Research Article Microsatellites in the Genome of the

Research ArticleMicrosatellites in the Genome of the EdibleMushroom Volvariella volvacea

Ying Wang1 Mingjie Chen1 Hong Wang1 Jing-Fang Wang2 and Dapeng Bao1

1 National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and UtilizationMinistry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible FungiShanghai Academy of Agriculture Science Shanghai 201403 China

2 Key Laboratory of Systems Biomedicine Shanghai Center for Systems Biomedicine Shanghai Jiao Tong UniversityShanghai 200240 China

Correspondence should be addressed to Jing-Fang Wang jfwang8113gmailcom and Dapeng Bao baodphotmailcom

Received 2 October 2013 Revised 23 October 2013 Accepted 23 October 2013 Published 19 January 2014

Academic Editor Yudong Cai

Copyright copy 2014 Ying Wang et al This is an open access article distributed under the Creative Commons Attribution Licensewhich permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited

Using bioinformatics software and database we have characterized the microsatellite pattern in the V volvacea genome andcompared it with microsatellite patterns found in the genomes of four other edible fungi Coprinopsis cinerea Schizophyllumcommune Agaricus bisporus and Pleurotus ostreatus A total of 1346 microsatellites have been identified with mono-nucleotidesbeing the most frequent motif The relative abundance of microsatellites was lower in coding regions with 21NoMb Howeverthe microsatellites in the V volvacea gene models showed a greater tendency to be located in the CDS regions There was also ahigher preponderance of trinucleotide repeats especially in the kinase genes which implied a possible role in phenotypic variationAmong the five fungal genomes microsatellite abundance appeared to be unrelated to genome size Furthermore the short motifs(mono- to tri-nucleotides) outnumbered other categories although these differed in proportion Data analysis indicated a possiblerelationship between the most frequent microsatellite types and the genetic distance between the five fungal genomes

1 Introduction

Volvariella volvacea the Chinese straw mushroom is anedible straw-degrading basidiomycetous fungus that hasbeen cultivated for over 300 years Currently ranked thirdin terms of production worldwide [1 2] this mushroomhas commercial importance that continues to increase dueto its delicious flavor and texture nutritional attributesmedicinal properties and short cultivation cycle V volvaceais rich in protein essential amino acids vitamin C andother bioactive components [3 4] According to traditionalChinese medicine consuming the mushroom is good for theliver [5] and stomach relieves summer heats and enrichesmilk production in women following childbirth Further-more antioxidants from V volvacea are reported to enhanceimmunity reduce cholesterol levels and prevent atheroscle-rosis [6] V volvacea also plays an important ecologicalrole by degrading the various agricultural wastes such asrice and wheat straw cottonseed hulls sugar cane bagasse

oil palm pericarp banana leaves and other carbonaceousmaterials used for cultivation [3 7] However in spite of thesenutritional medicinal and environmental benefits relativelylittle is known about themolecular biology of thismushroom

Microsatellites also known as simple sequence repeats(SSRs) or short tandem repeats (STRs) are 1ndash6 base-pair nucleotide motifs repeated in tandem at least fivetimes They are distributed in both coding and noncodingregions of eukaryotic and prokaryotic genomes [8 9] andexhibit high levels of polymorphism Since the late 1980smany microsatellites have been used as genetic makers forspecies identification [10] and classification and in genomefingerprinting and mapping studies [11ndash14] Subsequentresearch has revealed that microsatellites are involved ingene regulation and organism development and evolution[15 16] In most cases the effects of microsatellites aredetermined by their genomic location For example muta-tions to microsatellites located in coding and promoterregions lead to phenotype modification [17ndash20] while in

Hindawi Publishing CorporationBioMed Research InternationalVolume 2014 Article ID 281912 10 pageshttpdxdoiorg1011552014281912

2 BioMed Research International

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51015840-untranslated regions (51015840-UTRs) they affect gene transcrip-tion or regulation In intron regions microsatellite mutationsimpact gene transcription regulation mRNA splicing andgene silencing and in 31015840-UTRs they are involved in genesilencing and transcription slippage [16 21] Moreover sincethe frequency of these elements in genomes is proportionalto the genome coverage they can help explain how genomesare organized [11] However there are major drawbacksassociated with microsatellite research including the timeand costs associated with isolating microsatellites from thewhole genome [22] a process that involves the screening ofsmall insert genomic DNA libraries or the construction ofSSR-enriched libraries [23] However our previous researchinto the degradation and sexual reproduction mechanismsadopted by V volvacea has resulted in the sequencing of thewhole genome [1] thereby facilitating genome-wide analysesof microsatellite distribution

In this study the entire genome of a monokaryoticV volvacea strain (V23-1) has been screened to determinethe distribution and density of microsatellites in differentgenomic regions Particular emphasis has been given tomicrosatellites located in genes with molecular functionsand microsatellites in the V volvacea genome have alsobeen compared with those present in the genomes of fourother edible fungi For this purpose we designed 100 primerpairs based on identified microsatellites loci used for geneticmapping Our data will serve to establish the functional andevolutionary significance of these sequences and contributeto their future use as molecular markers

2 Materials and Methods

The complete genome sequence of V volvacea strainV23 was downloaded from the FTP site of GenBank

Information relating to the location of the gene mod-els introns coding sequences (CDSs) 51015840-untranslated-(51015840-UTRs) 31015840-untranslated-(31015840-UTRs) and intergenic regionswere obtained from the V volvacea genome study group 51015840-UTRs are defined as the sequence located between a tran-scription start point and the beginning of the start codonof the transcript 31015840-UTRs are defined as the sequencebetween the stop codon and the last base of the transcriptExcept introns CDSs and UTRs all the other regions inthe genome are classified as intergenic regions Coprinuscinereus Schizophyllum commune Agaricus bisporus andPleurotus ostreatus genome sequences used in this study(Table S1) (See Supplementary material available onlineat httpdxdoiorg1011552014281912) were downloadedfrom the Joint Genome Institute (JGI) website

MISA software (httppgrcipk-gaterslebendemisa)was used to locate and identify both perfect microsatellitesand compound microsatellites interrupted by a certainnumber of bases Mono- to hexanucleotide microsatellitemotifs were identified using the following default parametersmono- with at least 10 repeats di- with at least six repeatstri- penta- and hexa- with at least five repeats themaximumnumber of bases between two microsatellites was 100 bp[18 24] Unit patterns of repeats with circular permutationswere considered as one type for statistical analysis Thesame conditions were used to identify microsatellites inall the genome assemblies [25 26] To more accuratelycompare all the repeat types existing in different genomicregions the relative abundance (mean of the number ofmicrosatellites per Mb of the sequence analyzed) and therelative density (mean of the microsatellite length in bp perMb of the sequence analyzed) were calculated separately[27] Since longer microsatellites may display higher levels ofpolymorphism primers for these loci were designed usingthe Primer3 software (httpfrodowimiteduprimer3)

Genemodels havingmicrosatellites in exons introns andUTRs were isolated and then scanned for InterPro domainsand gene ontology (GO) annotation The latter was used toassign each gene-encoded protein to one of the three definedcategories (molecular function biological process or cellularcomponent) and WEGO (Web Gene Ontology AnnotationPlot) [28] was used to plot the GO annotation data

3 Results

31 Identification and Location of Microsatellites in the V vol-vacea Genome The V volvacea genome contained a total of1346 microsatellites with a relative abundance of 38 micro-satellites per Mbp (Table 1) Microsatellites with periodsranging from 1 to 6 (ie mono- to hexa-) accounted for 574(773) 82 (110) 297 (400) 14 (19) 10 (14) and 22(30) of the total respectively From these 100 microsatelliteloci were selected and 100 primers were designed accordingly(Table S2)

The entire genome (3572Mb) was divided into fiveregional types consisting of 51015840UTRs (069Mb) CDSs(1742Mb) introns (571Mb) 31015840UTRs (16Mb) andintergenic (1031Mb) Microsatellites were more numerousin the intergenic regions with a relative abundance of

BioMed Research International 3

Table 1 Number percentage and relative abundance of microsatellites in the different regions of the V volvacea genome

51015840

UTR CDS Introns 31015840

UTR Intergenic regions TotalGenome sizeMb 069 1742 571 161 1031 3572Percentage of the genome 193 4877 1599 451 2886 100Mono No 8 32 231 49 453 773

103 414 2988 634 5860 100NoMb 12 2 40 30 44 22

Di No 1 16 21 2 70 110 091 1455 1909 182 6364 100NoMb 1 1 4 1 7 3

Tri No 6 299 29 15 51 400 15 7475 725 375 1275 100NoMb 9 17 5 9 5 11

Tetra No 2 mdash 3 2 12 19 1053 mdash 1579 1053 6316 100NoMb 3 mdash mdash 1 1 1

Penta No mdash 2 4 4 4 14 mdash 1429 2857 2857 2857 100NoMb mdash mdash 1 2 mdash 0

Hexa No mdash 16 4 2 8 30 mdash 5333 1333 667 2667 100NoMb mdash 1 1 1 1 1

All SSRs No 17 365 292 74 598 1346 126 2712 2169 550 4443 100NoMb 25 21 51 46 58 38

58NoMb (Table 1) Over 50 of the mono- di- andtetranucleotides were located in the intergenic regionswhereas tri- and hexanucleotides appeared more frequentlyin the CDSs Pentanucleotide microsatellites were fairlyevenly distributed within the CDSs introns 31015840UTRs andintergenic regions No penta- and hexanucleotides werefound in the 51015840UTRs and no tetranucleotides were found inCDSs

The fourteen most abundant microsatellite types(ge10motifs) detected in the V volvacea genome constituted947 of the total (Figure 1) AT occurred at the highestfrequency (516) followed by ACCGGT (934) andCG (911) With the exception of the mononucleotidemotifs the majority of these most abundant microsatellitesmotifs were repeated less than 10 times Only 13 (1)microsatellite motifs exhibited a large repeat numberTrinucleotides were the primary types among the abovefourteen most abundant microsatellites types but theirdistribution was highly variable with a wide range (from086 to 934) of frequencies In addition there werefifteen tetranucleotide types twelve pentanucleotide typesand twenty-five hexanucleotide types identified within thewhole genome but none of these contained more thanten different motifs Among the fourteen most abundantmicrosatellites types (Figure 1) the longest motifs wereT (61 bp) CAC (42 bp) GAG (39 bp) TGA (30 bp) AAT(27 bp) AAG (24 bp) ACG (24 bp) TCA (24 bp) CTG(24 bp) AT (22 bp) C (21 bp) AG (20 bp) CCG (18 bp) andGT (14 bp) respectively

32 Distribution of Microsatellites in the V volvacea GeneModels and Functional Properties of the Genes ContainingMicrosatellites Of the 11084 genes identified in the wholegenome of V volvacea 649 (59) contained 748 microsatel-lites with 72 of these containing more than one microsatel-lite The relative abundance of microsatellites in the genemodels was 29 NoMb Altogether 365 microsatellites weredetected in the CDSs of 323 genes (29 of the total)contributing 271 of the total in the entire V volvaceagenome Trinucleotides (299) were the most abundant cate-gory (819) in all the gene models and with the exceptionof themononucleotidemicrosatellites the trinucleotide CACwas the most frequent (with 35motifs) followed by CAG(24motifs) GAC (20motifs) and CCA (16motifs) All thesemotifs encoded aliphatic amino acids such as valine leucineand glycine InterPro and KEGG database scanning revealedthat of the 649 gene models containing microsatellites 365contained at least one known domain 190 participated in abiological pathway and 147 had been annotated definitivelyThese genes encoded proteins including cytochrome P450monooxygenases carbohydrate-degrading enzymes kinasesdehydrogenases and transport proteins Thorough analysisof the microsatellite distribution and motif type among the147 annotated genes revealed that the microsatellites weremore frequent within the CDS regions of the kinase genesand that trinucleotides were the most abundant motif (TableS3) However these conditions did not apply to other genecategories In terms of molecular function the annotatedgenes included three with electron carrier activity 23 with


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catalytic activity five involved in binding two with struc-tural molecule activity and two with transporter activity(Table 2) Some genes contained more than one microsatel-lite For example four different types of microsatellite motifs(GAC)5 (GCT)5 (GAC)5 and (CCGCAC)6 were detectedin the CDS of the CAMKCAMK1 protein kinase gene TheCa2+ transporting ATPase gene also contained four micro-satellites three in the CDS and one in the intron regionswhile two or threemicrosatellites were identified in either theCDS or intron regions of other genes

The whole genome of V volvacea and the genes havingmicrosatellites were categorized on the basis of their homol-ogous gene function by the Gene Ontology ConsortiumGene ontology numbers for the best homologous hits wereused to determine molecular function cellular componentand biological process ontology for these sequences Aninferred putative gene ontology annotation was found for5161 genes in the genome of which only 320 (254 associatedwith cellular components 243 with biological processes and242 with molecular function) contained microsatellite lociThe GO terms in the three ontologies of the whole genometotaled 105 with 73 in the genes having microsatellites Inthe cellular component ontology the cell (762 in wholegenome and 794 in genes containing microsatellites) andthe cell part (762 and 794) were the two main types ofGO term followed by the organelle (568 and 609) andorganelle part (308 and 388) In the biological processontology cellular process (699 759) and metabolicprocess (701 688) were the two main GO terms andin the Molecular Function ontology the functions of themajor components were binding (655 756) and cat-alytic activity (588 525) Compared with the wholegenome some GO terms were not present in genes having

microsatellites including cell apex (GO0045177) exter-nal encapsulating structure (GO0044462) intracellularimmature spore (GO0042763) protein serinethreoninephosphatase complex (GO0008287) synapse (0045202)nutrient reservoir activity (GO0045735) and locomotion(GO0040011) (Figure 2) Most of the absent GO terms wereconcentrated in the cellular component ontology

33 Comparison of Microsatellite Distribution in the Genomesof V Volvacea and Four Other Edible Fungi The number andtypes of microsatellites in the V volvacea genome and fourother fully sequenced edible fungal genomes that varied insize from 302Mb (Agaricus bisporus) to 386Mb (Schizo-phyllum commune) were compared (Table 3) Microsatellitecontent in these species was not directly proportional to thesize of the genome since A bisporus contained the highestnumber (3134 relative abundance 1038 per Mbp) comparedwith only 1206 in S commune (relative abundance 312 perMbp) The C cinereus and P ostreatus genomes contained2050 and 1314microsatellites respectivelyHowever althoughV volvacea and P ostreatus showed the same relative abun-dance of microsatellites (38 per Mbp) the relative densitieswere different because the total length of microsatellitesin P ostreatus was longer Yet based on the comparisonof microsatellites in the wholegenomes the microsatellitecontent in the V volvacea genome exhibited closer similarityto P ostreatus and S commune than to the A bisporus and Ccinereus

The five fungal genomes exhibited considerable dif-ferences with respect to the number relative abundanceand relative density of mono- di- tri- tetra- penta- andhexanucleotides (Table 4 Figure 3) For example mononu-cleotide motifs outnumbered all other microsatellite classes


Table 2 Microsatellites in the gene models with some molecular functions in V volvacea

Molecular function Gene product Location

Electron carrier activityCYP547B1 IntronCYP5080B3b IntronCYP627A1 Intron

Catalytic activity

Nonribosomal peptide synthetase 12 IntronProtoporphyrinogen oxidase IntronGlycoside hydrolase family 13 protein CDSATP citrate lyase isoform 2 3

1015840

UTRAdenylate cyclase CDSXylanase CDSPyruvate dehydrogenase CDSModular protein with glycoside hydrolase family 13 and glycosyltransferase family 5domains Intron

long-chain-fatty-acid-CoA ligase 31015840

UTRGlycoside hydrolase family 18 protein CDS intronGlycoside hydrolase family 15 protein IntronGlycoside hydrolase family 35 protein IntronAMP dependent CoA ligase IntronSerine palmitoyltransferase 2 CDSIMP dehydrogenase CDS intronTrehalase IntronDNA helicase CDSExo-beta-13-glucanase IntronGlycoside hydrolase family 10 and carbohydrate-binding module family 1 protein IntronPotassiumsodium efflux P-type ATPase CDS times 3 IntronGlycoside hydrolase family 38 protein IntronSodium transport ATPase IntronFructose-bisphosphate aldolase CDS intron

Binding

Sec7 guanine nucleotide exchange factor 31015840

UTRCOP8 CDSSTESTE11cdc15 protein kinase CDSClathrin-coated vesicle protein IntronCarnitineacyl carnitine carrier Intron

Structural molecule activity Beta-tubulin 2 tubb2 IntronIron sulfur assembly protein 1 Intron

Transporter activity Urea transporter 31015840

UTRVacuole protein Intron

Table 3 Overview of the five edible fungal genomes

V volvacea C cinereus S commune A bisporus P ostreatusSequence analyzed (Mb) 357 362 386 302 343GC contents () 488 5167 575 4648 5094No of SSRs 1346 2050 1206 3134 1314Relative abundance (NoMb) 38 56 31 104 38Total length of SSRs (bp) 19347 32601 21538 44690 25265Relative density (bpMb) 541 898 558 1478 737Genome content () 005 009 006 015 007


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in theV volvacea andA bisporus genomes with 2030 (648of the total) detected in the latter However trinucleotidemicrosatellites (followed by mononucleotides) were the mostcommon motifs in S commune and C cinereus whiletrinucleotidemicrosatellites (followed by dinucleotides) weremost frequent in P ostreatus Comparison of the relativeabundance (Figure 3(a)) and the relative density (Figure 3(b))of the six microsatellite categories revealed general agree-ment except in the case of the P ostreatus genome wherehexanucleotide microsatellites were infrequent but relativelydense In contrast to the clear disparity in the total numberof microsatellites in the V volvacea and A bisporus genomes

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the proportion of the six microsatellite categories was verysimilar (Figure 4)

The number of motif types of 17 different microsatellitesin each of the fivemushroom species is shown in Figure 5Themononucleotide AT was the most frequent in the majorityof species and only the S commune genome contained


Table 4 Occurrence relative abundance total length and relative density of microsatellites in the five edible fungal genomes

V volvacea C cinereus S commune A bisporus P ostreatusMono

No 773 761 346 2030 251NoMb 22 21 9 67 7Length (bp) 9440 9950 4425 26065 3131BpMb 264 275 115 863 91

DiNo 110 375 200 354 272NoMb 3 10 5 12 8Length (bp) 1464 5354 2664 4980 3904BpMb 41 148 69 165 114

TriNo 400 843 593 701 640NoMb 11 23 15 23 19Length (bp) 6660 14655 10299 12267 11295BpMb 187 405 267 406 329

TetraNo 19 38 24 22 42NoMb 1 1 1 1 1Length (bp) 392 812 568 460 940BpMb 11 22 15 15 27

PentaNo 14 10 15 10 21NoMb 0 0 0 0 1Length (bp) 425 300 450 270 565BpMb 12 8 12 9 16

HexaNo 30 23 28 17 88NoMb 1 1 1 1 3Length (bp) 966 1530 3132 648 5430BpMb 27 42 81 21 158

more CG than AT Of the dinucleotide motifs CG wascommon in C cinereus S commune and P ostreatus butleast frequent in V volvacea and A bisporus Converselythe trinucleotide AATATT was comparatively common inV volvacea and A bisporus but rare in C cinereus S com-mune and P ostreatus Furthermore only eight AACGTTtrinucleotide motifs were detected in V volvacea and in Scommune compared with more than 35 in C cinereus Postreatus and A bisporus Tetra- penta- and hexanucleotideSSR densities were very low and only the hexanucleotideAACCCTATTGGG was relatively common with at least10 motifs identified in both S commune and P ostreatusThe longest motifs varied from 34 repeats of the dinu-cleotideAGCT and the hexanucleotideAACCCTATTGGGin A bisporus and C cinereus respectively to 61 repeatsof the mononucleotide AT in V volvacea (Table 5) AAC-CCTATTGGG was also the longest microsatellite identifiedin S commune and P ostreatus with 36 and 38 repeatsrespectively

4 Discussion

Microsatellites have contributed significantly to studies inpopulation genetics [29 30] and molecular ecology [11] haveserved to explain the phenomenon of genome expansion incertain species [31] influenced the expression of quantitativegenetic traits [32] and have been used to analyze the humangenome for human diseases [33 34] Considerable progresshas been made in microsatellite development includingassociated bioinformatics For example several studies havefocused on the basic distribution patterns and diversityacross whole genomes to better understand the role ofmicrosatellites However since relatively little comprehensiveanalysis of microsatellites in the genomes of edible fungi hasbeen undertaken we have used computational analysis tocharacterize and compare the microsatellites in the entiregenome of V volvacea and the genomes of four other ediblefungi (Table S1) Information on the relative abundance ofthesemicrosatellites combinedwith the distribution patterns


Table 5 The longest microsatellite motifs in the five edible fungalgenomes

Longest microsatellitesMotif Repeats Size

V volvacea AT 61 61C cinereus AACCCTATTGGG 34 204S commune AACCCTATTGGG 36 216A bisporus AGCT 34 68P ostreatus AACCCTATTGGG 38 228

in both the coding and noncoding regions of the genomemay provide clues to the functionality of microsatellites ingene regulation

At present there is no standard cut-off limit for theminimum length of microsatellites [35] Adopting slippagerate changes of around 10 bases for mono- and dinucleotiderepetitions universal thresholds of 8ndash10 bp and 7ndash10 bp wereproposed for mononucleotide microsatellites in yeast [36]and eukaryotes [37] respectively However the thresholdfor human microsatellites was found to depend on theirmotif size (9 repeats for mononucleotide and 4 repeats fordi- tri- and tetranucleotide microsatellites) [38] Accord-ingly and in order to compare our data with previousstudies of other fungi we identified mono- di- tri- tetra-penta- and hexanucleotide microsatellite motifs at minimumrepeat numbers of 10 6 5 5 5 and 5 respectively Ofthe 1346 microsatellites identified 729 were embedded innoncoding DNA (corresponding to 5123 of the genomeassembly) and 61 were located in the intergenic regions(289 of the genome assembly) This distribution patternwhich is common in fungal genomes has been attributedto negative selection against frame-shift mutations in codingregions [39] and possibly accounts for the small numberof microsatellites in fungi Another contributing factor isthe relatively smaller amount of noncoding DNA in fungidue to the high density of genes within the fungi genomecompared with higher eukaryotes This distribution impliesthat microsatellites are generated in intergenic regions byduplication or transposition

In addition to possible relevance as evolutionary neutralDNAmarkers [40] microsatellites have some functional sig-nificance including effects on chromatin organization regu-lation of gene activity recombination DNA replication cellcycle and mismatch repair systems [41 42] Firstly we canestimate the function of a microsatellite by its position Judg-ing fromprevious experiencemicrosatellites located in CDSscan alter the function of the protein [20] those located inintrons can affect gene transcription those located in 51015840UTRscan regulate gene expression and those located in 31015840UTRsmay cause transcription slippage [43] In V volvacea 556of the total number of microsatellites were scattered in genemodels and nearly half of thesemicrosatellites were located incoding regions Due to the high mutation rate of microsatel-lites genes containing microsatellites in their coding regionswould not be conserved Close inspection of the great major-ity of microsatellites appearing in kinase-encoding geneswas located in CDSs suggesting these genes are capable

of undergoing mutation Microsatellites were also found inthe introns 51015840UTRs and 31015840UTRs of CYPs carbohydrate-degrading enzymes dehydrogenases and transport proteinsEarlier studies have shown that microsatellites located inpromoter regions may affect gene activity [44] In additionsome long microsatellites located in intergenic regions mayhave special functions For instance long microsatellitesinvolved in sister chromatid cohesion which indirectly assistkinetochore formation are highly clustered in the centromere[45] Excess numbers of microsatellite repeats may playimportant roles both in genomic stability and also in theevolution of additional genomic features Consequently thelongest motifs (T)61 (CAC)14 and (GAG)13 in V volvaceamerit close attention with respect to possible functionality

Comparative analyses of the microsatellite distribution inthe genomes ofV volvacea and four edible fungi revealed thatin all cases the majority of the microsatellites were mono-di- and trinucleotides accounting for up to approximately90 of all the microsatellites identified However theirrespective percentages varied in the different genomes Vvolvacea and A bisporus showed a great affinity for mononu-cleotide repeats compared to the other three genomes inwhich trinucleotide microsatellites were the predominanttype Furthermore microsatellites in the S commune Ccinereus and P ostreatus genomes were comparatively longerThis was unexpected especially in the case of P ostreatus (thesecond smallest genome of the five) since an earlier studyhad concluded that microsatellites in larger genomes werelonger compared with those in smaller genomes [27] Henceneither the abundance nor the length of the microsatellitesin these fungi was correlated with genome size In the caseof microsatellite types few trends were evident AT werethe most frequent mononucleotide repeats in A bisporus Vvolvacea C cinereus and P ostreatus whereas CG was mostfrequent in the S commune genome Among the dinucleotidemotifs ACGT AGCT and ATAT were present at higherfrequencies in A bisporus V volvacea C cinereus andP ostreatus whereas CGCG was the most common in Scommune The reason for the difference may be attributablein part to the higher GC content in the S commune genomeand to its distant phylogenetic position

5 Conclusion

Comprehensive analysis of microsatellites in the V volvaceaand four other completely sequenced edible fungal genomeswill provide better understanding of the nature of theseimportant sequences Such understanding of the character-istics of microsatellites in the genomes of V volvacea and theother edible fungi will serve many useful purposes includingthe isolation and development of variable markers and willfacilitate research on the role of microsatellites in genomeorganization

Conflict of Interests

The authors declare that there is no conflict of interestsregarding the publication of this paper


Acknowledgments

This study was supported by the Shanghai Committee ofScience and Technology China (Grant no 10dz2212400)Chinese National Science and Technology Support Program(Grant no 2013BAD16B02) and Shanghai Key Scientific andTechnological Project for Agriculture The authors thank DrJohn Buswell for linguistic revision of the paper

References

[1] D Bao M Gong H Zheng et al ldquoSequencing and comparativeanalysis of the strawmushroom (Volvariella volvacea) genomerdquoPLoS ONE vol 8 no 3 Article ID e58294 2013

[2] G Thiribhuvanamala S Krishnamoorthy K ManoranjithamV Praksasm and SKrishnan ldquoImproved techniques to enhancethe yield of paddy straw mushroom (Volvariella volvacea) forcommercial cultivationrdquo African Journal of Biotechnology vol11 no 64 pp 12740ndash12748 2012

[3] Y J Cai S J Chapman J A Buswell and S-T Chang ldquoPro-duction and distribution of endoglucanase cellobiohydrolaseand 120573- glucosidase components of the cellulolytic system ofVolvariella volvacea the edible straw mushroomrdquo Applied andEnvironmental Microbiology vol 65 no 2 pp 553ndash559 1999

[4] S T Chang ldquoMushroom research and development-equalityand mutual benefitrdquo Mushroom Biology and Mushroom Prod-ucts pp 1ndash10 1996

[5] S V Kalava and S G Menon ldquoProtective efficacy of the extractof volvariella volvacea (bulliard ex fries) singer against carbontetrachloride induced hepatic injuryrdquo International Journal ofPharmaceutical Sciences and Research vol 3 no 8 pp 2849ndash2856 2012

[6] L Ramkumar T Ramanathan and J Johnprabagaran ldquoEval-uation of nutrients trace metals and antioxidant activity inVolvariella volvacea (Bull Ex Fr) SingrdquoEmirates Journal of Foodand Agriculture vol 24 no 2 pp 113ndash119 2012

[7] B Z Chen F Gui B G Xie F Zou Y J Jiang and Y J DengldquoSequence and comparative analysis of theMIP gene in Chinesestraw mushroom Volvariella volvaceardquo Genome vol 55 no 9pp 667ndash672 2012

[8] D Field and C Wills ldquoLong polymorphic microsatellites insimple organismsrdquo Proceedings of the Royal Society B vol 263no 1367 pp 209ndash215 1996

[9] G Toth Z Gaspari and J Jurka ldquoMicrosatellites in differenteukaryotic genomes surveys and analysisrdquo Genome Researchvol 10 no 7 pp 967ndash981 2000

[10] S Rufai M M Hanafi M Y Rafii S Ahmad I W Arolu andJ Ferdous ldquoGenetic dissection of new genotypes of drumsticktree (Moringa oleifera Lam) using random amplified polymor-phic DNA markerrdquo BioMed Research International vol 2013Article ID 604598 6 pages 2013

[11] H Ellegren ldquoMicrosatellites simple sequences with complexevolutionrdquo Nature Reviews Genetics vol 5 no 6 pp 435ndash4452004

[12] E Guichoux L Lagache S Wagner et al ldquoCurrent trends inmicrosatellite genotypingrdquoMolecular Ecology Resources vol 11no 4 pp 591ndash611 2011

[13] N Mittal and A K Dubey ldquoMicrosatellite markersmdasha newpractice of DNA based markers in molecular geneticsrdquo Phar-macognosy Reviews vol 3 no 6 pp 235ndash246 2009

[14] C Spampinato and D Leonardi ldquoMolecular fingerprints toidentify Candida speciesrdquo BioMed Research International vol2013 Article ID 923742 10 pages 2013

[15] J Labbe CMurat EMorin F Le Tacon and FMartin ldquoSurveyand analysis of simple sequence repeats in the Laccaria bicolorgenome with development of microsatellite markersrdquo CurrentGenetics vol 57 no 2 pp 75ndash88 2011

[16] M J Lawson and L Zhang ldquoDistinct patterns of SSR distri-bution in the Arabidopsis thaliana and rice genomesrdquo GenomeBiology vol 7 no 2 article R14 2006

[17] J J Rudd J Antoniw R Marshall J Motteram B Fraaije andK Hammond-Kosack ldquoIdentification and characterisation ofMycosphaerella graminicola secreted or surface-associated pro-teins with variable intragenic coding repeatsrdquo Fungal Geneticsand Biology vol 47 no 1 pp 19ndash32 2010

[18] C Murat C Riccioni B Belfiori et al ldquoDistribution andlocalization of microsatellites in the Perigord black trufflegenome and identification of new molecular markersrdquo FungalGenetics and Biology vol 48 no 6 pp 592ndash601 2011

[19] J G Gibbons and A Rokas ldquoComparative and functionalcharacterization of intragenic tandem repeats in 10 Aspergillusgenomesrdquo Molecular Biology and Evolution vol 26 no 3 pp591ndash602 2009

[20] K J Verstrepen A Jansen F Lewitter and G R Fink ldquoIntra-genic tandem repeats generate functional variabilityrdquo NatureGenetics vol 37 no 9 pp 986ndash990 2005

[21] Y C Li A B Korol T Fahima and E Nevo ldquoMicrosatelliteswithin genes structure function and evolutionrdquo MolecularBiology and Evolution vol 21 no 6 pp 991ndash1007 2004

[22] S Feng H Tong Y Chen et al ldquoDevelopment of pineapplemicrosatellite markers and germplasm genetic diversity analy-sisrdquo BioMed Research International vol 2013 Article ID 31791211 pages 2013

[23] C Dutech J Enjalbert E Fournier et al ldquoChallenges ofmicrosatellite isolation in fungirdquo Fungal Genetics and Biologyvol 44 no 10 pp 933ndash949 2007

[24] J Qian H Xu J Song J Xu Y Zhu and S Chen ldquoGenome-wide analysis of simple sequence repeats in themodelmedicinalmushroom Ganoderma lucidumrdquo Gene vol 512 no 2 pp 331ndash336 2013

[25] J Jurka and C Pethiyagoda ldquoSimple repetitive DNA sequencesfrom primates compilation and analysisrdquo Journal of MolecularEvolution vol 40 no 2 pp 120ndash126 1995

[26] C Y Li L Liu J Yang et al ldquoGenome-wide analysis ofmicrosatellite sequence in seven filamentous fungirdquo Interdisci-plinary Sciences vol 1 no 2 pp 141ndash150 2009

[27] H Karaoglu C M Y Lee and W Meyer ldquoSurvey of simplesequence repeats in completed fungal genomesrdquo MolecularBiology and Evolution vol 22 no 3 pp 639ndash649 2005

[28] J Ye L Fang H Zheng et al ldquoWEGO a web tool for plottingGO annotationsrdquo Nucleic Acids Research vol 34 pp W293ndashW297 2006

[29] P Jarne and P J L Lagoda ldquoMicrosatellites from molecules topopulations and backrdquo Trends in Ecology and Evolution vol 11no 10 pp 424ndash429 1996

[30] G Luikart P R England D Tallmon S Jordan and PTaberlet ldquoThe power and promise of population genomicsfrom genotyping to genome typingrdquo Nature Reviews Geneticsvol 4 no 12 pp 981ndash994 2003

[31] F Martin A Kohler C Murat et al ldquoPerigord black trufflegenome uncovers evolutionary origins and mechanisms ofsymbiosisrdquo Nature vol 464 no 7291 pp 1033ndash1038 2010


[32] V Albanese N F Biguet H Kiefer E Bayard J Mallet andR Meloni ldquoQuantitative effects on gene silencing by allelicvariation at a tetranucleotide microsatelliterdquo Human MolecularGenetics vol 10 no 17 pp 1785ndash1792 2001

[33] Y D Kelkar N Strubczewski S E Hile F Chiaromonte KA Eckert and K D Makova ldquoWhat is a microsatellite acomputational and experimental definition based upon repeatmutational behavior at AT and GTAC repeatsrdquo GenomeBiology and Evolution vol 2 no 1 pp 620ndash635 2010

[34] C E Pearson K N Edamura and J D Cleary ldquoRepeatinstability mechanisms of dynamic mutationsrdquoNature ReviewsGenetics vol 6 no 10 pp 729ndash742 2005

[35] E Meglecz G Neve E Biffin and M G Gardner ldquoBreakdownof phylogenetic signal a survey of microsatellite densities in454 shotgun sequences from 154 nonmodel eukaryote speciesrdquoPLoS ONE vol 7 no 7 Article ID e40861 2012

[36] O Rose and D Falush ldquoA threshold size for microsatelliteexpansionrdquo Molecular Biology and Evolution vol 15 no 5 pp613ndash615 1998

[37] K J Dechering K Cuelenaere R N H Konings and J AM Leunissen ldquoDistinct frequency-distributions of homopoly-meric DNA tracts in different genomesrdquoNucleic Acids Researchvol 26 no 17 pp 4056ndash4062 1998

[38] Y Lai and F Sun ldquoThe relationship between microsatellite slip-page mutation rate and the number of repeat unitsrdquo MolecularBiology and Evolution vol 20 no 12 pp 2123ndash2131 2003

[39] D Metzgar J Bytof and C Wills ldquoSelection against frameshiftmutations limits microsatellite expansion in coding DNArdquoGenome Research vol 10 no 1 pp 72ndash80 2000

[40] S Temnykh G DeClerck A Lukashova L Lipovich S Cart-inhour and S McCouch ldquoComputational and experimentalanalysis of microsatellites in rice (Oryza sativa L) frequencylength variation transposon associations and genetic markerpotentialrdquo Genome Research vol 11 no 8 pp 1441ndash1452 2001

[41] Y C Li A B Korol T Fahima A Beiles and E NevoldquoMicrosatellites genomic distribution putative functions andmutational mechanisms a reviewrdquo Molecular Ecology vol 11no 12 pp 2453ndash2465 2002

[42] S Subramanian R K Mishra and L Singh ldquoGenome-wideanalysis of microsatellite repeats in humans their abundanceand density in specific genomic regionsrdquo Genome Biology vol4 no 2 p R13 2003

[43] D E Riley and J N Krieger ldquoUTR dinucleotide simplesequence repeat evolution exhibits recurring patterns includingregulatory sequencemotif replacementsrdquoGene vol 429 no 1-2pp 80ndash86 2009

[44] M D Vinces M Legendre M Caldara M Hagihara and KJ Verstrepen ldquoUnstable tandem repeats in promoters confertranscriptional evolvabilityrdquo Science vol 324 no 5931 pp 1213ndash1216 2009

[45] T D Murphy and G H Karpen ldquoLocalization of centromerefunction in a Drosophila minichromosomerdquo Cell vol 82 no 4pp 599ndash609 1995

Submit your manuscripts athttpwwwhindawicom

Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014

Anatomy Research International

PeptidesInternational Journal of


Hindawi Publishing Corporation httpwwwhindawicom

International Journal of

Volume 2014

Zoology


Molecular Biology International

GenomicsInternational Journal of


The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014


BioinformaticsAdvances in

Marine BiologyJournal of



Signal TransductionJournal of


BioMed Research International

Evolutionary BiologyInternational Journal of



Biochemistry Research International

ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014


Genetics Research International


Advances in

Virolog y

Hindawi Publishing Corporationhttpwwwhindawicom

Nucleic AcidsJournal of

Volume 2014

Stem CellsInternational



Enzyme Research



Microbiology


ATCGACG

TAGC

TATA

T

AAGCTT

AATATT

ACCGGT

ACGCTG

ACTATG

AGCCGT

AGGCCT

AGTATC

CCGCGG

TotalN

umbe

r of m

icro

sate

llite

s

0100

200300

400500600

700

800

900

1000

1100

1200

1300

Figure 1

51015840-untranslated regions (51015840-UTRs) they affect gene transcrip-tion or regulation In intron regions microsatellite mutationsimpact gene transcription regulation mRNA splicing andgene silencing and in 31015840-UTRs they are involved in genesilencing and transcription slippage [16 21] Moreover sincethe frequency of these elements in genomes is proportionalto the genome coverage they can help explain how genomesare organized [11] However there are major drawbacksassociated with microsatellite research including the timeand costs associated with isolating microsatellites from thewhole genome [22] a process that involves the screening ofsmall insert genomic DNA libraries or the construction ofSSR-enriched libraries [23] However our previous researchinto the degradation and sexual reproduction mechanismsadopted by V volvacea has resulted in the sequencing of thewhole genome [1] thereby facilitating genome-wide analysesof microsatellite distribution

In this study the entire genome of a monokaryoticV volvacea strain (V23-1) has been screened to determinethe distribution and density of microsatellites in differentgenomic regions Particular emphasis has been given tomicrosatellites located in genes with molecular functionsand microsatellites in the V volvacea genome have alsobeen compared with those present in the genomes of fourother edible fungi For this purpose we designed 100 primerpairs based on identified microsatellites loci used for geneticmapping Our data will serve to establish the functional andevolutionary significance of these sequences and contributeto their future use as molecular markers

2 Materials and Methods

The complete genome sequence of V volvacea strainV23 was downloaded from the FTP site of GenBank

Information relating to the location of the gene mod-els introns coding sequences (CDSs) 51015840-untranslated-(51015840-UTRs) 31015840-untranslated-(31015840-UTRs) and intergenic regionswere obtained from the V volvacea genome study group 51015840-UTRs are defined as the sequence located between a tran-scription start point and the beginning of the start codonof the transcript 31015840-UTRs are defined as the sequencebetween the stop codon and the last base of the transcriptExcept introns CDSs and UTRs all the other regions inthe genome are classified as intergenic regions Coprinuscinereus Schizophyllum commune Agaricus bisporus andPleurotus ostreatus genome sequences used in this study(Table S1) (See Supplementary material available onlineat httpdxdoiorg1011552014281912) were downloadedfrom the Joint Genome Institute (JGI) website

MISA software (httppgrcipk-gaterslebendemisa)was used to locate and identify both perfect microsatellitesand compound microsatellites interrupted by a certainnumber of bases Mono- to hexanucleotide microsatellitemotifs were identified using the following default parametersmono- with at least 10 repeats di- with at least six repeatstri- penta- and hexa- with at least five repeats themaximumnumber of bases between two microsatellites was 100 bp[18 24] Unit patterns of repeats with circular permutationswere considered as one type for statistical analysis Thesame conditions were used to identify microsatellites inall the genome assemblies [25 26] To more accuratelycompare all the repeat types existing in different genomicregions the relative abundance (mean of the number ofmicrosatellites per Mb of the sequence analyzed) and therelative density (mean of the microsatellite length in bp perMb of the sequence analyzed) were calculated separately[27] Since longer microsatellites may display higher levels ofpolymorphism primers for these loci were designed usingthe Primer3 software (httpfrodowimiteduprimer3)

Genemodels havingmicrosatellites in exons introns andUTRs were isolated and then scanned for InterPro domainsand gene ontology (GO) annotation The latter was used toassign each gene-encoded protein to one of the three definedcategories (molecular function biological process or cellularcomponent) and WEGO (Web Gene Ontology AnnotationPlot) [28] was used to plot the GO annotation data

3 Results

31 Identification and Location of Microsatellites in the V vol-vacea Genome The V volvacea genome contained a total of1346 microsatellites with a relative abundance of 38 micro-satellites per Mbp (Table 1) Microsatellites with periodsranging from 1 to 6 (ie mono- to hexa-) accounted for 574(773) 82 (110) 297 (400) 14 (19) 10 (14) and 22(30) of the total respectively From these 100 microsatelliteloci were selected and 100 primers were designed accordingly(Table S2)

The entire genome (3572Mb) was divided into fiveregional types consisting of 51015840UTRs (069Mb) CDSs(1742Mb) introns (571Mb) 31015840UTRs (16Mb) andintergenic (1031Mb) Microsatellites were more numerousin the intergenic regions with a relative abundance of



51015840



103 414 2988 634 5860 100NoMb 12 2 40 30 44 22

Di No 1 16 21 2 70 110 091 1455 1909 182 6364 100NoMb 1 1 4 1 7 3

Tri No 6 299 29 15 51 400 15 7475 725 375 1275 100NoMb 9 17 5 9 5 11




All SSRs No 17 365 292 74 598 1346 126 2712 2169 550 4443 100NoMb 25 21 51 46 58 38





100

10

1

01

001

Gen

es (

)5161320

513

00

Num

ber o

f gen

es


Apic

al p

art o

f cel

lA

xone

me

Cel

lC

ell d

ivisi

on si

teC

ell d

ivisi

on si

te p

art

Cel

l env

elope

Cel

l fra

ctio

nC

ell l

eadi

ng ed

geC

ell p

art

Cel

l pro

ject

ion

Cel

l pro

ject

ion

part

Cel

l sep

tum

Cel

l som

aC

ell s

urfa

ceC

ellu

lar b

udEn

dom

embr

ane s

yste

mEn

velo

peEx

tern

al en

caps

ulat

ing

struc

ture

Exte

rnal

enca

psul

atin

g str

uctu

re p

art

Extr

acel

lula

r mat

rixEx

trac

ellu

lar m

atrix

par

tEx

trac

ellu

lar r

egio

nEx

trac

ellu

lar r

egio

n pa

rtEx

trac

ellu

lar s

pace

Extr

aorg

anism

al sp

ace

Hos

t cel

lH

ost c

ell p

art

Inte

rcel

lula

r brid

geIn

trac

ellu

lar

Intr

acel

lula

r im

mat

ure s

pore

Intr

acel

lula

r org

anel

leIn

trac

ellu

lar o

rgan

elle

par

tIn

trac

ellu

lar p

art

Mac

rom

olec

ular

com

plex

Mem

bran

eM

embr

ane p

art

Mem

bran

e-bo

unde

d or

gane

lleM

embr

ane-

enclo

sed

lum

enM

idbo

dyM

olyb

dopt

erin

synt

hase

com

plex

Neu

rom

uscu

lar j

unct

ion

Non

-mem

bran

e-bo

unde

d or

gane

lleO

rgan

elle

Org

anel

le en

velo

peO

rgan

elle

enve

lope

lum

enO

rgan

elle

lum

enO

rgan

elle

mem

bran

eO

rgan

elle

par

tPe

ripla

smic

spac

ePo

stsyn

aptic

den

sity

Posts

ynap

tic m

embr

ane

Prot

ein

com

plex

Prot

ein

serin

eth

reon

ine p

hosp

hata

se co

mpl

exPr

otei

n-D

NA

com

plex

Ribo

flavi

n sy

ntha

se co

mpl

exRi

bonu

cleop

rote

in co

mpl

exSi

te o

f pol

ariz

ed g

row

thSy

naps

eSy

naps

e par

tSy

napt

ic v

esic

leVe

sicle

Vira

l cap

sidVi

rion

Virio

n pa

rtA

ntio

xida

ntBi

ndin

gCa

taly

ticEl

ectro

n ca

rrie

rEn

zym

e reg

ulat

orM

olec

ular

tran

sduc

erN

utrie

nt re

serv

oir

Prot

ein

tag

Stru

ctur

al m

olec

ule

Tran

scrip

tion

regu

lator

Tran

slatio

n re

gulat

orTr

ansp

orte

rA

nato

mic

al st

ruct

ure f

orm

atio

nBi

olog

ical

adhe

sion

Biol

ogic

al re

gula

tion

Cel

l kill

ing

Cel

lula

r com

pone

nt b

ioge

nesis

Cel

lula

r com

pone

nt o

rgan

izat

ion

Cel

lula

r pro

cess

Dea

thD

evelo

pmen

tal p

roce

ssEs

tabl

ishm

ent o

f loc

aliz

atio

nG

row

thIm

mun

e sys

tem

pro

cess

Loca

lizat

ion

Loco

mot

ion

Met

abol

ic p

roce

ssM

ultio

rgan

ism p

roce

ssM

ultic

ellu

lar o

rgan

ismal

pro

cess

Pigm

enta

tion

Repr

oduc

tion

Repr

oduc

tive p

roce

ssRe

spon

se to

stim

ulus

Rhyt

hmic

pro

cess

Vira

l rep

rodu

ctio

n


Figure 2










Catalytic activity


1015840




Binding









Volva

riella

volva

cea

Copr

inus

cine

reus

Schi

zoph

yllum

com

mun

e

Agar

icus b

ispor

us

Pleu

rotu

s ostr

eatu

s

0

15

30

45

60

75

HexaPenta

TetraTri

DiMono

Relat

ive a

bund

ance

(No

Mb)

(a)

Volva

riella

volva

cea

Copr

inus

cine

reus

Schi

zoph

yllum

com

mun

e

Agar

icus b

ispor

us

Pleu

rotu

s ostr

eatu

s

HexaPenta

TetraTri

DiMono

SSR

dens

ity (b

pM

b)

900

800

700

600

500

400

300

200

100

0

(b)

Figure 3

0 20 40 60 80 100

MonoDiTri

TetraPentaHexa

()

V olacea

C cinereus

S commune

A bisporus

P ostreatus

Figure 4


2000

1800

1600

1400

1200

1000

800

600

400

200

0N

umbe

r of m

icro

sate

llite


Coprinus cinereus


Pleurotus ostreatus

Agaricus bisporus

AT

CG

ACG

TAG

CT

ATA

TCG

CG

AAC

GTT

AAG

CTT

AAT

ATT

ACG

CTG

ACC

GGT

ACT

ATG

AGC

CGT

AGG

CCT

AGT

ATC

CCG

CGG

AACC

CTA

TTGG

G

Figure 5













4 Discussion











5 Conclusion





Acknowledgments


References






















































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology



51015840



103 414 2988 634 5860 100NoMb 12 2 40 30 44 22

Di No 1 16 21 2 70 110 091 1455 1909 182 6364 100NoMb 1 1 4 1 7 3

Tri No 6 299 29 15 51 400 15 7475 725 375 1275 100NoMb 9 17 5 9 5 11




All SSRs No 17 365 292 74 598 1346 126 2712 2169 550 4443 100NoMb 25 21 51 46 58 38





100

10

1

01

001

Gen

es (

)5161320

513

00

Num

ber o

f gen

es


Apic

al p

art o

f cel

lA

xone

me

Cel

lC

ell d

ivisi

on si

teC

ell d

ivisi

on si

te p

art

Cel

l env

elope

Cel

l fra

ctio

nC

ell l

eadi

ng ed

geC

ell p

art

Cel

l pro

ject

ion

Cel

l pro

ject

ion

part

Cel

l sep

tum

Cel

l som

aC

ell s

urfa

ceC

ellu

lar b

udEn

dom

embr

ane s

yste

mEn

velo

peEx

tern

al en

caps

ulat

ing

struc

ture

Exte

rnal

enca

psul

atin

g str

uctu

re p

art

Extr

acel

lula

r mat

rixEx

trac

ellu

lar m

atrix

par

tEx

trac

ellu

lar r

egio

nEx

trac

ellu

lar r

egio

n pa

rtEx

trac

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tran

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Prot

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tag

Stru

ctur

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olec

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Tran

scrip

tion

regu

lator

Tran

slatio

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orTr

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nato

mic

al st

ruct

ure f

orm

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nBi

olog

ical

adhe

sion

Biol

ogic

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gula

tion

Cel

l kill

ing

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lula

r com

pone

nt b

ioge

nesis

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lula

r com

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izat

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lula

r pro

cess

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thD

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tabl

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mot

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abol

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pro

cess

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enta

tion

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oduc

tion

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oduc

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roce

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se to

stim

ulus

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hmic

pro

cess

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l rep

rodu

ctio

n


Figure 2










Catalytic activity


1015840




Binding









Volva

riella

volva

cea

Copr

inus

cine

reus

Schi

zoph

yllum

com

mun

e

Agar

icus b

ispor

us

Pleu

rotu

s ostr

eatu

s

0

15

30

45

60

75

HexaPenta

TetraTri

DiMono

Relat

ive a

bund

ance

(No

Mb)

(a)

Volva

riella

volva

cea

Copr

inus

cine

reus

Schi

zoph

yllum

com

mun

e

Agar

icus b

ispor

us

Pleu

rotu

s ostr

eatu

s

HexaPenta

TetraTri

DiMono

SSR

dens

ity (b

pM

b)

900

800

700

600

500

400

300

200

100

0

(b)

Figure 3

0 20 40 60 80 100

MonoDiTri

TetraPentaHexa

()

V olacea

C cinereus

S commune

A bisporus

P ostreatus

Figure 4


2000

1800

1600

1400

1200

1000

800

600

400

200

0N

umbe

r of m

icro

sate

llite


Coprinus cinereus


Pleurotus ostreatus

Agaricus bisporus

AT

CG

ACG

TAG

CT

ATA

TCG

CG

AAC

GTT

AAG

CTT

AAT

ATT

ACG

CTG

ACC

GGT

ACT

ATG

AGC

CGT

AGG

CCT

AGT

ATC

CCG

CGG

AACC

CTA

TTGG

G

Figure 5













4 Discussion











5 Conclusion





Acknowledgments


References






















































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


100

10

1

01

001

Gen

es (

)5161320

513

00

Num

ber o

f gen

es


Apic

al p

art o

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me

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pace

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Hos

t cel

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geIn

trac

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lar

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mat

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ynap

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embr

ane

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reon

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plex

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nt re

serv

oir

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tag

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ctur

al m

olec

ule

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scrip

tion

regu

lator

Tran

slatio

n re

gulat

orTr

ansp

orte

rA

nato

mic

al st

ruct

ure f

orm

atio

nBi

olog

ical

adhe

sion

Biol

ogic

al re

gula

tion

Cel

l kill

ing

Cel

lula

r com

pone

nt b

ioge

nesis

Cel

lula

r com

pone

nt o

rgan

izat

ion

Cel

lula

r pro

cess

Dea

thD

evelo

pmen

tal p

roce

ssEs

tabl

ishm

ent o

f loc

aliz

atio

nG

row

thIm

mun

e sys

tem

pro

cess

Loca

lizat

ion

Loco

mot

ion

Met

abol

ic p

roce

ssM

ultio

rgan

ism p

roce

ssM

ultic

ellu

lar o

rgan

ismal

pro

cess

Pigm

enta

tion

Repr

oduc

tion

Repr

oduc

tive p

roce

ssRe

spon

se to

stim

ulus

Rhyt

hmic

pro

cess

Vira

l rep

rodu

ctio

n


Figure 2










Catalytic activity


1015840




Binding









Volva

riella

volva

cea

Copr

inus

cine

reus

Schi

zoph

yllum

com

mun

e

Agar

icus b

ispor

us

Pleu

rotu

s ostr

eatu

s

0

15

30

45

60

75

HexaPenta

TetraTri

DiMono

Relat

ive a

bund

ance

(No

Mb)

(a)

Volva

riella

volva

cea

Copr

inus

cine

reus

Schi

zoph

yllum

com

mun

e

Agar

icus b

ispor

us

Pleu

rotu

s ostr

eatu

s

HexaPenta

TetraTri

DiMono

SSR

dens

ity (b

pM

b)

900

800

700

600

500

400

300

200

100

0

(b)

Figure 3

0 20 40 60 80 100

MonoDiTri

TetraPentaHexa

()

V olacea

C cinereus

S commune

A bisporus

P ostreatus

Figure 4


2000

1800

1600

1400

1200

1000

800

600

400

200

0N

umbe

r of m

icro

sate

llite


Coprinus cinereus


Pleurotus ostreatus

Agaricus bisporus

AT

CG

ACG

TAG

CT

ATA

TCG

CG

AAC

GTT

AAG

CTT

AAT

ATT

ACG

CTG

ACC

GGT

ACT

ATG

AGC

CGT

AGG

CCT

AGT

ATC

CCG

CGG

AACC

CTA

TTGG

G

Figure 5













4 Discussion











5 Conclusion





Acknowledgments


References






















































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology





Catalytic activity


1015840




Binding









Volva

riella

volva

cea

Copr

inus

cine

reus

Schi

zoph

yllum

com

mun

e

Agar

icus b

ispor

us

Pleu

rotu

s ostr

eatu

s

0

15

30

45

60

75

HexaPenta

TetraTri

DiMono

Relat

ive a

bund

ance

(No

Mb)

(a)

Volva

riella

volva

cea

Copr

inus

cine

reus

Schi

zoph

yllum

com

mun

e

Agar

icus b

ispor

us

Pleu

rotu

s ostr

eatu

s

HexaPenta

TetraTri

DiMono

SSR

dens

ity (b

pM

b)

900

800

700

600

500

400

300

200

100

0

(b)

Figure 3

0 20 40 60 80 100

MonoDiTri

TetraPentaHexa

()

V olacea

C cinereus

S commune

A bisporus

P ostreatus

Figure 4


2000

1800

1600

1400

1200

1000

800

600

400

200

0N

umbe

r of m

icro

sate

llite


Coprinus cinereus


Pleurotus ostreatus

Agaricus bisporus

AT

CG

ACG

TAG

CT

ATA

TCG

CG

AAC

GTT

AAG

CTT

AAT

ATT

ACG

CTG

ACC

GGT

ACT

ATG

AGC

CGT

AGG

CCT

AGT

ATC

CCG

CGG

AACC

CTA

TTGG

G

Figure 5













4 Discussion











5 Conclusion





Acknowledgments


References






















































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


Volva

riella

volva

cea

Copr

inus

cine

reus

Schi

zoph

yllum

com

mun

e

Agar

icus b

ispor

us

Pleu

rotu

s ostr

eatu

s

0

15

30

45

60

75

HexaPenta

TetraTri

DiMono

Relat

ive a

bund

ance

(No

Mb)

(a)

Volva

riella

volva

cea

Copr

inus

cine

reus

Schi

zoph

yllum

com

mun

e

Agar

icus b

ispor

us

Pleu

rotu

s ostr

eatu

s

HexaPenta

TetraTri

DiMono

SSR

dens

ity (b

pM

b)

900

800

700

600

500

400

300

200

100

0

(b)

Figure 3

0 20 40 60 80 100

MonoDiTri

TetraPentaHexa

()

V olacea

C cinereus

S commune

A bisporus

P ostreatus

Figure 4


2000

1800

1600

1400

1200

1000

800

600

400

200

0N

umbe

r of m

icro

sate

llite


Coprinus cinereus


Pleurotus ostreatus

Agaricus bisporus

AT

CG

ACG

TAG

CT

ATA

TCG

CG

AAC

GTT

AAG

CTT

AAT

ATT

ACG

CTG

ACC

GGT

ACT

ATG

AGC

CGT

AGG

CCT

AGT

ATC

CCG

CGG

AACC

CTA

TTGG

G

Figure 5













4 Discussion











5 Conclusion





Acknowledgments


References






















































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology











4 Discussion











5 Conclusion





Acknowledgments


References






















































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology










5 Conclusion





Acknowledgments


References






















































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


Acknowledgments


References






















































Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology























Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology








Volume 2014

Zoology






















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology

Documents

Research Article Microsatellites in the Genome of the