Supplementary Materials of Article

A long-read transcriptome assembly of cotton (Gossypium hirsutum) and intraspecific SNP discovery

Hamid Ashrafi1*, Amanda M. Hulse-Kemp2, Fei Wang2, Joshua Udall3, Don Jones4, Marta Matvienko5, Keithanne Mockaitis6, David M. Stelly2, Allen Van Deynze1

1- University of California-Davis, Department of Plant Sciences and Seed Biotechnology Center, One Shields Ave, Davis CA 956162- Texas A&M University, Department of Soil and Crop Sciences, College Station, TX 778433- Brigham Young University, Plant and Wildlife Science Department, Provo, UT 840624- Cotton Incorporated, Cary, NC 275135- University of California-Davis, Genome Center, One Shields Ave, Davis CA 95616 Current Address: CLC bio, Cambridge, Massachusetts, United States of America6- Department of Biology, Indiana University, 915 E. Third St., Bloomington IN 47405

Fig. S1

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Number of sequences with length X

Length of Sequences

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N50=1100

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Fig. S2

No BLAST No BLAST hit No Mapping No Annotation Annotated Total0

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Distribution of GO terms derived from each database

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Distribution of GO terms derived from each database

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Dirstribution of Number of Sequences with GO Terms

Number of GOs

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Sequence Length

Percent of Anotated Sequences Relative to Sequence Length

Fig. S5

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IEA

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SequencesEviden

ce Codes

Fig. S6

Vitis viniferaGlycine max

Populus trichocarpaArabidopsis thaliana

Cucumis sativusPrunus persica

Ricinus communisSolanum lycopersicum

Fragaria vescaMedicago truncatula

Oryza sativaArabidopsis lyrata

Zea maysSorghum bicolorCapsella rubella

Brachypodium distachyonLotus japonicus

Hordeum vulgareGossypium hirsutum

Aegilops tauschiiPicea sitchensisTriticum urartu

Nicotiana tabacumSolanum tuberosum

Malus xSelaginella moellendorffii

Physcomitrella patensThellungiella halophila

unknownothers

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Number of BLAST Hits to Available GenBank Species Sequences

Number of hits

Species

Fig. S7

Vitis vinifera

Populus trichocarpa

Glycine max

Fragaria vesca

Medicago truncatula

Arabidopsis thaliana

Oryza sativa

Lotus japonicus

Sorghum bicolor

Jatropha curcas

Hevea brasiliensis

Nicotiana tabacum

Gossypium raimondii

Citrus sinensis

Brachypodium distachyon

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Number of BLAST Top-Hits to Available Sequences Available in GenBank

Number of Hits

Species

Fig. S8

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Fig. S11

Chr 1

Fig. S12-a. Alignment of TM-1 454 and EST sequences to the genome of G. raimondii. a-d) alignment of G. raimondii genes, CDS, Gene based expression and translated region expression to its own genome sequence, respectively. e), f) depicts the left and right had side of break points when TM-1 Reads mapped to G. raimondii genome. g) large InDels h) structural variants.

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Chr 2

Fig. S12-b

Chr 3

Fig. S12-c

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Chr 6

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Chr 7

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Chr 8

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Chr 9

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Chr 10

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Chr 11

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Chr 12

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Chr 13

Fig. S12-m