Summer Internship Project in Academia Sinica

Biodiversity of nematode Caenorhabditis in Taiwan

Distribution of transposons in fire ants chromosomes&

Summer intern student: Chun Yu Chen

Biodiversity of nematode Caenorhabditis in Taiwan

Introduction to genus CaenorhabditisCaenorhabditis elegans - genome sequenced in 1998Caenorhabditis briggsae - genome sequence finished 2003

Living in bacteria-rich environments like compost piles, decaying dead animals and rotting fruit

C. elegans and C. briggsae are both male and hermaphrodite sexes whereas most other species male and female sexes

Discovery of new species of Caenorhabditis nematode has surged in recent years

MethodCollect rotting fruit from

field Put samples on plates

Pick or Chunk worms from plates

Isolate: Pick one pregnant female or hermaphrodite on

one plateLysis(Extract DNA)-PCR-

Sequence-BLAST

Result-OverviewAll Samples in lab My Samples

Caenorhabditis 33 7Oscheius 73 18Panagrolaimus 20 2Pristionchus 12 8Others 37 9No worms 55 11Not finish yet 57 9Toatal 287 64

Result-Analysis of relationship between placed time and dominant species

Caenorhabditis Oscheius Panagrolaimus Pristionchus Others

1-10 5 1 0 0 1

11-20 17 30 5 6 15

21-30 4 26 2 4 14

31-40 7 16 13 1 7

Species T-test

Caenorhabditis vs. Oscheius 0.24664735

Caenorhabditis vs. Panagrolaimus 0.000467427

Caenorhabditis vs. Pristionchus 0.607262216

Caenorhabditis vs. Others 0.284358149

Result-Analysis of relationship between altitude and dominant species

Low Altitude Intermediate Altitude

High Altitude

Caenorhabditis 13 14 6

Oscheius 13 16 44

Panagrolaimus 6 3 10

Pristionchus 0 1 10

Others 2 8 27

Chi-square p-value

5.27E-05

Distribution of transposons in fire ants chromosomes

Introduction to fire ant social chromosome and transposon sequenced data

J. Wang et al., “A Y-like social chromosome causes alternative colony organization in fire ants,”Nature, doi:10.1038/nature11832, 2013.

Transposon primers:Mariner1_ivPCR_F: AACGCCGATAAAAATTCACAACTGCAATGAMariner2_ivPCR_F: TTAAGTGAACATTCAAAATGGCCGAGCTTGBarcode:Name 8bp barcodeSneaky01_F GTGCAGTAGGGATAACAGGGTAAT ATCGCCAG *TSneaky02_F GTGCAGTAGGGATAACAGGGTAAT ATCCTATT *TSneaky03_F GTGCAGTAGGGATAACAGGGTAAT ATATAGGA *TSneaky04_F GTGCAGTAGGGATAACAGGGTAAT CCTTTACA *TSneaky05_F GTGCAGTAGGGATAACAGGGTAAT GAGTTAAC *TSneaky06_F GTGCAGTAGGGATAACAGGGTAAT GTCCATTA *TSneaky07_F GTGCAGTAGGGATAACAGGGTAAT TGAATTCG *TSneaky08_F GTGCAGTAGGGATAACAGGGTAAT AATGCTGA *TSneaky09_F GTGCAGTAGGGATAACAGGGTAAT AATCACAC *TSneaky10_F GTGCAGTAGGGATAACAGGGTAAT AAGATTGC *TSneaky11_F GTGCAGTAGGGATAACAGGGTAAT AAGCGGTC *TSneaky12_F GTGCAGTAGGGATAACAGGGTAAT AACCGTGT *TSneaky13_F GTGCAGTAGGGATAACAGGGTAAT GCAGCCTC *TSneaky14_F GTGCAGTAGGGATAACAGGGTAAT GTTGTCCC *TSneaky15_F GTGCAGTAGGGATAACAGGGTAAT ACAGTGCA *TSneaky16_F GTGCAGTAGGGATAACAGGGTAAT CAATCATC *T*Sneaky11 did not use in this time

Example:1. Barcode Sneaky01, TWSIMariner01AACGCCGATAAAAATTCACAACTGCAATGATAAGGAATTGTTGCCAGATGCCCAACCTTACATTTAAAATTTTTGATCTAACGTTTGGCGCCAGCATTTACCGCTGGCGCCATCTACTGGAAAACGGCGGTTTTCAATTTGTACTCCTAATA-----------------------(genome sequence)-----------------------ACTGGCGATATTACCCTGTTATCCCTACTGCAC

2. Barcode Sneaky01, Mariner2_DFTTAAGTGAACATTCAAAATGGCCGAGCTTGTCGGCATAAGTGAGAGACATGAGTACCAACATAACGCCACAAAAAGATCGAAATTCGAATATGCGTAACCCGCGAAAATTCAAAATTCGCGATACTTTTTGAACACACCTCG-----------------------(genome sequence)-----------------------ACTGGCGATATTACCCTGTTATCCCTACTGCAC

Method

Download the sequenced data

Identify homology across highly

divergent samples by pyRAD

Analysis pyRAD products to get

credible transposon fragments

BLAST transposon fragments with fire

ants genome

Match the BLAST results with fire ant

chromosome

Try to find out the chromosomes

position of scaffolds or contigs

Result-Cluster overviewtaxa total dpt.me dpt.sd d>5.tot d>5.me d>5.sd badpairsMariner1_ivPCR_F 21385 9.22 86.522 724 239.073 407.955 0Mariner2_ivPCR_R 48079 4.122 24.139 1428 100.396 100.284 0

Result-BLAST result

Result-Distribution of transposonsMariner1_ivPCR_F_250

Mariner1_ivPCR_F_500

Mariner2_ivPCR_R_100

Mariner2_ivPCR_R_250

Mariner2_ivPCR_R_500

ch1 3 6 28 1 0ch2 0 3 20 2 0ch3 1 3 23 2 0ch4 3 6 18 3 0ch5 1 0 1 0 0ch6 0 0 7 1 0ch7 1 4 8 0 0ch8 1 2 13 2 0ch9 1 1 9 0 0ch10 1 0 5 0 0ch11 1 2 6 2 0ch12 1 5 10 2 0ch13 1 0 6 0 0ch14 0 2 5 1 0ch15 0 0 4 0 0ch16 1 0 12 0 0

Conclusion• C. elegans are more prevalent in compost and C. remanei in apples,

possibly as a consequence of competition between the two taxa.• Their analysis suggests at least some influence from certain abiotic

factors like humidity and rain.• It is likely that biotic factors are additionally a major determinant of

Caenorhabditis prevalence.

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