Summer Internship Project in Academia Sinica
-
Upload
yoyo-chen- -
Category
Science
-
view
115 -
download
2
Transcript of 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.
Thank you for your listening!