My little project. 2014.7~8

1. Biodiversity of nematode
Caenorhabditis in Taiwan
Distribution of transposons in fire
ants chromosomes&
Summer intern student: Chun Yu Chen

2. Biodiversity of nematode
Caenorhabditis in Taiwan

3. Introduction to genus Caenorhabditis
Caenorhabditis elegans - genome
sequenced in 1998
Caenorhabditis 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

4. Method
Collect rotting fruit
from field
Put samples on
plates
Pick or Chunk
worms from plates
Isolate: Pick one
pregnant female or
hermaphrodite on one
plate
Lysis(Extract DNA)-
PCR-Sequence-
BLAST
Freeze worms

5. Result-Overview
All Samples in lab My Samples
Caenorhabditis 33 7
Oscheius 73 18
Panagrolaimus 20 2
Pristionchus 12 8
Others 37 9
No worms 55 11
Not finish yet 57 9
Toatal 287 64

7. 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

8. Species T-test
Caenorhabditis vs. Oscheius 0.24664735
Caenorhabditis vs. Panagrolaimus 0.000467427
Caenorhabditis vs. Pristionchus 0.607262216
Caenorhabditis vs. Others 0.284358149

9. 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

11. Distribution of transposons in fire
ants chromosomes

12. 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.

13. Transposon primers:
Mariner1_ivPCR_F: AACGCCGATAAAAATTCACAACTGCAATGA
Mariner2_ivPCR_F: TTAAGTGAACATTCAAAATGGCCGAGCTTG
Barcode:
Name 8bp barcode
Sneaky01_F GTGCAGTAGGGATAACAGGGTAAT ATCGCCAG *T
Sneaky02_F GTGCAGTAGGGATAACAGGGTAAT ATCCTATT *T
Sneaky03_F GTGCAGTAGGGATAACAGGGTAAT ATATAGGA *T
Sneaky04_F GTGCAGTAGGGATAACAGGGTAAT CCTTTACA *T
Sneaky05_F GTGCAGTAGGGATAACAGGGTAAT GAGTTAAC *T
Sneaky06_F GTGCAGTAGGGATAACAGGGTAAT GTCCATTA *T
Sneaky07_F GTGCAGTAGGGATAACAGGGTAAT TGAATTCG *T
Sneaky08_F GTGCAGTAGGGATAACAGGGTAAT AATGCTGA *T
Sneaky09_F GTGCAGTAGGGATAACAGGGTAAT AATCACAC *T
Sneaky10_F GTGCAGTAGGGATAACAGGGTAAT AAGATTGC *T
Sneaky11_F GTGCAGTAGGGATAACAGGGTAAT AAGCGGTC *T
Sneaky12_F GTGCAGTAGGGATAACAGGGTAAT AACCGTGT *T
Sneaky13_F GTGCAGTAGGGATAACAGGGTAAT GCAGCCTC *T
Sneaky14_F GTGCAGTAGGGATAACAGGGTAAT GTTGTCCC *T
Sneaky15_F GTGCAGTAGGGATAACAGGGTAAT ACAGTGCA *T
Sneaky16_F GTGCAGTAGGGATAACAGGGTAAT CAATCATC *T
*Sneaky11 did not use in this time

14. Example:
1. Barcode Sneaky01, TWSIMariner01
AACGCCGATAAAAATTCACAACTGCAATGATAAGGAATTGTTGCCAGATGCCCAACCTT
ACATTTAAAATTTTTGATCTAACGTTTGGCGCCAGCATTTACCGCTGGCGCCATCTACTG
GAAAACGGCGGTTTTCAATTTGTACTCCTAATA-----------------------(genome
sequence)-----------------------ACTGGCGATATTACCCTGTTATCCCTACTGCAC
2. Barcode Sneaky01, Mariner2_DF
TTAAGTGAACATTCAAAATGGCCGAGCTTGTCGGCATAAGTGAGAGACATGAGTACCA
ACATAACGCCACAAAAAGATCGAAATTCGAATATGCGTAACCCGCGAAAATTCAAAATT
CGCGATACTTTTTGAACACACCTCG-----------------------(genome sequence)-----------
------------ACTGGCGATATTACCCTGTTATCCCTACTGCAC

15. 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

16. Result-Cluster overview
taxa total dpt.me dpt.sd d>5.tot d>5.me d>5.sd badpairs
Mariner1_ivPCR_F 21385 9.22 86.522 724 239.073 407.955 0
Mariner2_ivPCR_R 48079 4.122 24.139 1428 100.396 100.284 0

17. Result-BLAST result

18. Result-Distribution of transposons
Mariner1_ivPCR_F_
250
Mariner1_ivPCR_F_
500
Mariner2_ivPCR_R_
100
Mariner2_ivPCR_R_
250
Mariner2_ivPCR_R_
500
ch1 3 6 28 1 0
ch2 0 3 20 2 0
ch3 1 3 23 2 0
ch4 3 6 18 3 0
ch5 1 0 1 0 0
ch6 0 0 7 1 0
ch7 1 4 8 0 0
ch8 1 2 13 2 0
ch9 1 1 9 0 0
ch10 1 0 5 0 0
ch11 1 2 6 2 0
ch12 1 5 10 2 0
ch13 1 0 6 0 0
ch14 0 2 5 1 0
ch15 0 0 4 0 0
ch16 1 0 12 0 0

23. 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.

24. Thank you for your listening!