Nucleotide diversity and selection signature in the domesticated silkworm, Bombyx mori, and wild silkworm, Bombyx mandarina

Journal of Insect Science

Volumn 11, Issue , 2011, Pages

  Guo, Yi ^a   Shen, Yi Hong ^a   Sun, Wei ^a   Kishino, Hirohisa ^b   Xiang, Zhong Huai ^a   Zhang, Ze ^a,c  

^a SOUTHWEST UNIVERSITY   (China)

^b UNIVERSITY OF TOKYO   (Japan)

^c CHONGQING UNIVERSITY   (China)

Author keywords

Bottleneck; Domestication; Nucleotide diversity; Selection

Indexed keywords

BOMBYCIDAE; BOMBYX MANDARINA; BOMBYX MORI; LEPIDOPTERA;

ANIMAL; ARTICLE; COMPARATIVE STUDY; GENE; GENE LINKAGE DISEQUILIBRIUM; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; GENETICS; SILKWORM;

ANIMALS; BOMBYX; GENES, INSECT; GENETIC VARIATION; LINKAGE DISEQUILIBRIUM; RECOMBINATION, GENETIC; SELECTION, GENETIC;

EID: 84857247513     PISSN: None     EISSN: 15362442     Source Type: Journal    
DOI: 10.1673/031.011.15501     Document Type: Article

References (44)

1. Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437(7062): 1149-1152. (Pubitemid 41509351)
2. Banno Y, Nakamura T, Nagashima E, Fujii H, Doira H. 2004. M chromosome of the wild silkworm, Bombyx mandarina (n = 27), corresponds to two chromosomes in the domesticated silkworm, Bombyx mori (n =28). Genome 47(1): 96-101. (Pubitemid 38504135)
3. Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, et.al. 2007. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genetics 3: e163.
4. Charlesworth D, Bartolomé C, Schierup MH, Mable BK. 2003. Haplotype structure of the stigmatic self-incompatibility gene in natural populations of Arabidopsis lyrata. Molecular Biology and Evolution. 20(11): 1741-1753. (Pubitemid 37420927)
5. Counterman B, Araujo-Perez F, Hines H, Baxter S, Morrison C, Lindstrom1 D, Papa R, Ferguson L, Joron M, Ffrench-Constant R, et al. 2010. Genomic hotspots for adaptation: the population genetics of mullerian mimicry in Heliconius erato. PLoS Genetics 6: e1000796.
6. Eyre-Walker AR, Gaut L, Hilton H, Eldman DL, Gaut BS. 1998. Investigation of the bottleneck leading to the domestication of maize. Proceedings of the National Academy of Sciences 95(8): 4441-4446. (Pubitemid 28207931)
7. Garris AJ, McCouch SR, Kresovich S. 2003. Population structure and its effects on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.). Genetics 165(2): 759-769. (Pubitemid 37337641)
8. Goldsmith MR, Shimada T, Abe H. 2005. The genetics and genomics of the silkworm. Bombyx mori. Annual Review of Entomology 50: 71-100.
9. Hall TA. 1999. Bioedita user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
10. Hamblin MT, Casa AM, Sun H, Murray SC, Paterson AH, Aquadro CF, Kresovich S. 2006. Challenges of Detecting Directional Selection After a Bottleneck: Lessons From Sorghum bicolor. Genetics 173(2): 953-964. (Pubitemid 43945910)
11. Haudry A, Cenci A, Ravel C, Bataillon T, Brunel D, Poncet C, Hochu I, Poirier S, Santoni S, Glemin S, David J. 2007. Grinding up wheat: a massive loss of nucleotide diversity since domestication. Molecular Biology and Evolution. 24(7): 1506-1517. (Pubitemid 47216606)
12. Hill WG, Robertson A. 1968. Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 38(6): 226-231.
13. Hudson RR, Kaplan NL. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111(1): 147-164. (Pubitemid 16248827)
14. Hudson RR. 1987. Estimating the recombination parameter of a finite population model without selection. Gentical Research 50(3): 245-250. (Pubitemid 18042123)
15. Hudson, RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18(2): 337-338. (Pubitemid 34183119)
16. Kolkman JM, Berry ST, Leon AJ, Slabaugh MB, Tang S, Gao W, Shintani DK, Burke JM, Knapp SJ. 2007. Single nucleotide polymorphisms and linkage disequilibrium in sunflower. Genetics 177(1): 457-468. (Pubitemid 47555863)
17. Labate JA, Robertson LD, Baldo AM. 2009. Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.). Heredity 103(3): 257-267.
18. Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research. 18(11): 1851-1858.
19. Li X, Tan L, Zhu Z, Huang H, Liu Y, Hu S, Sun C. 2009. Patterns of nucleotide diversity in wild and cultivated rice. Plant systematics and evolution 281: 97-106.
20. Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11): 1451-1452.
21. Liu A, Burke JM. 2006. Patterns of nucleotide diversity in wild and cultivated sunflower. Genetics 173(1): 321-330. (Pubitemid 43800205)
22. Lu C, Yu SH, Xiang ZH. 2002. Molecular systematic studies on Chinese mandarina silkworm (Bombyx manderina M.) and domestic silkworm (Bombyx mori L.). Scieatia Agricultura Sinica 35(1): 94-101.
23. Matzkin LM. 2008. The molecular basis of host adaptation in Cactophilic Drosophila: molecular evolution of a Glutathione STransferase gene (GstD1) in Drosophila mojavensis. Genetics 178(2): 1073-1083. (Pubitemid 351398814)
24. Olsen KM, Caicedo AL, Polato N, McClung A, McCouch S, Purugganan MD. 2006. Selection under domestication: evidence for a sweep in the rice waxy genomic region. Genetics 173(2): 975-983. (Pubitemid 43945912)
25. Pool J, Hellmann I, Jensen J, Nielsen R. 2010. Population genetic inference from genomic sequence variation. Genome Research 20(3): 291-300.
26. Raymond M, Rousset F. 1995. GENEPOP (version 1.2), population genetics software for exact tests and ecumenicism. Journal of Heredity 86(3): 248-249.
27. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler IV ES. 2001. Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proceedings of the National Academy of Sciences 98(20): 11479-11484. (Pubitemid 32928754)
28. Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nature Biotechnology 26(10): 1135-1145.
29. Tanaka H, Ishibash J, Fujita K, Nakajima Y, Sagisaka A, Tomimoto K, Suzuki N, Yoshiyama M, Kaneko Y, Iwasaki T, et al. 2008. A genome-wide analysis of genes and gene families involved in innate immunity of Bombyx mori. Insect Biochemistry and Molecular Biology 38(12): 1087-1110.
30. Tang T, Lu J, Huang J, He J, McCouch SR, Shen Y, Kai Z, Purugganan MD, Shi S, Wu CI. 2006. Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication. Plos Genetics 2: e199.
31. Tanksley S, McCouch SR. 1997. Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277(5329): 1063-1066. (Pubitemid 27371620)
32. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS. 2001. Patterns Nature of the Drugs of the Peal Bag in Songs (Zea mays ssp. mays L.). Proceedings of the National Academy of Sciences 98(16): 9161-9166.
33. Tenaillon MI, U'ren J, Tenaillon O, Gaut BS. 2004. Selection versus demography: a multilocus investigation of the domestication process in maize. Molecular Biology and Evolution 21(7): 1214-1225. (Pubitemid 38823724)
34. Thompson, JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25(24): 4876-4882. (Pubitemid 28022245)
35. Tian F, Stevens NM, Buckler IV ES. 2009. Tracking footprints of maize Higginson syringe. Proceedings of the National Academy of Sciences 106(Supplement 1): 9979-9986.
36. Vigouroux Y, McMullen M, Hittinger CT, Houchins K, Schulz L, Kresovich S, Matsuoka Y, Doebley J. 2002. Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proceedings of the National Academy of Sciences 99(15): 9650-9655. (Pubitemid 34831102)
37. Weiss, G, Haeseler A. 1998 Inference of population history using a likelihood approach. Genetics 149(3): 1539-1546. (Pubitemid 28334543)
38. Wilcoxon F. 1945. Individual comparisons by ranking methods. Biometrics 1(6): 80-83.
39. White GM, Hamblin MT, Kresovich S. 2004. Molecular evolution oagronomic cropreplacement evolution. Molecular Biology and Evolution 21(4): 716-723.
40. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS. 2005. The effects of artificial selection of the maize genome. Science 308(5726): 1310-1314. (Pubitemid 40746127)
41. Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, Dai F, Li Y, Cheng D, Li R, et al. 2009. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326(5951): 433-436.
42. Xiang ZH, Huang JT, Xia JG, Lu C. 2005. Biology of Sericulture. China Forestry Publishing House.
43. Zhu Q, Zheng X, Luo J, Gaut BS, Ge S. 2007. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Molecular Biology and Evolution 24(3): 875-888. (Pubitemid 46355812)
44. Zhu YL, Song QJ, Hyten DL, Von Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB. 2003. Single-nucleotide polymorphisms in soybean. Genetics 163(3): 1123-1134. (Pubitemid 36417952)