SSRs(Simple sequence repeats)是一类广泛存在于动植物基因组的DNA短串联重复序列,是重要的基因组分子标记。比较不同基因组同源SSR的差异,有利于了解相近物种间的进化过程。文章使用雷蒙德氏棉基因组(D5)、亚洲棉基因组(A2)全基因组序列和陆地棉(AD1)的限制性酶切基因组测序数据,进行全基因组SSR扫描,比较了A组和D组的SSR分布情况,通过识别3个基因组之间的同源SSR,比较它们之间同源SSR重复序列的差异。结果发现,A组和D组同源SSR的分布规律非常相似,但A组与AD组的同源SSR保守性比D组与AD组同源SSR的保守性强。与AD组同源SSR相比,A组中重复序列长度增长的SSR数量约为长度缩短的SSR数量的5倍,在D组中这一比值约为3倍。可以推测,四倍体AD组在与A组、D组的平行进化过程中,由于基因组融合,导致SSR的重复序列长度变化速率与二倍体A、D组有差异,同时这种差异可能导致了AD组SSR重复序列长度在进化过程中与二倍体相比有变短的趋势。文章首次对3个棉花基因组的同源SSR进行了系统地比较,发现了同源SSR在棉属四倍体基因组和二倍体基因组中的显著差异,为进一步揭示棉属基因组的进化规律提供了基础。
Simple sequence repeats (SSRs)are a class of repetitive DNA sequences, which are commonly used for genome analysis. Comparison of the homologous SSRs among different genomes is helpful to understand the evolutionary process in relative species. In this study, SSR scanning was performed to investigate their distribution and length variation among the genomes of G. raimondii (D5), G. arboretum (A2) and G. hirsutum (AD1). The results demonstrated that the distribution of SSRs in A genome was very similar with that in D genome, while the length variation of homologous SSRs between A and AD genome was more conserved than that between D and AD genome. Compared with SSRs in AD genome, the number of SSRs with longer motif length in A genome was about five times of those with shorter motif length, while it was about three times in D genome. This implied that the length variation rates of homologous SSRs between diploid cotton and tetraploid cotton were different during the parallel evolution due to the subgenome fusion, and the motif length of most SSRs in tetraoploid genome tended to become shorter than homologous SSRs in diploid genome during the process of evolution. This study comprehensively compared the SSRs in three cotton genomes and revealed the significant difference among them, providing a foundation for further evolutionary study of Gossypium genome.
[1] Ellegren H. Microsatellites: simple sequences with complex evolution. Nat Rev Genet , 2004, 5(6): 435-445.
[2] Morgante M, Olivieri AM. PCR-amplified microsatellites as markers in plant genetics. Plant J , 1993, 3(1): 175-182. Ellegren H, Moore S, Robinson N, Byrne K, Ward W, Sheldon BC. Microsatellite evolution-a reciprocal study of repeat lengths at homologous loci in cattle and sheep. Mol Biol Evol , 1997, 14(8): 854-860.
[3] Webster MT, Smith NGC, Ellegren H. Microsatellite evolution inferred from human-chimpanzee genomic sequence alignments. Proc Natl Acad Sci USA , 2002, 99(13): 8748- 8753.
[4] Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL. High resolution of human evolutionary trees with polymorphic microsatellites. Nature , 1994, 368(6470): 455-457.
[5] 杨弘, 李大宇, 曹祥, 邹芝英, 肖炜, 祝璟琳. 微卫星标记分析罗非鱼群体的遗传潜力. 遗传, 2011, 33(7): 768-775.
[6] Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A. Cross-species amplification of soybean ( Glycine max ) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol Biol Evol , 1998, 15(10): 1275-1287.
[7] Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet , 2002, 30(2): 194-200.
[8] Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S. Computational and experimental analysis of microsatellites in rice ( Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res , 2001, 11(8): 1441-1452.
[9] 谢文刚, 张新全, 马啸, 彭燕, 黄琳凯. 鸭茅种质遗传变异及亲缘关系的SSR分析. 遗传, 2009, 31(6): 654-662.
[10] Vowles EJ, Amos W. Quantifying ascertainment bias and species-specific length differences in human and chimpanzee microsatellites using genome sequences. Mol Biol Evol , 2006, 23(3): 598-607.
[11] Kelkar YD, Tyekucheva S, Chiaromonte F, Makova KD. The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Res , 2008, 18(1): 30-38. Chistiakov DA, Hellemans B, Volckaert FAM. Microsatellites and their genomic distribution, evolution, function and applications: a review with special reference to fish genetics. Aquaculture , 2006, 255(1-4): 1-29.
[12] La Rota M, Kantety RV, Yu JK, Sorrells ME. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics , 2005, 6(1): 23.
[13] Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL, Myers RM. Worldwide human relationships inferred from genome-wide patterns of variation. Science , 2008, 319(5866): 1100-1104.
[14] Sonah H, Deshmukh RK, Sharma A, Singh VP, Gupta DK, Gacche RN, Rana JC, Singh NK, Sharma TR. Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium . PLoS One , 2011, 6(6): e21298.
[15] Wang HT, Li XM, Gao WH, Jin X, Zhang XL, Lin ZX. Comparison and development of EST-SSRs from two 454 sequencing libraries of Gossypium barbadense . Euphytica , 2014, 198(2): 277-288. Han ZG, Wang CB, Song XL, Guo WZ, Gou ZY, Li CH, Chen XY, Zhang TZ. Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet , 2006, 112(3): 430-439.
[16] Wang CB, Guo WZ, Cai CP, Zhang TZ. Characterization, development and exploitation of EST-derived microsatellites in Gossypium raimondii Ulbrich. Chin Sci Bull , 2006, 51(5): 557-561.
[17] Lacape JM, Dessauw D, Rajab M, Noyer JL, Hau B. Microsatellite diversity in tetraploid Gossypium germplasm : assembling a highly informative genotyping set of cotton SSRs. Mol Breeding , 2007, 19(1): 45-58.
[18] Alves MF, Barroso PA, Ciampi AY, Hoffmann LV, Azevedo VC, Cavalcante U. Diversity and genetic structure among subpopulations of Gossypium mustelinum (Malvaceae). G
