Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping.
Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping.
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薏苡和薏苡的差异基因组进化和物种形成。
DOI：
10.1186/1471-2164-15-1025
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发表时间：
2014-11-25
期刊：
影响因子：
4.4
通讯作者：
Jin W
中科院分区：
文献类型：
--
作者：
Cai Z;Liu H;He Q;Pu M;Chen J;Lai J;Li X;Jin W
薏苡仁、高粱和玉米是菊科亚族中关系密切的植物属。薏苡仁有9 ~ 11种不同倍性水平（2n = 10、20、30、40）。专门栽培的C. lacryma-jobi L. （2n = 20）广泛用于东亚和东南亚的食品和医药应用。三种可育细胞型（2n = 10、20和40）已被报道。最近在广西发现了一种与水草（C. aquatica）密切相关的不育细胞型（2n = 30）。这个假定的杂交种被命名为C. aquatica HG （hybrid广西）。目前，对泪鱼和水鱼的基因组组成和进化史尚不清楚。通过低覆盖率基因组测序和相似度聚类分析，可以发现，约76%的C. lacryma-jobi基因组和73%的C. aquatica HG基因组是重复DNA序列。此外，长末端重复序列（long terminal repeat， LTR）逆转录转座元件是这两个基因组中的优势重复序列，许多重复序列在全基因组中的比例在两个物种之间差异很大，表明它们在进化上存在分歧。我们还发现了一种新的102 bp的着丝粒卫星重复序列CentX和另外两个卫星只出现在水草中。重复序列探针鸡尾酒的FISH分析结果和减数分裂中期染色体配对数据表明，泪草可能是二倍体的古四倍体物种，水草可能是新近形成的杂交物种。此外，泪草和水草与高粱的重复家族共存较多，序列相似性高于玉米。细核型分析和染色体配对结果表明，泪鱼在进化过程中发生了二倍体化，泪鱼是新近形成的杂交种。重复序列的全基因组比较表明，薏苡米的重复序列与高粱的重复序列更相似，而与玉米的重复序列更相似，这与前人报道的系统发育关系一致。本文的在线版本（doi:10.1186/1471-2164-15-1025）包含补充材料，可供授权用户使用。
Coix, Sorghum and Zea are closely related plant genera in the subtribe Maydeae. Coix comprises 9–11 species with different ploidy levels (2n = 10, 20, 30, and 40). The exclusively cultivated C. lacryma-jobi L. (2n = 20) is widely used in East and Southeast Asia for food and medicinal applications. Three fertile cytotypes (2n = 10, 20, and 40) have been reported for C. aquatica Roxb. One sterile cytotype (2n = 30) closely related to C. aquatica has been recently found in Guangxi of China. This putative hybrid has been named C. aquatica HG (Hybrid Guangxi). The genome composition and the evolutionary history of C. lacryma-jobi and C. aquatica HG are largely unclear. About 76% of the genome of C. lacryma-jobi and 73% of the genome of C. aquatica HG are repetitive DNA sequences as shown by low coverage genome sequencing followed by similarity-based cluster analysis. In addition, long terminal repeat (LTR) retrotransposable elements are dominant repetitive sequences in these two genomes, and the proportions of many repetitive sequences in whole genome varied greatly between the two species, indicating evolutionary divergence of them. We also found that a novel 102 bp variant of centromeric satellite repeat CentX and two other satellites only appeared in C. aquatica HG. The results from FISH analysis with repeat probe cocktails and the data from chromosomes pairing in meiosis metaphase showed that C. lacryma-jobi is likely a diploidized paleotetraploid species and C. aquatica HG is possibly a recently formed hybrid. Furthermore, C. lacryma-jobi and C. aquatica HG shared more co-existing repeat families and higher sequence similarity with Sorghum than with Zea. The composition and abundance of repetitive sequences are divergent between the genomes of C. lacryma-jobi and C. aquatica HG. The results from fine karyotyping analysis and chromosome pairing suggested diploidization of C. lacryma-jobi during evolution and C. aquatica HG is a recently formed hybrid. The genome-wide comparison of repetitive sequences indicated that the repeats in Coix were more similar to those in Sorghum than to those in Zea, which is consistent with the phylogenetic relationship reported by previous work. The online version of this article (doi:10.1186/1471-2164-15-1025) contains supplementary material, which is available to authorized users.
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影响因子：
1.7
作者：
Albert, P. S.;Gao, Z.;Birchler, J. A.
通讯作者：
Birchler, J. A.
DOI：
10.1073/pnas.97.13.7002
发表时间：
2000-06-20
影响因子：
11.1
作者：
Fedoroff, N
通讯作者：
Fedoroff, N
影响因子：
3.3
作者：
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4.5
作者：
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通讯作者：
Bennetzen JL
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影响因子：
1.6
作者：
Han, Yonghua;Wang, Guixiang;Jin, Weiwei
通讯作者：
Jin, Weiwei