Differential genome evolution and speciation of Coix lacryma-jobi L. and Coix aquatica Roxb. hybrid guangxi revealed by repetitive sequence analysis and fine karyotyping
文献类型: 外文期刊
第一作者: Cai, Zexi
作者: Cai, Zexi;Liu, Huijun;He, Qunyan;Pu, Mingwei;Jin, Weiwei;He, Qunyan;Chen, Jian;Lai, Jinsheng;Chen, Jian;Lai, Jinsheng;Li, Xuexian
作者机构:
关键词: Coix;Next-generation sequencing;Repeat element;Genome structure;Karyotyping;Polyploidy;Evolution
期刊名称:BMC GENOMICS ( 影响因子:3.969; 五年影响因子:4.478 )
ISSN: 1471-2164
年卷期: 2014 年 15 卷
页码:
收录情况: SCI
摘要: Background: 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. Results: 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. Conclusions: 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.
分类号:
- 相关文献
作者其他论文 更多>>
-
Metabolomics and ionomics reveal the quality differences among peach, acacia and karaya gums
作者:Zhang, Kaiwei;Yu, Xiangyang;Zhang, Kaiwei;Chen, Meng;Zhang, Xue;Chen, Jian;Chen, Xiaolong;Li, Yong;Yu, Xiangyang;Zhang, Kaiwei;Chen, Meng;Zhang, Xue;Chen, Jian;Chen, Xiaolong;Li, Yong;Yu, Xiangyang;Liu, Xin
关键词:Gum; Metabolomics; Flavonoids; Total phenols content; Metabolites
-
Epigenetics in the modern era of crop improvements
作者:Xue, Yan;Deng, Xing Wang;Cao, Xiaofeng;Deng, Xian;Cao, Xiaofeng;Deng, Xian;Chen, Xiangsong;Yang, Hongchun;Ding, Yong;Dong, Aiwu;Liu, Bing;Ren, Guodong;Zhang, Yijing;Duan, Cheng-Guo;Fang, Xiaofeng;Qi, Yijun;Gong, Lei;Liu, Bao;Xu, Zheng-Yi;Gong, Zhizhong;Gong, Zhizhong;Gu, Xiaofeng;He, Chongsheng;He, Hang;He, Shengbo;He, Xin-Jian;He, Yan;Tian, Zhixi;He, Yuehui;Jia, Guifang;Wang, Yuan;Jiang, Danhua;Song, Xianwei;Jiang, Jianjun;Lai, Jinsheng;Lai, Jinsheng;Lai, Jinsheng;Lai, Jinsheng;Lai, Jinsheng;Lang, Zhaobo;Zhu, Jian-Kang;Li, Chenlong;Li, Qing;Li, Xingwang;Yan, Wenhao;Zhou, Dao-Xiu;Luo, Xiao;Qian, Weiqiang;Song, Qingxin;Wang, Jia-Wei;Xu, Lin;Wu, Liang;Wu, Zhe;Xia, Rui;Xiao, Jun;Zhao, Yusheng;Zhai, Jixian;Zhong, Xuehua;Zhou, Dao-Xiu;Zhou, Ming;Zhou, Yue;Zhu, Bo;Liu, Qikun
关键词:epigenetics; plant development; plant immunity; crop improvement; stress responses
-
Subtilisin-like protease 4 regulates cold tolerance through cell wall modification in rice
作者:Liu, Jingyan;He, Fei;Liu, Meng;Wang, Ying;Cai, Yumeng;Du, Jin;Jin, Weiwei;Liu, Xuejun;Chen, Zhicai;Xiao, Yingni
关键词:
-
Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs
作者:Xu, Zhiting;Lin, Qing;Cai, Xiaodian;Zhong, Zhanming;Teng, Jinyan;Zeng, Haonan;Gao, Yahui;Wei, Chen;Zhou, Jun;Zhang, Wenjing;Zhang, Xiaoke;Shi, Shaolei;Wu, Jun;Diao, Shuqi;Liu, Yuqiang;Pan, Xiangchun;Feng, Xueyan;Liu, Ruiqi;Su, Zhanqin;Chang, Chengjie;Zhu, Qianghui;Wu, Yuwei;Zhang, Hao;Yuan, Xiaolong;Li, Jiaqi;Zhang, Zhe;Li, Bingjie;Gao, Yahui;Liu, George E.;Gao, Yahui;Ma, Li;Cai, Zexi;Bai, Zhonghao;Su, Guosheng;Sahana, Goutam;Lund, Mogens Sando;Fang, Lingzhao;Wang, Xiaoqing;Shi, Liangyu;Zhao, Fuping;Wang, Xue;Wang, Yi;Zhang, Zipeng;Ding, Xiangdong;Lin, Yu;Tang, Guoqing;Li, Mingzhou;Li, Xuewei;Liu, Shuli;Yin, Hongwei;Bai, Lijing;Li, Kui;Zhou, Zhongyin;Wang, Qishan;Pan, Yuchun;Xu, Zhong;Peng, Xianwen;Mei, Shuqi;Mo, Delin;Liu, Xiaohong;Chen, Yaosheng;Liu, Yang;Xiang, Ruidong;Xiang, Ruidong;Shen, Xia;Shen, Xia;Shen, Xia;Li, Pinghua;Huang, Ruihua;Li, Pinghua;Huang, Ruihua;Ballester, Maria;Crespo-Piazuelo, Daniel;Amills, Marcel;Clop, Alex;Amills, Marcel;Karlskov-Mortensen, Peter;Fredholm, Merete;Zhang, Qin;Zhao, Yunxiang
关键词:pig; meta-GWAS; PigGTEx; molQTL; complex traits
-
Genetic Mapping of QTL Associated with 100-Kernel Weight Using a DH Population in Maize
作者:Li, Huawei;Li, Hao;Chen, Jian;Song, Weibin;Lai, Jinsheng;Zhao, Haiming;Chen, Jian;Song, Weibin;Lai, Jinsheng;Zhao, Haiming;Zhang, Xiangbo;Wang, Baobao;Zhi, Shujun;Guan, Haiying;Gao, Rixin
关键词:maize (
Zea mays L.); QTL mapping; 100-kernel weight; DH population -
Preparation, characterization, and antibacterial application of cross-linked nanoparticles composite films
作者:Zhao, Yuxin;Li, Kaimian;Ye, Jianqiu;Zhang, Jie;Zhao, Yuxin;Yao, Guanglong;Chen, Jian;Zhao, Yuxin;Yao, Guanglong;Chen, Jian;Zhao, Yuxin;Yao, Guanglong;Chen, Jian
关键词:Antibacterial activity; Cross-linked tapioca starch; Silver nanoparticles; ZnO nanoparticles
-
Physiological and molecular mechanisms of exogenous salicylic acid in enhancing salt tolerance in tobacco seedlings by regulating antioxidant defence system and gene expression
作者:Song, Xiliang;Xu, Can;Chen, Jian;Cai, Xianjie;Song, Wenjing;Chang, Aixia;Zhang, Yu;Luo, Chenggang
关键词:soil salinity; iron toxicity; oxidative damage; salicylic acid; salt tolerance