Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes.
Gene space dynamics during the evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor genomes.
复制标题
aegilops tauschii，胸臂式distachyon，oryza sativa和高粱双色基因组进化过程中的基因空间动力学。
DOI：
10.1093/molbev/msr080
复制
发表时间：
2011-09
影响因子：
10.7
通讯作者：
Devos KM
中科院分区：
文献类型：
--
作者：
Massa AN;Wanjugi H;Deal KR;O'Brien K;You FM;Maiti R;Chan AP;Gu YQ;Luo MC;Anderson OD;Rabinowicz PD;Dvorak J;Devos KM
利用桑格测序技术对粗山羊草基因组的9个不同区域共9.7 Mb进行了测序，并与直序短柄草、水稻和高粱的基因组序列进行了比较。在这些地区的祖先基因的内容进行推断，并用于估计基因缺失和基因重复率沿着每个分支的系统发育树有关的四个物种。现存的Ae. tauschii的基因组估计为36，371。利用基因缺失率、基因重复率和基因总数估计系统树各节点的基因总数。据估计，Brachypodieae和Triticeae谱系的共同祖先有28，558个基因，而Panicoideae，Ehrhartoideae和Pooideae亚科的共同祖先估计有27，152或28，350个基因，这取决于祖先基因方案。相对于Brachypodieae和Triticeae的共同祖先，B的基因数目减少。二穗型增加了3，026个基因，并且在Ae. tauschii有7,813个基因基因缺失率和基因重复率之和反映了基因同线性丢失率，与结构染色体重排率相关，并且在Ae中最高。tauschii谱系和最低的水稻谱系。基因空间进化的高速率在Ae。tauschii血统占的事实是，与预期相反，水平的共线性之间的同源性更相关的Ae。tauschii和B.二穗型基因组之间的同线性水平相似的Ae。tauschii的基因组和不太相关的水稻和高粱的基因组。这四种草的基因重复率与基因缺失率的比值与一个物种的基因总数和整个基因组的大小密切相关。由于整个基因组的大小在很大程度上是基因组中重复序列含量的函数，我们认为重复序列的数量和活性是决定基因组中基因数量的重要因素。
Nine different regions totaling 9.7 Mb of the 4.02 Gb Aegilops tauschii genome were sequenced using the Sanger sequencing technology and compared with orthologous Brachypodium distachyon, Oryza sativa (rice), and Sorghum bicolor (sorghum) genomic sequences. The ancestral gene content in these regions was inferred and used to estimate gene deletion and gene duplication rates along each branch of the phylogenetic tree relating the four species. The total gene number in the extant Ae. tauschii genome was estimated to be 36,371. The gene deletion and gene duplication rates and total gene numbers in the four genomes were used to estimate the total gene number in each node of the phylogenetic tree. The common ancestor of the Brachypodieae and Triticeae lineages was estimated to have had 28,558 genes, and the common ancestor of the Panicoideae, Ehrhartoideae, and Pooideae subfamilies was estimated to have had 27,152 or 28,350 genes, depending on the ancestral gene scenario. Relative to the Brachypodieae and Triticeae common ancestor, the gene number was reduced in B. distachyon by 3,026 genes and increased in Ae. tauschii by 7,813 genes. The sum of gene deletion and gene duplication rates, which reflects the rate of gene synteny loss, was correlated with the rate of structural chromosome rearrangements and was highest in the Ae. tauschii lineage and lowest in the rice lineage. The high rate of gene space evolution in the Ae. tauschii lineage accounts for the fact that, contrary to the expectations, the level of synteny between the phylogenetically more related Ae. tauschii and B. distachyon genomes is similar to the level of synteny between the Ae. tauschii genome and the genomes of the less related rice and sorghum. The ratio of gene duplication to gene deletion rates in these four grass species closely parallels both the total number of genes in a species and the overall genome size. Because the overall genome size is to a large extent a function of the repeated sequence content in a genome, we suggest that the amount and activity of repeated sequences are important factors determining the number of genes in a genome.
登录
查看更多内容
DOI：
10.1007/978-0-387-77489-3_23
发表时间：
2009-01-01
期刊：
GENETICS AND GENOMICS OF THE TRITICEAE
影响因子：
--
作者：
Dvorak, Jan
通讯作者：
Dvorak, Jan
DOI：
10.1073/pnas.94.13.6809
发表时间：
1997-06-24
影响因子：
11.1
作者：
Gaut, BS;Doebley, JF
通讯作者：
Doebley, JF
DOI：
10.1073/pnas.0502923102
发表时间：
2005-06-21
影响因子：
11.1
作者：
Lai, JS;Li, YB;Dooner, HK
通讯作者：
Dooner, HK
影响因子：
7
作者：
Ma, JX;Devos, KM;Bennetzen, JL
通讯作者：
Bennetzen, JL
影响因子：
11.6
作者：
Choulet, Frederic;Wicker, Thomas;Feuillet, Catherine
通讯作者：
Feuillet, Catherine