The genome of Rhizobium leguminosarum has recognizable core and accessory components.
The genome of Rhizobium leguminosarum has recognizable core and accessory components.
复制标题
DOI：
10.1186/gb-2006-7-4-r34
复制
发表时间：
2006
期刊：
影响因子：
12.3
通讯作者：
Parkhill J
中科院分区：
文献类型：
--
作者：
Young JP;Crossman LC;Johnston AW;Thomson NR;Ghazoui ZF;Hull KH;Wexler M;Curson AR;Todd JD;Poole PS;Mauchline TH;East AK;Quail MA;Churcher C;Arrowsmith C;Cherevach I;Chillingworth T;Clarke K;Cronin A;Davis P;Fraser A;Hance Z;Hauser H;Jagels K;Moule S;Mungall K;Norbertczak H;Rabbinowitsch E;Sanders M;Simmonds M;Whitehead S;Parkhill J
描述了豆科植物固氮共生菌Rhizobium leguminosarum的基因组序列，揭示了一个“核心”和一个“附属”组分。豆科根瘤菌（Rhizobium leguminosarum）是豆科植物的一种α-蛋白细菌固氮共生体，已经有一千多篇出版物。与植物共生相互作用的基因已经得到了很好的研究，但允许在土壤环境中生存和生长的适应性却知之甚少。我们已经测定了R.蚕豆生物变种3841菌株。7.75 Mb的基因组包括一个环状染色体和六个环状质粒，总的G+C为61%。所有三个rRNA操纵子和52个tRNA基因都在染色体上;编码必需蛋白质的基因大部分在染色体上，但大多数功能类别也发生在质粒上。在7，263个蛋白质编码基因中，2，056个在三个相关基因组（根癌农杆菌、苜蓿中华根瘤菌和百脉根中慢生根瘤菌）中的每一个中具有直系同源物，并且这些基因在染色体中过量表达，并且具有高于平均水平的G+C。大多数支持基于rRNA的基因组学，证实了A. tumefaciens是这些亲缘关系中最接近的，但有347个基因与这种同源性不相容;这些基因分散在整个基因组中，但在质粒上过度表达。出乎意料的是，这三种根瘤菌共有大量的基因，而A.根瘤菌总的来说，基因组可以被认为有两个主要组成部分：“核心”，G+C较高，主要是染色体，与相关生物共享，并具有一致的同源性;和“辅助”组成部分，分散分布，G+C较低，位于质粒和染色体岛上。尽管存在很长的共存历史，但辅助基因组具有与核心不同的核苷酸组成。
The genome sequence of the α-proteobacterial N2-fixing symbiont of legumes, Rhizobium leguminosarum, is described, revealing a 'core' and an 'accessory' component. Rhizobium leguminosarum is an α-proteobacterial N2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841. The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were over-represented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens. Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.
登录
查看更多内容
DOI：
10.1073/pnas.221575398
发表时间：
2002-01-08
影响因子：
11.1
作者：
DelVecchio, VG;Kapatral, V;Overbeek, R
通讯作者：
Overbeek, R
影响因子：
3.2
作者：
Chain, P;Lamerdin, J;Arp, D
通讯作者：
Arp, D
影响因子：
12.3
作者：
Daubin V;Lerat E;Perrière G
通讯作者：
Perrière G
影响因子：
5.8
作者：
Carver, TJ;Rutherford, KM;Parkhill, J
通讯作者：
Parkhill, J
DOI：
10.1073/pnas.0305659101
发表时间：
2004-06-29
影响因子：
11.1
作者：
Alsmark, CM;Frank, AC;Andersson, SGE
通讯作者：
Andersson, SGE