Analysis of genome sequence and symbiotic ability of rhizobial strains isolated from seeds of common bean (Phaseolus vulgaris).
Analysis of genome sequence and symbiotic ability of rhizobial strains isolated from seeds of common bean (Phaseolus vulgaris).
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DOI：
10.1186/s12864-018-5023-0
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发表时间：
2018-08-30
期刊：
影响因子：
4.4
通讯作者：
Peralta H
中科院分区：
文献类型：
--
作者：
Aguilar A;Mora Y;Dávalos A;Girard L;Mora J;Peralta H
根瘤菌是常见于土壤和豆科植物根瘤中的α-变形菌。最近报道固氮根瘤菌也栖息在豆科植物种子中。在这项研究中，我们研究了从普通菜豆种子中分离的七株根瘤菌的全基因组序列。本研究所用的根瘤菌分属于菜豆根瘤菌Rhizobium phaseoli、R.豆科（R. leguminosarum）和豆科（R.格拉汉姆。基因组序列分析显示，其中6个菌株形成了3对高度相关的菌株。组成一对的两个菌株共享除一个质粒外的所有质粒。在三对中的两对中，其中一个成员菌株在固氮和固氮方面是有效的，而另一个是无效的。每一对中无效菌株的基因组缺少负责共生的几个基因，包括nod、nif和fix基因，而有效菌株的基因组则含有成簇的相应基因，这表明重组事件引起无效菌株的基因丢失。种子菌株和根瘤菌株的基因组序列的比较表明，染色体序列的保守性较高，质粒序列的保守性较低。大约70%的基因在每个物种的菌株之间共享。然而，旁系同源物更丰富的种子菌株比根瘤菌株。功能分析表明，种子菌株特别丰富的基因参与运输和代谢的氨基酸和碳水化合物，生物合成的辅因子和转座子和原噬菌体。种子株基因组中含有多个完整的原噬菌体，其中一个原噬菌体在三株R. phaseoli和R.豆科植物中华民国grahamii菌株携带类似于基因转移剂（GTA）的原噬菌体;这代表了该属报道的第一个GTA。种子代表了细菌的生态位;根瘤菌进入种子可能会引发细菌的感染、重组、质粒的丢失或获得以及共生基因的丢失。这个过程可能代表了持续的进化，最终将这些菌株转化为专性内生菌。本文的在线版本（10.1186/s12864-018-5023-0）包含补充材料，可供授权用户使用。
Rhizobia are alpha-proteobacteria commonly found in soil and root nodules of legumes. It was recently reported that nitrogen-fixing rhizobia also inhabit legume seeds. In this study, we examined whole-genome sequences of seven strains of rhizobia isolated from seeds of common bean (Phaseolus vulgaris). Rhizobial strains included in this study belonged to three different species, including Rhizobium phaseoli, R. leguminosarum, and R. grahamii. Genome sequence analyses revealed that six of the strains formed three pairs of highly related strains. Both strains comprising a pair shared all but one plasmid. In two out of three pairs, one of the member strains was effective in nodulation and nitrogen fixation, whereas the other was ineffective. The genome of the ineffective strain in each pair lacked several genes responsible for symbiosis, including nod, nif, and fix genes, whereas that of the effective strain harbored the corresponding genes in clusters, suggesting that recombination events provoked gene loss in ineffective strains. Comparisons of genomic sequences between seed strains and nodule strains of the same species showed high conservation of chromosomal sequences and lower conservation of plasmid sequences. Approximately 70% of all genes were shared among the strains of each species. However, paralogs were more abundant in seed strains than in nodule strains. Functional analysis showed that seed strains were particularly enriched in genes involved in the transport and metabolism of amino acids and carbohydrates, biosynthesis of cofactors and in transposons and prophages. Genomes of seed strains harbored several intact prophages, one of which was inserted at exactly the same genomic position in three strains of R. phaseoli and R. leguminosarum. The R. grahamii strain carried a prophage similar to a gene transfer agent (GTA); this represents the first GTA reported for this genus. Seeds represent a niche for bacteria; their access by rhizobia possibly triggered the infection of phages, recombination, loss or gain of plasmids, and loss of symbiosis genes. This process probably represents ongoing evolution that will eventually convert these strains into obligate endophytes. The online version of this article (10.1186/s12864-018-5023-0) contains supplementary material, which is available to authorized users.
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影响因子：
5.2
作者：
Aguilar A;Peralta H;Mora Y;Díaz R;Vargas-Lagunas C;Girard L;Mora J
通讯作者：
Mora J
影响因子：
3.2
作者：
BROM, S;DELOSSANTOS, AG;PALACIOS, R
通讯作者：
PALACIOS, R
影响因子：
3.2
作者：
Cevallos, MA;Encarnacion, S;Mora, J
通讯作者：
Mora, J
影响因子：
11.3
作者：
Juhas M;van der Meer JR;Gaillard M;Harding RM;Hood DW;Crook DW
通讯作者：
Crook DW
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.