State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
BMC Genomics. 2020 Feb 27;21(1):186. doi: 10.1186/s12864-020-6578-0.
Phaseolus vulgaris (common bean) microsymbionts belonging to the bacterial genera Rhizobium, Bradyrhizobium, and Ensifer (Sinorhizobium) have been isolated across the globe. Individual symbiosis genes (e.g., nodC) of these rhizobia can be different within each genus and among distinct genera. Little information is available about the symbiotic structure of indigenous Rhizobium strains nodulating introduced bean plants or the emergence of a symbiotic ability to associate with bean plants in Bradyrhizobium and Ensifer strains. Here, we sequenced the genomes of 29 representative bean microsymbionts (21 Rhizobium, four Ensifer, and four Bradyrhizobium) and compared them with closely related reference strains to estimate the origins of symbiosis genes among these Chinese bean microsymbionts.
Comparative genomics demonstrated horizontal gene transfer exclusively at the plasmid level, leading to expanded diversity of bean-nodulating Rhizobium strains. Analysis of vertically transferred genes uncovered 191 (out of the 2654) single-copy core genes with phylogenies strictly consistent with the taxonomic status of bacterial species, but none were found on symbiosis plasmids. A common symbiotic region was wholly conserved within the Rhizobium genus yet different from those of the other two genera. A single strain of Ensifer and two Bradyrhizobium strains shared similar gene content with soybean microsymbionts in both chromosomes and symbiotic regions.
The 19 native bean Rhizobium microsymbionts were assigned to four defined species and six putative novel species. The symbiosis genes of R. phaseoli, R. sophoriradicis, and R. esperanzae strains that originated from Mexican bean-nodulating strains were possibly introduced alongside bean seeds. R. anhuiense strains displayed distinct host ranges, indicating transition into bean microsymbionts. Among the six putative novel species exclusive to China, horizontal transfer of symbiosis genes suggested symbiosis with other indigenous legumes and loss of originally symbiotic regions or non-symbionts before the introduction of common bean into China. Genome data for Ensifer and Bradyrhizobium strains indicated symbiotic compatibility between microsymbionts of common bean and other hosts such as soybean.
在全球范围内，已从菜豆属植物中分离出属于细菌属根瘤菌、慢生根瘤菌和中华根瘤菌（根瘤菌属）的小扁豆共生体。这些根瘤菌的个别共生基因（例如 nodC）在每个属内以及不同属之间可能不同。关于结瘤豆科植物的本土根瘤菌菌株的共生结构或慢生根瘤菌和中华根瘤菌菌株与豆科植物共生能力的出现的信息很少。在这里，我们对 29 个代表性的豆类共生体（21 个根瘤菌、4 个中华根瘤菌和 4 个慢生根瘤菌）进行了基因组测序，并将其与密切相关的参考菌株进行了比较，以估计这些中国豆类共生体中共生基因的起源。
比较基因组学表明，水平基因转移仅发生在质粒水平，导致结瘤根瘤菌菌株的多样性扩大。垂直转移基因的分析揭示了 191 个（2654 个）单拷贝核心基因，其系统发育与细菌物种的分类地位严格一致，但在共生质粒上没有发现。一个共同的共生区域在根瘤菌属内完全保守，但与其他两个属的不同。一个中华根瘤菌菌株和两个慢生根瘤菌菌株在染色体和共生区域与大豆共生体具有相似的基因含量。
19 种本土豆类根瘤菌共生体被分配到四个确定的种和六个假定的新种。源自墨西哥豆类结瘤菌株的 R. phaseoli、R. sophoriradicis 和 R. esperanzae 菌株的共生基因可能是随着豆类种子一起引入的。R. anhuiense 菌株表现出不同的宿主范围，表明其已转变为豆类共生体。在仅在中国特有的六个假定的新种中，共生基因的水平转移表明与其他本土豆科植物的共生关系以及在大豆引入中国之前失去了原本的共生区域或非共生体。中华根瘤菌和慢生根瘤菌菌株的基因组数据表明，普通菜豆的共生体与其他宿主（如大豆）之间具有共生相容性。
