Exploring Genetic Diversity and Signatures of Horizontal Gene Transfer in Nodule Bacteria Associated with Lotus japonicus in Natural Environments
Exploring Genetic Diversity and Signatures of Horizontal Gene Transfer in Nodule Bacteria Associated with Lotus japonicus in Natural Environments
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DOI：
10.1094/mpmi-02-19-0039-r
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发表时间：
2019-09-01
影响因子：
3.5
通讯作者：
Tsuchimatsu, Takashi
中科院分区：
文献类型：
--
作者：
Bamba, Masaru;Aoki, Seishiro;Tsuchimatsu, Takashi
摘要为了研究日本莲花（Lotus japonicus）结瘤菌的遗传多样性，了解其水平基因转移（HGT）过程，我们分析了来自日本广泛地区的3个管家基因和5个共生基因的序列。整理基因的系统发育分析表明，自然环境下的日本乳杆菌与不同的中根瘤菌谱系相关，而菌株之间的共生基因序列高度相似，导致同义位点和非同义位点的核苷酸多样性都很低。共生基因的鸟嘌呤-胞嘧啶含量较低，共生基因之间的相对重组频率也低于内务基因之间的相对重组频率。分子变异分析表明，共生基因和内务基因在种群间存在显著的遗传分化。这些结果证实了与L. japonicus共生所需的中根瘤菌基因表现为一个基因组岛（即共生岛），并表明该岛通过自然环境中的HGT事件扩散到不同的中根瘤菌基因组背景中。此外，我们的数据汇编显示，与其他物种相比，日本l.a japonicus相关共生基因的遗传多样性是最低的，这可能与日本l.a japonicus种群最近的种群扩张有关。
To investigate the genetic diversity and understand the process of horizontal gene transfer (HGT) in nodule bacteria associated with Lotus japonicus, we analyzed sequences of three housekeeping and five symbiotic genes using samples from a geographically wide range in Japan. A phylogenetic analysis of the housekeeping genes indicated that L. japonicus in natural environments was associated with diverse lineages of Mesorhizobium spp., whereas the sequences of symbiotic genes were highly similar between strains, resulting in remarkably low nucleotide diversity at both synonymous and nonsynonymous sites. Guanine-cytosine content values were lower in symbiotic genes, and relative frequencies of recombination between symbiotic genes were also lower than those between housekeeping genes. An analysis of molecular variance showed significant genetic differentiation among populations in both symbiotic and housekeeping genes. These results confirm that the Mesorhizobium genes required for symbiosis with L. japonicus behave as a genomic island (i.e., a symbiosis island) and suggest that this island has spread into diverse genomic backgrounds of Mesorhizobium via HGT events in natural environments. Furthermore, our data compilation revealed that the genetic diversity of symbiotic genes in L. japonicus-associated symbionts was among the lowest compared with reports of other species, which may be related to the recent population expansion proposed in Japanese populations of L. japonicus.