Defining the Rhizobium leguminosarum Species Complex.
Defining the Rhizobium leguminosarum Species Complex.
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DOI：
10.3390/genes12010111
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发表时间：
2021-01-18
期刊：
影响因子：
3.5
通讯作者：
Tian CF
中科院分区：
文献类型：
--
作者：
Young JPW;Moeskjær S;Afonin A;Rahi P;Maluk M;James EK;Cavassim MIA;Rashid MH;Aserse AA;Perry BJ;Wang ET;Velázquez E;Andronov EE;Tampakaki A;Flores Félix JD;Rivas González R;Youseif SH;Lepetit M;Boivin S;Jorrin B;Kenicer GJ;Peix Á;Hynes MF;Ramírez-Bahena MH;Gulati A;Tian CF
目前豆根瘤菌中的细菌种类繁多，不能被视为单一物种，因此我们可以将其称为物种复合体（Rlc）。我们发现了 429 个属于 Rlc 的公开基因组序列，这些序列表明 Rlc 是一个独特的实体，与该属的其他物种完全分开。它的姐妹分类单元是R. anhuiense。我们基于 120 个通用（核心）基因的串联序列构建了系统发育，并计算了所有基因组之间的成对平均核苷酸同一性 (ANI)。从这些分析中，我们得出结论，Rlc 包括 18 个不同的基因种，加上 7 个未归入这些基因种的独特菌株。每个基因种的 ANI 值之间存在明显的差距，通常约为 96% ANI，这意味着它是一个“自然”单位。其中五个基因种包括指定物种的模式菌株：R. laguerreae、R. sophorae、R. ruizarguesonis、“R. indicum”和 R. leguminosarum 本身。 16S 核糖体 RNA 序列在 Rlc 内显着多样化，但不能区分基因种。管家基因的部分序列经常用于表征分离株集合，大多数可以明确地分配给基因种，但基因种内的等位基因并不总是形成进化枝，因此单个基因并不能可靠地指导菌株的真实系统发育。我们的结论是，获取大量基因组序列是表征细菌多样性的有力工具，分类学结论应基于所有可用的基因组序列，而不仅仅是典型菌株的基因组序列。
Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a ‘natural’ unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, “R. indicum” and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.
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影响因子：
10.7
作者：
Darriba, Diego;Posada, David;Flouri, Tomas
通讯作者：
Flouri, Tomas
影响因子：
56.9
作者：
FLEISCHMANN, RD;ADAMS, MD;VENTER, JC
通讯作者：
VENTER, JC
DOI：
10.1111/nph.16392
发表时间：
2020-04
期刊：
The New phytologist
影响因子：
--
作者：
Boivin S;Ait Lahmidi N;Sherlock D;Bonhomme M;Dijon D;Heulin-Gotty K;Le-Queré A;Pervent M;Tauzin M;Carlsson G;Jensen E;Journet EP;Lopez-Bellido R;Seidenglanz M;Marinkovic J;Colella S;Brunel B;Young P;Lepetit M
通讯作者：
Lepetit M
DOI：
10.1126/science.1127573
发表时间：
2007-01-26
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Fraser C;Hanage WP;Spratt BG
通讯作者：
Spratt BG
影响因子：
3
作者：
Camacho C;Coulouris G;Avagyan V;Ma N;Papadopoulos J;Bealer K;Madden TL
通讯作者：
Madden TL