The genome sequence of hairy root Rhizobium rhizogenes strain LBA9402: Bioinformatics analysis suggests the presence of a new opine system in the agropine Ri plasmid,MicrobiologyOpen

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The genome sequence of hairy root Rhizobium rhizogenes strain LBA9402: Bioinformatics analysis suggests the presence of a new opine system in the agropine Ri plasmid
MicrobiologyOpen ( IF 3.9 ) Pub Date : 2021-05-01 , DOI: 10.1002/mbo3.1180
Marjolein J G Hooykaas ₁ , Paul J J Hooykaas ₁

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We report here the complete genome sequence of the Rhizobium rhizogenes (formerly Agrobacterium rhizogenes) strain LBA9402 (NCPPB1855rifR), a pathogenic strain causing hairy root disease. To assemble a complete genome, we obtained short reads from Illumina sequencing and long reads from Oxford Nanopore Technology sequencing. The genome consists of a 3,958,212 bp chromosome, a 2,005,144 bp chromid (secondary chromosome) and a 252,168 bp Ri plasmid (pRi1855), respectively. The primary chromosome was very similar to that of the avirulent biocontrol strain K84, but the chromid showed a 724 kbp deletion accompanied by a large 1.8 Mbp inversion revealing the dynamic nature of these secondary chromosomes. The sequence of the agropine Ri plasmid was compared to other types of Ri and Ti plasmids. Thus, we identified the genes responsible for agropine catabolism, but also a unique segment adjacent to the TL region that has the signature of a new opine catabolic gene cluster including the three genes that encode the three subunits of an opine dehydrogenase. Our sequence analysis also revealed a novel gene at the very right end of the TL‐DNA, which is unique for the agropine Ri plasmid. The protein encoded by this gene was most related to the succinamopine synthases of chrysopine and agropine Ti plasmids and thus may be involved in the synthesis of the unknown opine that can be degraded by the adjacent catabolic cluster. The available sequence will facilitate the use of R. rhizogenes and especially LBA9402 in both the laboratory and for biotechnological purposes.

中文翻译：

发根根瘤菌菌株 LBA9402 的基因组序列：生物信息学分析表明 agropine Ri 质粒中存在新的 opine 系统

我们在这里报告的完整基因组序列根瘤菌 发根农杆菌 （原农杆菌 发根）菌株 LBA9402 (NCPPB1855rifR)，一种引起毛根病的致病菌株。为了组装一个完整的基因组，我们从 Illumina 测序中获得了短读长，从牛津纳米孔技术测序中获得了长读长。该基因组分别由 3,958,212 bp 染色体、2,005,144 bp chromid（二级染色体）和 252,168 bp Ri 质粒 (pRi1855) 组成。初级染色体与无毒生物防治菌株 K84 的非常相似，但染色质显示 724 kbp 缺失，并伴有 1.8 Mbp 的大倒置，揭示了这些次级染色体的动态特性。将 agropine Ri 质粒的序列与其他类型的 Ri 和 Ti 质粒进行比较。因此，我们确定了负责 agropine 分解代谢的基因，还有一个与 TL 区域相邻的独特片段，它具有新的鸦片分解代谢基因簇的特征，包括编码鸦片脱氢酶三个亚基的三个基因。我们的序列分析还揭示了 TL-DNA 最右端的一个新基因，这是 agropine Ri 质粒所独有的。由该基因编码的蛋白质与 chrysopine 和 agropine Ti 质粒的琥珀酰氨平合酶最相关，因此可能参与了可被相邻分解代谢簇降解的未知鸦片的合成。可用的序列将有助于使用由该基因编码的蛋白质与 chrysopine 和 agropine Ti 质粒的琥珀酰氨平合酶最相关，因此可能参与了可被相邻分解代谢簇降解的未知鸦片的合成。可用的序列将有助于使用由该基因编码的蛋白质与 chrysopine 和 agropine Ti 质粒的琥珀酰氨平合酶最相关，因此可能参与了可被相邻分解代谢簇降解的未知鸦片的合成。可用的序列将有助于使用R。发根农杆菌并同时在实验室和生物技术为目的特别LBA9402。

更新日期：2021-05-03

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