NDLI: Highly active repeat-mediated recombination in the mitogenome of the aquatic grass Hygroryza aristata

Content Provider	Springer Nature : BioMed Central
Author	Wang, Huijun Wu, Zhigang Li, Tao Zhao, Jindong
Abstract	Background Floating bamboo (Hygroryza aristata) is an endangered species with a narrow native distribution and is renowned for its unique aesthetic qualities, which holds significant ecological and ornamental value. However, the lack of genetic information research, with only one complete plastome available, significantly hampers conservation efforts and further research for this species. Results In this research, we sequenced and assembled the organelle genomes of floating bamboo, including the mitogenome (587,847 bp) and plastome (135,675 bp). The mitogenome can recombine into various configurations, which are mediated by 25 repeat pairs (13 SRs, 6 MRs, 1 LR, and 5 CRs). LR1 and SR5 are particularly notable as they have the ability to combine with other contigs, forming complex repeat units that facilitate further homologous recombination. The rate of homologous recombination varies significantly among species, yet there is still a pronounced positive correlation observed between the length of these repeat pairs and the rate of recombination they mediate. The mitogenome integrates seven intact protein-coding genes from the chloroplast. The codon usage patterns in both organelles are similar, with a noticeable bias towards C and T on the third codon. The gene map of Poales shows the entire loss of rpl6, succinate dehydrogenase subunits (sdh3 and sdh4). Additionally, the BOP clade retained more variable genes compared to the PACMAD clade. Conclusions We provided a high-quality and well-annotated mitogenome for floating bamboo and demonstrated the presence of diverse configurations. Our study has revealed the correlation between repeat length and their corresponding recombination rate despite variations among species. Although the mitogenome can potentially exist in the form of a unicircular in vivo, this occurrence is rare and may not be stable.
Related Links	https://bmcplantbiol.biomedcentral.com/counter/pdf/10.1186/s12870-024-05331-x.pdf
Ending Page	15
Page Count	15
Starting Page	1
File Format	HTM / HTML
ISSN	14712229
DOI	10.1186/s12870-024-05331-x
Journal	BMC Plant Biology
Issue Number	1
Volume Number	24
Language	English
Publisher	BioMed Central
Publisher Date	2024-07-08
Access Restriction	Open
Subject Keyword	Plant Sciences Agriculture Tree Biology Hygroryza aristata Mitochondrial genome Repeat Homologous recombination Intracelluar gene transfer
Content Type	Text
Resource Type	Article
Subject	Plant Science
Journal Impact Factor	4.3/2023
5-Year Journal Impact Factor	5.2/2023

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