Author:
Wang Huijun,Wu Zhigang,Li Tao,Zhao Jindong
Abstract
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.
Funder
Strategic Priority Research Program of Chinese Academy of Sciences
Publisher
Springer Science and Business Media LLC
Reference78 articles.
1. Sun XZ, Simpson DA. Flora of China. Volume 9. Beijing: Science Press and Missouri Botanical Garden; 1992.
2. World Grass Species. descriptions, identification, and information retrieval. http://www.kew.org/data/grasses-db.html.
3. Hossain MM, Shahjahan M, Khan S, Juraimi AS, Uddin MK, Hasan M. Potentialities of the Asian watergrass (Hygroryza aristata) as feed in aquaculture. Sustainability. 2021;13(12):14.
4. Hossain MM, Rahman MH, Ali ML, Khan S, Haque MM, Shahjahan M. Development of a low-cost polyculture system utilizing Hygroryza aristata floating grass in the coastal wetlands of Bangladesh. Aquaculture 2020, 527.
5. Malik V, Mohammad I, Pranita. Ecology and conservation of rare Hygroryza aristata (Retz.) Nees Ex Wight & Arn. Biol Forum 2014, 6(1).