Assembly of the complete mitochondrial genome of an endemic plant, Scutellaria tsinyunensis, revealed the existence of two conformations generated by a repeat‑mediated recombination

Scutellaria tsinyunensis belongs to the family Lamiaceae, distributed only in the Jinyun Mountain, Chongqing, China. As a valuable endemic and small population species, it is regarded as a natural resource potentially with significant economic and ecological importance. In this study, we assembled a...

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Bibliographic Details
Published in:Planta 2021-08, Vol.254 (2), p.1-16, Article 36
Main Authors: Li, Jingling, Xu, Yicen, Shan, Yuanyu, Pei, Xiaoying, Yong, Shunyuan, Liu, Chang, Yu, Jie
Format: Article
Language:English
Subjects:
Agriculture
Atp9 gene
Base composition
Biomedical and Life Sciences
Ecology
Endemic plants
Endemic species
Forestry
Fragments
Gene sequencing
Genes
Genomes
Herbal medicine
Life Sciences
Medicinal plants
Mitochondria
Mountains
Natural resources
Negative selection
ORIGINAL ARTICLE
Plant Sciences
Positive selection
Proteins
Recombination
rRNA
Scutellaria
tRNA
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Summary:Scutellaria tsinyunensis belongs to the family Lamiaceae, distributed only in the Jinyun Mountain, Chongqing, China. As a valuable endemic and small population species, it is regarded as a natural resource potentially with significant economic and ecological importance. In this study, we assembled a complete and gap-free mitochondrial genome of S. tsinyunensis. This genome had a length of 354,073 bp and the base composition of the genome was A (27.44%), T (27.30%), C (22.58%), and G (22.68%). This genome encodes 59 genes, including 32 protein-coding genes, 24 tRNA genes, and 3 rRNA genes. The Sanger sequencing and Oxford Nanopore sequencing confirmed a pair of direct repeats had mediated genome recombination, resulting in the formation of two conformations. The gene conversation between plastome and mitochondrial genome was also observed in S. tsinyunensis by detecting gene migration, including six tRNA genes (namely, trnW-CCA, trnI-CAU, trnH-UUU, trnD-GUC, trnN-GUU, and trnM-CAU), five protein-coding gene fragments, and the fragments from 2 rRNA genes. Moreover, the dN/dS analysis revealed the atp9 gene had undergone strong negative selection, and four genes (atp4, mttB, ccmFc, and ccmB) probably had undergone positive selection during evolution in Lamiales. This work reported the first mitochondrial genome of S. tsinyunensis, which could be used as a reference genome for the important medicinal plants of the genus Scutellaria, and also provide much-desired information for molecular breeding.
ISSN:0032-0935
1432-2048
DOI:10.1007/s00425-021-03684-3