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

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We assembled the complete mitochondrial genome of Scutellaria tsinyunensis in this study. Repeat-mediated recombination resulted in the formation of two conformations of the mitochondrial genome in S. tsinyunensis.


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.

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Data availability

The raw sequencing data for the Illumina and Nanopore platforms and the mitogenome sequences have been deposited in NCBI ( with accession number: PRJNA680174, SAMN16871192, SRR13107290, SRR14924549 and MW553042.1, respectively. The sample has been deposited in the herbarium of Southwest University, Chongqing, China, with voucher number: 20200320CQ-1.



Polymerase chain reaction


Simple sequence repeat


Direct repeat




Bayesian inferences

dS :

Synonymous substitution rates

dN :

Non-synonymous substitution rates


Cetyl trimethylammonium bromide


National Center for Biotechnology Information


Basic Local Alignment Search Tool


Protein-coding gene sequences


Mitochondrial plastid DNA


Mitochondrial nuclear DNA


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We would like to thank GrandOmics and Novogene Technology Co., Ltd for technical support and genomic sequencing service.


This work was supported by the National Natural Science Foundation of China (31772260), The National Training Program of Innovation and Entrepreneurship for Undergraduates (X202010635443), and Chongqing Study Abroad Innovation Project (cx2019052). The funders were not involved in the study design, data collection and analysis, decision to publish, or manuscript preparation.

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Correspondence to Chang Liu or Jie Yu.

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The authors declare that they have no competing interests.

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Communicated by Anastasios Melis.

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Li, J., Xu, Y., Shan, Y. et al. Assembly of the complete mitochondrial genome of an endemic plant, Scutellaria tsinyunensis, revealed the existence of two conformations generated by a repeat-mediated recombination. Planta 254, 36 (2021).

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