Comparative analysis of mitochondrial genomes of Schisandra repanda and Kadsura japonica

Hyo Ju Lee; Yi Lee; Sang-Choon Lee; Chang-Kug Kim; Ji-Nam Kang; Soo-Jin Kwon; Sang-Ho Kang

doi:10.3389/fpls.2023.1183406

Comparative analysis of mitochondrial genomes of Schisandra repanda and Kadsura japonica

Front Plant Sci. 2023 Jul 3:14:1183406. doi: 10.3389/fpls.2023.1183406. eCollection 2023.

Authors

Hyo Ju Lee¹, Yi Lee², Sang-Choon Lee³, Chang-Kug Kim¹, Ji-Nam Kang¹, Soo-Jin Kwon¹, Sang-Ho Kang¹

Affiliations

¹ Genomics Division, National Institute of Agricultural Sciences, Jeonju, Republic of Korea.
² Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Republic of Korea.
³ Phyzen Genomics Institute, Seongnam, Republic of Korea.

Abstract

The family Schisandraceae is a basal angiosperm plant group distributed in East and Southeast Asia and includes many medicinal plant species such as Schisandra chinensis. In this study, mitochondrial genomes (mitogenomes) of two species, Schisandra repanda and Kadsura japonica, in the family were characterized through de novo assembly using sequencing data obtained with Oxford Nanopore and Illumina sequencing technologies. The mitogenomes of S. repanda were assembled into one circular contig (571,107 bp) and four linear contigs (10,898-607,430 bp), with a total of 60 genes: 38 protein-coding genes (PCGs), 19 tRNA genes, and 3 rRNA genes. The mitogenomes of K. japonica were assembled into five circular contigs (211,474-973,503 bp) and three linear contigs (8,010-72,712 bp), with a total of 66 genes: 44 PCGs, 19 tRNA genes, and 3 rRNA genes. The mitogenomes of the two species had complex structural features with high repeat numbers and chloroplast-derived sequences, as observed in other plant mitogenomes. Phylogenetic analysis based on PCGs revealed the taxonomical relationships of S. repanda and K. japonica with other species from Schisandraceae. Finally, molecular markers were developed to distinguish between S. repanda, K. japonica, and S. chinensis on the basis of InDel polymorphisms present in the mitogenomes. The mitogenomes of S. repanda and K. japonica will be valuable resources for molecular and taxonomic studies of plant species that belong to the family Schisandraceae.

Keywords: InDel markers; Kadsura japonica; Schisandra repanda; genome assembly; mitogenome.

Grants and funding

This study was supported by the Cooperative Research Program in the National Agricultural Genome Program (Grant No. PJ013490), Rural Development Administration (RDA), Republic of Korea.