Comparative Analysis of the Complete Mitochondrial Genomes of Apium graveolens and Apium leptophyllum Provide Insights into Evolution and Phylogeny Relationships

Author:

Li Xiaoyan1,Li Mengyao1ORCID,Li Weilong1,Zhou Jin1ORCID,Han Qiuju1,Lu Wei1,Luo Qin2,Zhu Shunhua2,Xiong Aisheng3ORCID,Tan Guofei2,Zheng Yangxia1

Affiliation:

1. College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China

2. Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China

3. College of Horticulture, Nanjing Agricultural University, Nanjing 611130, China

Abstract

The genus Apium, belonging to the family Apiaceae, comprises roughly 20 species. Only two species, Apium graveolens and Apium leptophyllum, are available in China and are both rich in nutrients and have favorable medicinal properties. However, the lack of genomic data has severely constrained the study of genetics and evolution in Apium plants. In this study, Illumina NovaSeq 6000 and Nanopore sequencing platforms were employed to identify the mitochondrial genomes of A. graveolens and A. leptophyllum. The complete lengths of the mitochondrial genomes of A. graveolens and A. leptophyllum were 263,017 bp and 260,164 bp, respectively, and contained 39 and 36 protein-coding genes, five and six rRNA genes, and 19 and 20 tRNA genes. Consistent with most angiosperms, both A. graveolens and A. leptophyllum showed a preference for codons encoding leucine (Leu). In the mitochondrial genome of A. graveolens, 335 SSRs were detected, which is higher than the 196 SSRs found in the mitochondrial genome of A. leptophyllum. Studies have shown that the most common RNA editing type is C-to-U, but, in our study, both A. graveolens and A. leptophyllum exhibited the U-C editing type. Furthermore, the transfer of the mitochondrial genomes of A. graveolens and A. leptophyllum into the chloroplast genomes revealed homologous sequences, accounting for 8.14% and 4.89% of the mitochondrial genome, respectively. Lastly, in comparing the mitochondrial genomes of 29 species, it was found that A. graveolens, A. leptophyllum, and Daucus carota form a sister group with a support rate of 100%. Overall, this investigation furnishes extensive insights into the mitochondrial genomes of A. graveolens and A. leptophyllum, thereby enhancing comprehension of the traits and evolutionary patterns within the Apium genus. Additionally, it offers supplementary data for evolutionary and comparative genomic analyses of other species within the Apiaceae family.

Funder

National Natural Science Foundation of China

National Natural Science Foundation of Sichuan Province

Project of Guizhou Provincial Department of Science and Technology “Construction and Utilization of Horticultural Platform of Plant GenBank Creation”

Shaanxi Provincial Department of Science and Technology

Project of Research and Demonstration of Key Technologies for Quality Improvement and Efficiency Enhancement of Vegetables in Bazhong City

Publisher

MDPI AG

Subject

Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis

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