Sequence Analysis of the Complete Mitochondrial Genome of a Medicinal Plant, Vitex rotundifolia Linnaeus f. (Lamiales: Lamiaceae)

Yu, Xiaoli; Zhong-gang, Duan; Wang, Yanjun; Zhang, Qingxin; Li, Wei

doi:10.3390/genes13050839

Cited by 18 publications

(13 citation statements)

References 34 publications

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“…6 ). This inference was consistent with the conclusions of other studies on angiosperms [ 6 , 34 ]. However, we also identified that four genes, atp8 , ccmB , mttB and sdh4 , may have undergone positive selection in the evolution of gymnosperms in most species.…”

Section: Discussionsupporting

confidence: 94%

Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

Xia

Zuo

et al. 2023

BMC Plant Biol

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Background The complex physical structure and abundant repeat sequences make it difficult to assemble the mitogenomes of seed plants, especially gymnosperms. Only approximately 33 mitogenomes of gymnosperms have been reported. However, as the most widely distributed and the second largest family among gymnosperms, Cupressaceae has only six assembled mitogenomes, including five draft mitogenomes and one complete mitogenome, which has greatly hindered the understanding of mitogenome evolution within this large family, even gymnosperms. Results In this study, we assembled and validated the complete mitogenome of Thuja sutchuenensis, with a size of 2.4 Mb. Multiple sequence units constituted its complex structure, which can be reduced to three linear contigs and one small circular contig. The analysis of repeat sequences indicated that the numbers of simple sequence repeats increased during the evolutionary history of gymnosperms, and the mitogenome of Thuja sutchuenensis harboured abundant extra-long repeats (more than 5 kb). Additionally, the longest repeat sequence identified in these seven gymnosperms also came from the mitogenome of Thuja sutchuenensis, with a length of up to 47 kb. The analysis of colinear blocks and gene clusters both revealed that the orders of mitochondrial genes within gymnosperms was not conserved. The comparative analysis showed that only four tRNAs were shared by seven gymnosperms, namely, trnD-GUC, trnE-UUC, trnI-CAU and trnY-GUA. Furthermore, four genes have undergone potential positive selection in most gymnosperm species, namely, atp8, ccmB, mttB and sdh4. Conclusion We successfully assembled the second complete mitogenome within Cupressaceae and verified that it consisted of multiple sequence units. Our study also indicated that abundant long repeats may contribute to the generation of the complex conformation of the mitogenome of Thuja sutchuenensis. The investigation of Thuja sutchuenensis’s mitogenome in our study provides new insight into further understanding the complex mitogenome architecture within gymnosperms.

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Section: Discussionsupporting

confidence: 94%

Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

Xia

Zuo

et al. 2023

BMC Plant Biol

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“…As shown in Figure 6 , the Ka/Ks ratios of most PCGs were less than 1 ( Figure 6 ), suggesting that these genes were highly conserved and had undergone neutral and negative selections in Actinidiaceae. These results were also supported in the report on Lamiales [ 78 ]. However, among the five Actinidiaceae plants, sdh3 with dN/dS values greater than 1.0 was found between the S. tristyla and kiwifruit mitogenomes, indicating that this gene may have suffered from positive selection during the evolution in Actinidiaceae.…”

Section: Discussionsupporting

confidence: 89%

A Comparative Genomics Approach for Analysis of Complete Mitogenomes of Five Actinidiaceae Plants

Yang

Ling

Zhang

et al. 2022

Genes

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Actinidiaceae, an economically important plant family, includes the Actinidia, Clematoclethra and Saurauia genus. Kiwifruit, with remarkably high vitamin C content, is an endemic species widely distributed in China with high economic value. Although many Actinidiaceae chloroplast genomes have been reported, few complete mitogenomes of Actinidiaceae have been studied. Here, complete circular mitogenomes of the four kiwifruit species and Saurauia tristyla were assembled. Codon usage, sequence repeats, RNA editing, gene transfers, selective pressure, and phylogenetic relationships in the four kiwifruit species and S. tristyla were comparatively analyzed. This research will contribute to the study of phylogenetic relationships within Actiniaceae and molecular barcoding in kiwifruit.

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“…The Ka/Ks ratio is typically applied to estimate the selective pressure to which specific mitogenome PCGs are subjected during evolution (Zhang et al, 2006). In general, most mt genes have undergone negative or neutral selection considering their high level of conservation, resulting in Ka/Ks values that do not exceed 1 (Bi et al, 2020;Cheng et al, 2021;Yu et al, 2022). From Ka/Ks analysis of all 36 unique PCGs from the H. citrina mitogenome with five other species, we detected that the majority of PCGs had undergone purifying selection during the evolutionary process (Figure 4).…”

Section: Discussionmentioning

confidence: 97%

Deciphering the mitochondrial genome of Hemerocallis citrina (Asphodelaceae) using a combined assembly and comparative genomic strategy

et al. 2022

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Hemerocallis citrina is a perennial herbaceous plant that is dedicated to mothers in Chinese culture and is widely distributed across the country. As a popular species with a long history of cultivation and utilization, it is renowned for its remarkable edible and medicinal value. In this study, we integrated Illumina short-read and Oxford Nanopore long-read sequencing to generate a complete mitochondrial genome (mitogenome) assembly of H. citrina. The H. citrina mitogenome has a multiple chromosomal structure consisting of three circular molecules that are 45,607 bp, 239,991 bp, and 182,864 bp long. We correspondingly annotated 66 genes, comprising 45 protein-coding genes (PCGs), 17 tRNA genes, and 4 rRNA genes. Comparative analysis of gene organization indicated that six syntenic gene clusters were conserved in the mitogenomes of the compared plants. The investigation of repeat content revealed repeat-rich nature of the H. citrina mitogenome, for which plentiful dispersed repeats were characterized to correlate with the size of the mitogenome. The codon usage behavior disclosed that Leucine (Leu) and Serine (Ser) were the most preferred amino acids in H. citrina, and nearly all of the codons with relative synonymous codon usage (RSCU) values greater than 1 showed the preference of A or T ending. Moreover, we inferred a total of 679 RNA editing sites in all mitochondrial PCGs, which presented perfect C-to-U types and tended to lead to the alteration of internal codons. Subsequent selective pressure analysis showed that the majority of the PCGs had undergone evolutionary negative selections, with atp9 in particular undergoing strong stabilizing selection, reflecting its indispensable function in mitogenomes. According to the phylogenetic analysis, H. citrina is close to the species Allium cepa (Amaryllidaceae) and Asparagus officinalis (Asparagaceae) in evolutionary terms. Overall, this project presents the first complete mitogenome of H. citrina, which could provide a reference genome for the comprehensive exploration of the Asphodelaceae family and can facilitate further genomic breeding and evolutionary research on this medicine–food homologous plant.

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Sequence Analysis of the Complete Mitochondrial Genome of a Medicinal Plant, Vitex rotundifolia Linnaeus f. (Lamiales: Lamiaceae)

Cited by 18 publications

References 34 publications

Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

A Comparative Genomics Approach for Analysis of Complete Mitogenomes of Five Actinidiaceae Plants

Deciphering the mitochondrial genome of Hemerocallis citrina (Asphodelaceae) using a combined assembly and comparative genomic strategy

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