Assessing the ecological and evolutionary processes underlyingcytonuclear interactions

Zhang, Xinxin; Zhou, Wei; Cheng, Xiang; Chen, XiaoYang; Hu, Xin‐Sheng; Hu, Ying; Wang, Xi

doi:10.1360/ssv-2019-0049

Cited by 3 publications

(3 citation statements)

References 38 publications

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“…Mitochondrial DNA differs from chloroplast DNA and nuclear DNA, with a generally lower substitution rate in plant mitochondria compared to chloroplast and nuclear DNA (Fan et al 2022). Mitochondrial DNA is commonly used to study evolutionary relationships, hybridization events, and nuclear interactions among species (Zhang et al 2019, , (Wang et al 2023).…”

Section: Introductionmentioning

confidence: 99%

The complete mitochondrial genome assembly of Capsicum pubescens reveals key evolutionary characteristics of mitochondrial genes of two Capsicum subspecies

Liu

et al. 2023

Preprint

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Pepper (Capsicum pubescens), one of the five domesticated pepper species, boasts unique characteristics such as numerous hairs on the epidermis of its leaves and stems, black seeds, and vibrant purple flowers. Previously, no studies have reported on the complete assembly of the mitochondrial genome (mitogenome) of C. pubescens. Understanding the mitogenome is crucial for further research on C. pubescens. In our study, we successfully assembled the first mitogenome of C. pubescens, which has been assigned the GenBank accession number OP957066. This mitogenome has a length of 454,165 bp and exhibits the typical circular structure observed in most mitogenomes. We have annotated a total of 70 genes, including 35 protein-coding genes (PCGs), 30 tRNA genes, 3 rRNA genes, and 2 pseudogenes. Compared to the other three pepper mitogenomes (KJ865409, KJ865410, and MN196478), C. pubescens OP957066 exhibits 4 unique PCGs (atp4, atp8, mttB, and rps1), while 2 PCGs (rpl10 and rps3) are absent. It's worth mentioning that each of the three pepper mitogenomes (KJ865409, KJ865410, and MN196478) experienced the loss of 4 PCGs (atp4, atp8, mttB, and rps1). To further explore the evolutionary relationships, we reconstructed a phylogenetic tree using the mitogenomes of C. pubescens and fourteen other species. The structural comparison and synteny analysis of the above four pepper mitogenomes showed that C. pubescens has a higher sequence similarity with KJ865409, and C. pubescens experienced rearrangements with the other three pepper mitogenomes. Interestingly, we observed 72 homologous sequences between the mitochondrial and chloroplast genomes, which accounted for 12.60% of the mitogenome, with a total length of 57,207 bp. These sequences encompassed 12 tRNA genes and the rRNA gene (rrn18). Remarkably, selective pressure analysis suggests that the nad5 gene underwent obvious positive selection. Furthermore, the single base mutation in three genes (nad1, nad2, and nad4) resulted in amino acid change. This study has provided a high-quality mitogenome of pepper, offering valuable molecular data for future investigations into the genetic information exchange between organelle genomes in pepper.

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Section: Introductionmentioning

confidence: 99%

The complete mitochondrial genome assembly of Capsicum pubescens reveals key evolutionary characteristics of mitochondrial genes of two Capsicum subspecies

Liu

et al. 2023

Preprint

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“…Compared with chloroplast and nuclear DNAs, mtDNA has generally a lower mutation rate in plants 30 . Thus, mtDNA sequences are useful for studying the long-term phylogenetic relationships at the level of species or higher order, and also for studying other perspectives of evolutionary relationships, such as lineage sorting, hybridization and cytonuclear interactions 31 .…”

Section: Introductionmentioning

confidence: 99%

A complete sequence of mitochondrial genome of Neolamarckia cadamba and its use for systematic analysis

Wang

Chen

et al. 2021

Sci Rep

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Neolamarckia cadamba is an important tropical and subtropical tree for timber industry in southern China and is also a medicinal plant because of the secondary product cadambine. N. cadamba belongs to Rubiaceae family and its taxonomic relationships with other species are not fully evaluated based on genome sequences. Here, we report the complete sequences of mitochondrial genome of N. cadamba, which is 414,980 bp in length and successfully assembled in two genome circles (109,836 bp and 305,144 bp). The mtDNA harbors 83 genes in total, including 40 protein-coding genes (PCGs), 31 transfer RNA genes, 6 ribosomal RNA genes, and 6 other genes. The base composition of the whole genome is estimated as 27.26% for base A, 22.63% for C, 22.53% for G, and 27.56% for T, with the A + T content of 54.82% (54.45% in the small circle and 54.79% in the large circle). Repetitive sequences account for ~ 0.14% of the whole genome. A maximum likelihood (ML) tree based on DNA sequences of 24 PCGs supports that N. cadamba belongs to order Gentianales. A ML tree based on rps3 gene of 60 species in family Rubiaceae shows that N. cadamba is more related to Cephalanthus accidentalis and Hymenodictyon parvifolium and belongs to the Cinchonoideae subfamily. The result indicates that N. cadamba is genetically distant from the species and genera of Rubiaceae in systematic position. As the first sequence of mitochondrial genome of N. cadamba, it will provide a useful resource to investigate genetic variation and develop molecular markers for genetic breeding in the future.

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“…Sousa和Hey [6] 系统地评价了应用基因组数据分析种间基因流的不同统计方法和模型. 王茜等人 [33] 讨论了应用核质分子标记的连锁不平衡来检测种间基因渐渗. [35] , 也有学者提倡不用这方法估计迁移数 [29] .…”

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Advances in the methods of detecting interspecific gene introgression and their applications

Li¹,

Cheng²,

Xiao³

et al. 2020

Sci. Sin.-Vitae

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Assessing the ecological and evolutionary processes underlyingcytonuclear interactions

Cited by 3 publications

References 38 publications

The complete mitochondrial genome assembly of Capsicum pubescens reveals key evolutionary characteristics of mitochondrial genes of two Capsicum subspecies

The complete mitochondrial genome assembly of Capsicum pubescens reveals key evolutionary characteristics of mitochondrial genes of two Capsicum subspecies

A complete sequence of mitochondrial genome of Neolamarckia cadamba and its use for systematic analysis

Advances in the methods of detecting interspecific gene introgression and their applications

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