Mitochondrial genome assembly of the Chinese endemic species of Camellia luteoflora and revealing its repetitive sequence mediated recombination, codon preferences and MTPTs DOI Creative Commons

Xu Xiao,

Zhaohui Ran,

Chao Yan

и другие.

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Апрель 5, 2025

Abstract Camellia luteoflora Y.K. Li ex Hung T. Chang & F.A. Zeng belongs to the L. genus (Theaceae Mirb.). As an endemic, rare, and critically endangered species in China, it holds significant ornamental economic value, garnering global attention due its ecological rarity. Despite conservation importance, genomic investigations on this remain limited, particularly organelle genomics, hindering progress phylogenetic classification population identification. In study, we employed high-throughput sequencing assemble first complete mitochondrial genome of C. reannotated chloroplast genome. Through integrated bioinformatics analyses, systematically characterized genome’s structural organization, gene content, interorganellar DNA transfer, sequence variation, evolutionary relationships.Key findings revealed a circular spanning 587,847 bp with GC content 44.63%. The harbors70 unique functional genes, including 40 protein-coding genes (PCGs), 27 tRNA 3 rRNA genes. Notably, 9 PCGs contained 22 intronic regions. Codon usage analysis demonstrated pronounced A/U bias synonymous codon selection. Structural features included 506 dispersed repeats 240 simple repeats. Comparative genomics identified 19 chloroplast-derived transfer events, contributing 29,534 (3.77% total DNA). RNA editing prediction 539 C-to-T conversion events across PCGs. Phylogenetic reconstruction using positioned closest proximity sinensis var. . Selection pressure (Ka/Ks ratios < 1 for 11 PCGs) nucleotide diversity assessment (Pi values: 0–0.00711) indicated strong purifying selection low divergence.This study provides comprehensive resource , offering critical insights germplasm conservation, comparative resolution, adaptation studies species.

Язык: Английский

Assembly and analysis of the complete mitochondrial genome of an endemic Camellia species of China, Camellia tachangensis DOI Creative Commons
Dong-hang Jiang, Lei Zhou,

Zhaohui Ran

и другие.

Research Square (Research Square), Год журнала: 2025, Номер unknown

Опубликована: Апрель 1, 2025

Abstract Background Camellia tachangensis F. C. Zhang is an endemic Camellia species of the junction Yunnan, Guizhou and Guangxi Provinces in China. It characterized by a primitive five-chambered ovary morphology serves as botanical source renowned “Pu’an Red Tea”. Unfortunately, populations have declined due to destruction their habitats human activities. The lack mitochondrial genomic resources has hindered research into molecular breeding phylogenetic evolution C. tachangensis. Result In this study, we had sequenced, assembled, annotated genome reveal its genetic characteristics relation with other species. assembly result indicated that sequence was 746,931 bp (GC content = 45.86%). consisted one multibranched (Chr1) circular (Chr2), Chr1 capable producing 7 substructures. comparative analysis chloroplast DNA revealed 23 pairs homologous fragments, 10 fully preserved tRNA genes within them. Comparison interspecies Ka/Ks mutations protein-coding (PCGs) were predominantly shaped purifying selection throughout (Ka/Ks < 1). tree constructed from CDS certain variants sinensis distinct species, forming clade relatively low support (BS 22%, PP 0.41). Meanwhile, genomes-based analyses most closely related taliensis, makuanica, gymnogyna, strong statistical 100, 1.00). Conclusions Our study deciphered structure tachangensis. These findings not only enhanced our comprehension complexity diversity structures but also established foundational data framework for future on programs relationship involving

Язык: Английский

Процитировано

0
Mitochondrial Genome Insights into Evolution and Gene Regulation in Phragmites australis DOI Open Access
Jipeng Cui, Qianhui Yang, Jiyue Zhang

и другие.

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(2), С. 546 - 546

Опубликована: Янв. 10, 2025

As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic environmental values. Here, we performed complete assembly annotation of the mitogenome P. using genomic data from PacBio BGI platforms. The is multibranched structure 501,134 bp, divided into two circular chromosomes 325,493 bp 175,641 respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which often translocated nuclear genome mitogenomes gramineous species. We also tissue-specific mitochondrial differentially expressed genes RNAseq data, providing new insights understanding energy allocation regulatory strategies long-term adaptive evolution mitochondria. In addition, studied features more detail, including repetitive sequences, Ka/Ks analyses, codon preferences, intracellular transfer, RNA editing, multispecies phylogenetic analyses. Our results provide an essential molecular resource for genetic characterisation research basis population genetics species Arundiaceae.

Язык: Английский

Процитировано

0
Mitochondrial genome and transcription of Shiraia-like species reveal evolutionary aspects in protein-coding genes DOI Creative Commons
X. SHEN,

Xue-Ting Cao,

Xiao-Bo Huang

и другие.

IMA Fungus, Год журнала: 2025, Номер 16

Опубликована: Фев. 20, 2025

Shiraia-related species are well-known bambusicolous fungi in Dothideomycetes class, with high value traditional medicine for producing hypocrellin, as an anticipated photosensitiser. The complete mitogenomes of hypocrellin-producing Pseudoshiraiaconidialis strains were analysed the present study, functional gene variations through comparative genomics and transcriptomics. Five (ZZZ816, CNUCC1353PR, JAP103846, CNUCC C72, C151) sequenced, which indicated similar genome characteristics. Two them possess extra atp6 gene, associated variable fragment "HSP1-HSP2-atp6_2" correlates closely hypocrellin production capacity. Therefore, these five divided into three groups: ZZZ816 CNUCC1353PR possessing efficiency, C72 JAP103846 low yield C151 a transition type. expression changes screened under various conditions. ZZZ816-related showed significant mitochondrial genes, especially HSP1, HSP2 atp6_2, linked to synthesis stress response; rps3 also consistently correlated production. group stable pattern divergently, except suppression by blue light. These findings would provide new insights secondary metabolite regulation ROS resistance. Above all, this study conducted comprehensive analysis Shiraia-like expression, can update understanding fungal evolution potential improved

Язык: Английский

Процитировано

0
Mitochondrial genome assembly of the Chinese endemic species of Camellia luteoflora and revealing its repetitive sequence mediated recombination, codon preferences and MTPTs DOI Creative Commons

Xu Xiao,

Zhaohui Ran,

Chao Yan

и другие.

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Апрель 5, 2025

Abstract Camellia luteoflora Y.K. Li ex Hung T. Chang & F.A. Zeng belongs to the L. genus (Theaceae Mirb.). As an endemic, rare, and critically endangered species in China, it holds significant ornamental economic value, garnering global attention due its ecological rarity. Despite conservation importance, genomic investigations on this remain limited, particularly organelle genomics, hindering progress phylogenetic classification population identification. In study, we employed high-throughput sequencing assemble first complete mitochondrial genome of C. reannotated chloroplast genome. Through integrated bioinformatics analyses, systematically characterized genome’s structural organization, gene content, interorganellar DNA transfer, sequence variation, evolutionary relationships.Key findings revealed a circular spanning 587,847 bp with GC content 44.63%. The harbors70 unique functional genes, including 40 protein-coding genes (PCGs), 27 tRNA 3 rRNA genes. Notably, 9 PCGs contained 22 intronic regions. Codon usage analysis demonstrated pronounced A/U bias synonymous codon selection. Structural features included 506 dispersed repeats 240 simple repeats. Comparative genomics identified 19 chloroplast-derived transfer events, contributing 29,534 (3.77% total DNA). RNA editing prediction 539 C-to-T conversion events across PCGs. Phylogenetic reconstruction using positioned closest proximity sinensis var. . Selection pressure (Ka/Ks ratios < 1 for 11 PCGs) nucleotide diversity assessment (Pi values: 0–0.00711) indicated strong purifying selection low divergence.This study provides comprehensive resource , offering critical insights germplasm conservation, comparative resolution, adaptation studies species.

Язык: Английский

Процитировано

0