The complete mitochondrial genome of Pontederia crassipes: using HiFi reads to investigate genome recombination and gene transfer from chloroplast genome DOI Creative Commons

Zhigang Hao,

Xiaoqi Jiang,

Lei Pan

и другие.

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Июнь 28, 2024

Water hyacinth ( Pontederia crassipes Mart.) is a monocotyledonous aquatic plant renowned for its rapid growth, extensive proliferation, biological invasiveness, and ecological resilience to variations in pH, nutrients, temperature. The International Union Conservation of Nature (IUCN) has listed P. among the top 100 invasive species. However, comprehensive genomic information, particularly concerning mitochondrial genome (mitogenome), remains surprisingly limited. In this study, complete mitogenome was analyzed using bioinformatics approaches. 399,263 bp long contains 38 protein-coding genes (PCGs), 24 tRNA genes, 3 rRNA genes. Sequence analysis revealed that species 3,289 dispersed repeats, 765 RNA editing sites possessed un-conserved structures, including sequence transfer between chloroplasts mitochondria. Our study on offers critical insights into evolutionary patterns phylogenetic relationships with related taxa. This research enhances our understanding species, known significant biomass overgrowth environments.

Язык: Английский

Characterization of the complete chloroplast genome assembly of Amorphophallus yunnanensis Engler, Pflanzenr (Araceae) from southwestern China DOI Creative Commons
Si Yin, Yong Gao

Mitochondrial DNA Part B, Год журнала: 2023, Номер 8(12), С. 1445 - 1449

Опубликована: Дек. 2, 2023

Southwestern China is a biodiversity hotspot due to its diverse topography and environment. Amorphophallus yunnanensis species of perennial herb that mainly distributed throughout southwestern China. The genetic diversity divergence in this have not been assessed largely lack genomic resources. To help with the phylogeographic study, we sequenced assembled first complete chloroplast genome sequence A. yunnanensis. length was 164,417 bp, an average GC content 36% (GenBank accession no. OR400247). possessed typical quadripartite structure, lengths large single-copy (LSC), small (SSC), two inverted repeat (IR) regions were 92,149 15,182 28,543bp, respectively. A total 128 genes annotated across genome, including 82 protein-coding genes, 8 rRNAs, 38 tRNAs. maximum likelihood (ML) phylogeny confirmed phylogenetic position within Araceae, forming single monophyletic clade high bootstrap value. ML tree also indicated most closely related coaetaneus. This newly assembly will aid future studies diversity, historical population dynamics, geographic differentiation patterns

Язык: Английский

Процитировано

6
Elucidating the multichromosomal structure within the Brasenia schreberi mitochondrial genome through assembly and analysis DOI Creative Commons

Yuanyu Shan,

Jingling Li,

Xinmei Duan

и другие.

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Апрель 29, 2024

Abstract Brasenia schreberi , a plant species traditionally utilized in Chinese medicine and cuisine, represents an early evolutionary stage among flowering plants (angiosperms). While the plastid genome of this has been published, its mitochondrial (mitogenome) not extensively explored, with notable absence thorough comparative analyses organellar genomes. In our study, we had assembled entire mitogenome B. utilizing sequencing data derived from both Illumina platform Oxford Nanopore. The mostly exists as six circular DNA molecules, largest being 628,257 base pairs (bp) smallest 110,220 bp, amounting to 1.49 megabases (Mb). Then annotated schreberi. encompasses total 71 genes: 40 these are coding proteins genes (PCGs), 28 for transfer RNA (tRNA), remaining 3 ribosomal (rRNA). analysis codon usage, noted unique preference specific each amino acid. most commonly used codons exhibited average RSCU 1.36, indicating noticeable bias selection. repeat sequence analysis, 553 simple repeats (SSRs) were identified, 1,822 dispersed (comprising 1,015 forward 807 palindromic repeats), 608 long terminal (LTRs). Additionally, homologous sequences between organelle genomes, detected 38 genome, exceeding 500 within genome. Notably, ten tRNA ( trnC-GCA trnM-CAU, trnI-CAU, trnQ-UUG, trnN-GUU, trnT-GGU, trnW-CCA trnA-UGC trnI-GAU trnV-GAC ) appear have completely transferred chloroplast mitogenome. Utilizing Deepred-mt predict editing sites mitogenome, identified 675 high-quality PCGs. final performed colinearity inferred phylogenetic relationship other angiosperms, PCGs basis. results showed that non-coding regions characterized by abundance repetitive exogenous sequences, is more closely related Euryale ferox .

Язык: Английский

Процитировано

2
The complete chloroplast genome assembly of Amorphophallus tonkinensis Engler and Gehrmann 1911 from southwestern China DOI Creative Commons
Si Yin, Huanhuan Chen,

Weijia Wu

и другие.

Mitochondrial DNA Part B, Год журнала: 2024, Номер 9(5), С. 592 - 596

Опубликована: Май 3, 2024

Species in the Amorphophallus genus are important cash crops many tropical and subtropical Asian countries. Although several molecular markers have been employed to determine relationships assess genetic variation genus, some conflicts remain infrageneric classification evolution. To aid phylogenetic research of we collected one sample tonkinensis Engler Gehrmann 1911 from southwestern China. We assembled first chloroplast genome this species using high-throughput sequencing. The was 169,341 bp long with a typical quadripartite structure (GenBank accession number: PP234804). lengths large single-copy region, small two inverted repeats were 90,705 bp, 15,640 31,498 respectively. annotated 129 genes across A. tonkinensis. trees suggested that distributed continental Asia split into main clades. reported our study provided valuable genomic resources for future genus.

Язык: Английский

Процитировано

2
Mitochondrial genome complexity in Stemona sessilifolia: nanopore sequencing reveals chloroplast gene transfer and DNA rearrangements DOI Creative Commons

Yuning Xie,

Wenqiong Liu,

Liwen Guo

и другие.

Frontiers in Genetics, Год журнала: 2024, Номер 15

Опубликована: Июнь 4, 2024

Mitochondria are semi-autonomous organelles in eukaryotic cells with their own genome. Plant mitogenomes differ from animal size, structure, and repetitive DNA sequences. Despite larger sizes, plant do not have significantly more genes. They exhibit diverse structures due to variations DNA, recombination frequencies, low gene densities, reduced nucleotide substitution rates. In this study, we analyzed the mitochondrial genome of Stemona sessilifolia using Nanopore Illumina sequencing. De-novo assembly annotation were conducted Unicycler, Geseq, tRNAscan-SE BLASTN, followed by codon usage, repeat sequence, RNA-editing, synteny, phylogenetic analyses. S. sessilifolia’s mitogenome consisted one linear contig six circular contigs totaling 724,751 bp. It had 39 protein-coding genes, 27 tRNA 3 rRNA Transfer chloroplast sequences accounted for 13.14% mitogenome. Various analyses provided insights into genetic characteristics, evolutionary dynamics, placement. Further investigations can explore transferred genes’ functions RNA-editing’s role expression .

Язык: Английский

Процитировано

2
The complete mitochondrial genome of Pontederia crassipes: using HiFi reads to investigate genome recombination and gene transfer from chloroplast genome DOI Creative Commons

Zhigang Hao,

Xiaoqi Jiang,

Lei Pan

и другие.

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Июнь 28, 2024

Water hyacinth ( Pontederia crassipes Mart.) is a monocotyledonous aquatic plant renowned for its rapid growth, extensive proliferation, biological invasiveness, and ecological resilience to variations in pH, nutrients, temperature. The International Union Conservation of Nature (IUCN) has listed P. among the top 100 invasive species. However, comprehensive genomic information, particularly concerning mitochondrial genome (mitogenome), remains surprisingly limited. In this study, complete mitogenome was analyzed using bioinformatics approaches. 399,263 bp long contains 38 protein-coding genes (PCGs), 24 tRNA genes, 3 rRNA genes. Sequence analysis revealed that species 3,289 dispersed repeats, 765 RNA editing sites possessed un-conserved structures, including sequence transfer between chloroplasts mitochondria. Our study on offers critical insights into evolutionary patterns phylogenetic relationships with related taxa. This research enhances our understanding species, known significant biomass overgrowth environments.

Язык: Английский

Процитировано

1