The Complete Chloroplast Genome Sequence of the Medicinal Moss Rhodobryum giganteum (Bryaceae, Bryophyta): Comparative Genomics and Phylogenetic Analyses

Genes, Journal Year: 2024, Volume and Issue: 15(7), P. 900 - 900

Published: July 10, 2024

(Bryaceae, Bryophyta), a rare medicinal bryophyte, is valued for its cardiovascular therapeutic properties in traditional Chinese medicine. This study presents the first complete chloroplast genome sequence of

Language: Английский

Complete Chloroplast Genome Structural Characterization and Comparative Analysis of Viburnum japonicum (Adoxaceae)

Forests, Journal Year: 2023, Volume and Issue: 14(9), P. 1819 - 1819

Published: Sept. 6, 2023

Viburnum japonicum (Thunb.) Sprengel is an endangered species endemic to coastal regions of eastern Asia (China, Japan, and South Korea). However, its systematic position has been controversial. In this study, we present the complete chloroplast (cp) genome V. (GenBank OP644292) sequenced using Illumina NovaSeq platform. The cp a total length 158,606 bp G+C contents 38.08%. It consists large single-copy (LSC) region, small (SSC) pair inverted repeats (IRs) measuring 87,060 bp, 18,510 26,516 respectively. A 131 genes were identified, including 87 protein-coding genes, 36 transfer RNA (tRNAs), 8 ribosomal genes(rRNAs). Additionally, 44 dispersed detected, three types: forward, palindromic, reverse. Among 38 SSR loci that discovered, majority mononucleotide composed A/T. Furthermore, found 15 (accD, atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rpoC1, rps12, rps16, trnA-UGC, trnI, trnK-UUU, trnL-UAA) contain one intron, while clpP ycf3 have two introns. relative synonymous codon usage (RSCU) analysis detected 31 high-frequency codons, where A/U bases accounted for 93.55% total, indicating asymmetry in gene presence bases. Comparative structure sequences data genomes comparison with other closely related demonstrated high level conservation their organization. mutation hotspots (psbH, rps19, trnL) which could be valuable future phylogenetic population genetic research. Phylogenetic revealed accessions are group setigerum, erosum, fordiae within genus. conclusion, study provides important insights accurately identifying understanding phylogeny through sequencing japonicum.

Language: Английский

Conserved Plastid Genomes of Pourthiaea Trees: Comparative Analyses and Phylogenetic Relationship

Forests, Journal Year: 2024, Volume and Issue: 15(10), P. 1811 - 1811

Published: Oct. 16, 2024

The genus Pourthiaea Decne., a deciduous woody group with high ornamental value, belongs to the family Rosaceae. Here, we reported newly sequenced plastid genome sequences of beauverdiana (C. K. Schneid.) Hatus., parvifolia E. Pritz., villosa (Thunb.) and Photinia glomerata Rehder & H. Wilson. plastomes these three species shared typical quadripartite structures, ranging in size from 159,903 bp (P. parvifolia) 160,090 beauverdiana). contained pair inverted repeat regions (26,394–26,399 bp), separated by small single-copy region (19,304–19,322 bp) large (87,811–87,973 bp). A total 113 unique genes were predicted for plastomes, including four ribosomal RNA genes, 30 transfer 79 protein-coding genes. Analyses repeat/single-copy boundary, mVISTA, nucleotide diversity, genetic distance showed that 13 (including 10 published plastomes) are highly conserved. number simple sequence repeats long is similar among species. non-coding (trnT-GGU-psbD, trnR-UCU-atpA, trnH-GUG-psbA) most divergent. Only one gene, rbcL, was under positive selection. Phylogenetic analyses based on 78 29 nrDNA strongly supported monophyly Pourthiaea. As relationship other genera our phylogenies, sister Malus plastome while it remaining phylogenies. Furthermore, significant cytonuclear discordance likely stems hybridization events within Pourthiaea, reflecting complex evolutionary dynamics genus. Our study provides valuable insights further phylogenetic, taxonomic, delimitation studies as well essential support horticultural improvement conservation germplasm resources.

Language: Английский