Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae

• Published in: BMC genomics Vol. 25; no. 1; p. 114
• Main Authors: Liu, Daliang, Zhang, Zhihan, Hao, Yanlin, Li, Mengge, Yu, Houlin, Zhang, Xingruo, Mi, Haoyang, Cheng, Lin, Zhao, Yiyong
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 25.01.2024; BioMed Central; BMC
• Subjects: Bats; Bias; Biodiversity; Biological evolution; Botanical research; Cell organelles; Chloroplast genome; Chloroplasts; Chloroplasts - genetics; Codon - genetics; Codon bias; Comparative analysis; Cyclooxygenase-2; Cytochrome; Decoding; Developmental biology; Dilleniidae; Divergence; Evolutionary genetics; Gene transfer; Genes; Genetic aspects; Genetic engineering; Genome, Chloroplast; Genomes; Genomics; Identification and classification; Inverted repeat; Mitochondrial genome; Natural history; Phylogenetics; Phylogeny; Proteins; RNA editing; RNA, Transfer - genetics; rRNA; Simple sequence repeats; Stewartia; Stewartia gemmate; Tea; Theaceae; Theaceae - genetics; Transfer RNA; China; Phylogenetics; Stewartia gemmate; Chloroplast genome; Mitochondrial genome
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-10016-8

Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of the earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin and evolutionary history. We sequenced the complete organelle genomes of Stewartia gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406 bp) exhibited a quadripartite structure including the large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, and four rRNAs. The mitochondrial genome (681,203 bp) exhibited alternative conformations alongside a monocyclic structure: 61 genes encoding 38 proteins, 20 tRNAs, three rRNAs, and RNA editing-impacting genes, including ATP6, RPL16, COX2, NAD4L, NAD5, NAD7, and RPS1. Comparative analyses revealed frequent recombination events and apparent rRNA gene gains and losses in the mitochondrial genome of Theaceae. In organelle genomes, the protein-coding genes exhibited a strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven codon bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic analysis confirmed Stewartieae's early divergence within Theaceae, shedding light on organelle genome characteristics and evolution in Theaceae. We studied the detailed characterization of organelle genomes, including genome structure, composition, and repeated sequences, along with the identification of lateral gene transfer (LGT) events and complexities. The discovery of a large number of repetitive sequences and simple sequence repeats (SSRs) has led to new insights into molecular phylogenetic markers. Decoding the Stewartia gemmata organellar genome provides valuable genomic resources for further studies in tea plant phylogenomics and evolutionary biology.