Jul 2026· Bartın University International Journal of Natural and Applied Sciences· 0 citations· 50 references
TL;DR
New methodologies were examined, including genome scanning, advanced assembly tools such as GetOrganelle, and multispecies merger phylogenetic reconstruction, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.
Abstract
The Brassicaceae family is important both scientifically and economically; however, its complex evolutionary history, characterized by rapid diversification, whole-genome duplications, and significant reticular evolution, makes its classification challenging. The advent of high-throughput next-generation sequencing technology has facilitated the shift from single-locus phylogenomics to whole-plastome phylogenomics, improving our understanding of the family's deep evolutionary relationships. This comprehensive review reinforces our understanding of Brassicaceae chloroplast genomes, highlighting the highly consistent gene content, distinctive base composition patterns, and highly conserved quadruple structure. Phylogenetically relevant structural changes, including temporal shifts in the boundaries of inverted repeats (IRs), lineage-specific gene losses (e.g., rps16), and the loss of ndh genes in response to local adaptive pressures, are investigated in this study. Furthermore, the effectiveness of plastid phylogenics in clarifying taxonomically complex clades was evaluated, while directly addressing common problems such as cytonuclear incompatibility, chloroplast capture, and soft polytomies at key backbone nodes. The article examined newly developed methodologies, including genome scanning, advanced assembly tools such as GetOrganelle, and multispecies merger phylogenetic reconstruction. Finally, potential future developments were discussed, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.
Pennisetum sinese, a perennial grass central to “Juncao Technology,” holds considerable promise for non-grain biomass production and ecological restoration. Despite its agronomic value, the cytoplasmic genetic architecture of this species, particularly its mitochondrial genome, remains uncharacterized. Here, we present the first complete mitochondrial genome of the P. sinese assembled via hybrid long- and short-read sequencing. The genome adopts a multi-branched conformation spanning 405,186 bp with a GC content of 43.98%, and encodes 32 unique protein-coding genes, 20 tRNA genes, and three rRNA genes. We detected significant codon usage bias, abundant tandem repeats, and dispersed repeats. In addition, 24 chloroplast-derived homologous fragments totaling 13,053 bp were identified. Phylogenetic analysis confirms the placement of the P. sinese within the Poaceae clade, whereas synteny analysis reveals extensive structural rearrangements in its mitochondrial genome compared with closely related species. Furthermore, we predicted 454 C−to−U RNA editing sites. These findings establish a foundational genetic resource for P. sinese cytoplasmic inheritance and laying a foundation for future investigations into the molecular mechanisms underlying its high biomass yield and stress tolerance, informing future germplasm innovation.
Xiaobing Hu, Dan Zhu, Xin Ning et al.· Frontiers in Plant Science· 0 citations
Background Rosa platyacantha is a rose species endemic to the high-altitude regions of Xinjiang in China. To date, no complete chloroplast genome has been reported for this species, limiting our understanding of its genomic characteristics and phylogenetic relationships within the genus Rosa. Methods This study employed Sequencing by Synthesis (SBS) technology to achieve the first complete sequencing, assembly, and annotation of the R. platyacantha chloroplast genome. Comparative genomics and phylogeny analyses were then conducted using this data alongside chloroplast genome data from other Rosa species. Results The chloroplast genome of R. platyacantha spans 157,133 bp, and it annotates 132 genes and has a total guanine cytosine (GC) content of 37.21%. Fifty-one simple sequence repeat (SSR) loci were identified, predominantly adenine/thymine (A/T)-type mononucleotide repeats. Codon usage preference analysis revealed a marked bias towards synonymous codons ending in adenine/uracil (A/U). Compared to closely related species, R. platyacantha exhibited higher nucleotide diversity (Pi) in non-coding regions and the large single copy (LSC) and small single copy (SSC) region. Potential adaptive hot spots were identified at ycf3-trnS -GCU (Pi = 0.29005), trnC-GCA, trnT-UGU, and trnV-UAC. Rose genus chloroplast genomes are generally conserved, with most species exhibiting identical inverted repeat regions a and b (IRa and IRb) lengths. However, only R. acicularis shows a 62 bp difference, and the associated fragment length of the duplicated gene ycf1 varies between species from 1,108 to 1,117 bp. Phylogeny analysis revealed that R. platyacantha did not cluster with the sympatric R. fedtschenkoana. This finding confirms their distant evolutionary relationship at the genome level, providing new insights into the evolutionary and dispersal pathways of Rosa species within the unique habitats of northwest China.
Gang Lu, Mengmeng Yu, Fazu Xu et al.· PeerJ· 0 citations
This study presents the largest plastome dataset for Chinese Begonia, identifies hypervariable markers, and resolves a specific taxonomic issue, clarifying the phylogenetic position.
Yang Huang, Wenxiu Tang, Secai Huang et al.· BMC Genomics· 0 citations
The results indicate that while the Ormosia plastomes retain the typical angiosperm quadripartite structure, they show a substantial expansion of the inverted repeat (IR) regions compared to the sister lineage of core genistoids (represented by Lupinus and Sophora), with the boundaries extending to the clpP gene.
Shihong Zhang, Fengcheng Deng, Yixiong Zhao et al.· Plant Systematics and Evolut...· 0 citations
This work offers novel insights into genomic diversity and evolutionary history of sampled Zehneria species, providing a critical molecular resource for future taxonomic and phylogenetic studies within Cucurbitaceae.
Michael Gichuru Karendi, Caroline Njambi Ndungu, Elijah Mkala Mbadi et al.· Genetica· 0 citations
This study provides the first comprehensive phylogenetic framework for Stellaria based on the chloroplast genome, establishing a robust foundation for future taxonomic revisions and evolutionary studies.
Wenqiao Wang, Mujie Shen, Zhiwei Su et al.· Frontiers in Plant Science· 0 citations