Assembly, annotation, and comparative analysis of the first complete mitochondrial genome of Pennisetum sinese

Characteristics, comparative genomics, and phylogenetic analysis of the chloroplast genome of Rosaplatyacantha

This study employed Sequencing by Synthesis (SBS) technology to achieve the first complete sequencing, assembly, and annotation of the R. platyacantha chloroplast genome, providing new insights into the evolutionary and dispersal pathways of Rosa species within the unique habitats of northwest China.

CHLOROPLAST GENOME SEQUENCING IN BRASSICACEAE AND ITS PHYLOGENETIC APPLICATIONS: A COMPREHENSIVE REVIEW

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.

Complete chloroplast genome analysis of critically endangered endemic Prangos denticulata and insights into its evolutionary dynamics

Prangos denticulata (Apiaceae) is a critically endangered and narrowly endemic species restricted to Ankara, Türkiye. To provide genomic resources for its conservation and evolutionary study, we sequenced, assembled, and annotated its complete chloroplast genome using short-read next-generation sequencing. The circular plastome was 153,486 bp in length, exhibiting the typical quadripartite structure with a large single-copy (86,440 bp), small single-copy (17,894 bp), and two inverted repeats (49,152 bp), and an overall GC content of 37.8%. A total of 116 genes were identified, including 92 protein-coding, 31 tRNA, and 5 rRNA genes, of which 20 contained introns. Comparative analyses with P. trifida, P. lipskyi, and P. fedtschenkoi revealed high structural conservation with lineage-specific variation at the Inverted Repeat/Small Single Copy boundaries and within ndh regions. Nucleotide diversity analysis identified several highly variable coding and intergenic regions with potential utility as molecular markers. Codon usage analysis showed a strong bias toward A/U-ending codons and moderate selection pressure influencing synonymous codon choice. Phylogenomic reconstruction based on complete chloroplast genomes confirmed P. denticulata as a distinct lineage forming a well-supported clade with P. trifida, closely related to Apium graveolens. This study provides the first complete plastome of P. denticulata, expanding genomic resources for the genus Prangos and offering valuable insights into its evolutionary dynamics, systematics, and future conservation strategies.

Characterization of the complete mitochondrial genome of Rhododendron simsii var. putuoense and its comparative evolutionary analysis

Rhododendron simsii var. putuoense is a coastal-endemic plant with significant ecological and genetic resource value. Although its chloroplast genome (cpDNA) was recently characterized, its mitochondrial genome (mtDNA) remains unexplored. Here, we report the first complete assembly and annotation of the R. simsii var. putuoense mtDNA using PacBio HiFi long-read sequencing. The genome sequence is 658,161 bp in length, organized as two subgenomic linear molecules (a major one of 633,105 bp and a minor one of 25,056 bp), and encodes 33 protein-coding genes (PCGs), 26 tRNAs, three rRNAs and 323 ORFs. Repeat analysis revealed a predominance of dispersed repeats (72%), alongside 128 SSRs and 20 tandem repeats. The mtDNA exhibits a strong A/U-ending codon usage bias, with 463 RNA editing sites predicted. Six homologous segments (0.91% of the mtDNA) provide evidence of interorganellar gene transfer (IGT). Notably, pairwise K a / K s analysis revealed an elevated ratio in the matR gene, suggesting at lineage-specific evolutionary dynamics that warrant further site-specific codon model testing. Phylogenetic and synteny analyses further confirmed a close relationship with R. simsii , while revealing structural divergence consistent with ecological specialization. Overall, these findings deepen our understanding of mitochondrial genomic diversity within Rhododendron and establish a genetic framework for conserving lineage-specific resources in this ecologically significant variety.

Comparative Analysis of Chloroplast Genomes Reveals Molecular Evolution and Phylogenetic Relationships in Fraxinus (Fraxinus mandshurica)

Fraxinus mandshurica (Manchurian ash) is an ecologically and economically valuable hardwood tree native to Northeast Asia, yet its genomic resources remain limited. We assembled its complete chloroplast (cp) genome (155,559 bp) using hybrid PacBio and Illumina sequencing and performed comparative, phylogenetic, and evolutionary analyses. The cp genome exhibits a typical quadripartite structure encoding 132 gene copies, comprising 114 unique genes (80 protein-coding, 30 tRNA, and 4 rRNA genes), with 18 genes duplicated in the inverted repeat (IR) regions. Simple sequence repeat analysis revealed dominance of mononucleotide A/T repeats. Phylogenetic analysis of 53 complete cp genomes strongly supported the monophyly of Oleaceae and resolved F. mandshurica as sister to the North American F. nigra, consistent with previously proposed Miocene intercontinental dispersal scenarios between East Asia and North America. Most protein-coding genes were under strong purifying selection (Ka/Ks << 1), whereas petB, rpl2, and several ndh genes showed elevated Ka/Ks values that are suggestive of altered selective constraint but are based on very few substitutions and are therefore not, on their own, evidence of positive selection. Nucleotide diversity (Pi) analysis identified 15 hypervariable intergenic spacers (mean Pi = 0.067), among which trnM-CAU-rps14, ndhJ-ndhK, and petL-petG represent promising candidate barcode regions requiring further validation. This study provides a high-quality, fully annotated cp genome of F. mandshurica and a valuable genomic resource for future phylogenetic, population genetic, and conservation studies of this important genus.

Mitochondrial genome and phylogenetic analysis of Aster Indicus L.