Aug 2026· Genetica· Vol 154· 0 citations· 74 references
Medicine
TL;DR
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.
The genus Stephania is a member of the family Menispermaceae within the angiosperms, possesses remarkable species diversity across south of China. To elucidate phylogenetic relationships within the genus Stephania at the chloroplast genome level, we sequenced the complete chloroplast genomes of four Stephania species, namely Stephania longipes, Stephania lincangensis, Stephania longa, and Stephania herbacea, using a combination of second- and third-generation sequencing technologies. The complete chloroplast genomes of four Stephania species sequenced in this study exhibited a conserved quadripartite circular structure, with total lengths ranging from 157,727 bp to 158,138 bp. These genomes comprised 130 functional genes, with a Guanine-cytosine (GC) content ranging from 38.24% to 38.28%. Among these, protein-coding genes displayed a significant A/U preference at the third codon position. Repetitive sequence analysis detected a total of 31 to 43 long repeat sequences and 74 to 96 simple sequence repeats (SSRs), with A/T type mononucleotide repeats constituting the largest proportion. The complete chloroplast genomes of Stephania exhibited a high degree of conservation, with no significant large-scale gene rearrangements or inversions observed, and the boundaries are relatively stable. Nucleotide diversity (Pi) analysis showed that the shared intergenic regions generally exhibited higher nucleotide polymorphism than the shared coding regions, and nine highly variable regions could serve as candidate barcode regions for species identification in Stephania. DNA barcoding analysis showed that the trnK-UUU-matK region could be successfully amplified in all tested samples, and the phylogenetic tree based on this region was highly consistent with that inferred from complete chloroplast genomes, indicating its potential as a candidate DNA barcode for Stephania. Phylogenetic analysis of chloroplast genomes revealed that the genus Stephania formed a distinct monophyletic clade, with S. longipes and S. lincangensis closely related, while S. longa and S. herbacea clustered together in another lineage. The phylogenetic relationships in the genus Stephania reflect the division of subgenera, but do not reveal section division within the genus. It is indicated that inflorescence and fruit morphological characteristics in Stephania are useful for taxonomic identification but may provide limited phylogenetic signal. Additionally, Stephania japonica var. timoriensis and Stephania japonica var. discolor showed a certain degree of differentiation from typical Stephania japonica, suggesting that their taxonomic status warrants further evaluation.
Fei Wang, Li-Li Wu, Gui-Zi Yang et al.· Scientific Reports· 0 citations
This study sequenced and comparatively analyzed the mitochondrial genomes of three agriculturally important Aulacophora pests: the polyphagous A. indica, the oligophagous A. lewisii, and the early-diverging A. nigripennis. All three mitogenomes contained the typical 37 genes with conserved gene order. However, total length varied substantially (15,258–18,766 bp), driven primarily by control region length variation. All species exhibited pronounced AT bias, and relative synonymous codon usage analysis revealed marked interspecific divergence. Phylogenetic analysis based on 13 protein-coding genes resolved A. nigripennis as the basal lineage and A. lewisii and A. indica as closely related sister species. Both widespread species displayed maximum haplotype diversity (Hd = 1.000); however, A. indica exhibited approximately 2.4-fold higher nucleotide diversity (Pi = 0.00478) than A. lewisii (Pi = 0.00198), indicating differential population genetic architectures between the two species. These findings established a comparative mitogenomic framework for Aulacophora and provide baseline data for future phylogenomic and phylogeographic investigations.
Liancheng Liu, Huanhuan Li, Gonghua Lin et al.· Life· 0 citations
Poa
L. (Poaceae), comprising over 500 species, is taxonomically challenging due to morphological plasticity, hybridization, and polyploidy. To clarify plastome architecture and phylogenetic relationships within the genus, we sequenced and annotated complete chloroplast genomes of
Poa angustifolia
(accessions P10, P14) and
Poa lipskyi
(P17) from Uzbekistan. The three plastomes (135,310–135,609 bp) shared the typical quadripartite structure and an identical complement of 130 genes across self-replication, photosynthesis, and other functional categories. Codon usage and amino acid composition were highly conserved, with a consistent bias toward A/T-ending codons and leucine, isoleucine, glycine, and serine as the dominant residues. Sliding-window analysis identified two nucleotide-diversity hotspots, in the
rpl32
–
trnL
-UAG and
trnC
-GCA–
rpoB
regions, and SSR profiling showed predominant mononucleotide A/T repeats alongside a few taxon-specific pentanucleotide motifs. Maximum-likelihood phylogenomic analysis placed the
P. angustifolia
accessions in a strongly supported clade sister to
P. lipskyi
, consistent with shared membership in sect.
Poa.
These results indicate that
Poa
plastomes are structurally conserved yet retain informative variable regions useful for phylogenetics and barcoding.
Shukhrat Abdullaev, Temur Asatulloyev, Ziyoviddin Yusupov et al.· F1000Research· 0 citations
Phylogenetic analyses recovered Veronica as a well-supported monophyletic lineage and clarified the plastid positions of the three newly sequenced species, providing plastome resources and molecular evidence for taxonomy, species identification, and future evolutionary studies of Veronica.
Ying Huang, Shihao Jiang, Yanru Zhang et al.· Frontiers in Plant Science· 0 citations
The utility of plastid genome data for resolving deep-level phylogenetic relationships within Hamamelidaceae is highlighted, providing a robust framework for future taxonomic and evolutionary studies of this globally distributed and taxonomically complex family.
Sadaf Habib, Yong Shi, Jie Zhang et al.· Frontiers in Plant Science· 0 citations
The complete plastome of C. erectus is characterized, providing the first complete cp genome resource for C. erectus, and offering a foundation for further phylogenomic and conservation studies within Arecaceae.
Sheikh Sunzid, S. Ahmed, Nusrat Jahan et al.· Korean Journal of Plant Taxo...· 0 citations
