The results provide plastome-scale evidence refining the phylogenetic placement of A. ficulneus with A. esculentus and identify validated loci for molecular marker development within Abelmoschus.
Abstract
Introduction The genus Abelmoschus (Malvaceae) includes cultivated okra (A. esculentus), yet its phylogenetic relationships remain unresolved using limited molecular markers. Methods In this study, complete chloroplast genomes of A. esculentus and the first complete plastome of A. ficulneus were assembled and analyzed together with published plastomes of three additional Abelmoschus species and Hibiscus rosasinensis as an outgroup Results and Discussion Plastome sizes ranged from 163, 119 to 163, 503 bp, with conserved quadripartite structures and GC content (~36.7%). A total of 751 and 755 simple sequence repeats (SSRs) were identified in AE12 and AF01, respectively, with hexanucleotide repeats as the dominant class (~25%) and a consistent enrichment in the LSC region (~62–64%). Codon usage analysis of 64 codons revealed a conserved bias toward A/U-ending codons, with no substantial interspecific variation. IR boundary analysis identified a genus-specific feature, with rps3 consistently located within IR regions in Abelmoschus, in contrast to rpl2 in Hibiscus. Polymorphism analysis across 271 genomic regions identified nine hypervariable loci, all exhibiting five haplotypes (Hap = 5) and maximum haplotype diversity (Hd = 1). Nucleotide diversity was low overall (mean p = 0.00116). Phylogenetic reconstruction based on complete plastomes resolved two strongly supported clades (SH-like ≥ 0.99) and consistently placed A. ficulneus with A. esculentus. Hypervariable loci including ycf1, trnK–rps16, atpH–atpI, ndhF, and ndhF–rpl32 reproduced the full plastome topology. These results provide plastome-scale evidence refining the phylogenetic placement of A. ficulneus and identify validated loci for molecular marker development within Abelmoschus.
This plastome provides a valuable genomic resource and reveals robust discordance between morphology-based classification and plastid phylogenetic placement in F. gasparriniana, providing a foundation for future nuclear-genomic and population-level tests of the alternative evolutionary scenarios underlying this discordance.
Yong Shi, Jie-Jun Liu, Lei Ren et al.· Genes· 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 sequenced and characterized the complete mitogenomes of Dasyhelea ludingensis and Forcipomyia taiwana to explore their genomic structure and phylogenetic relationships and provides essential genomic resources for future studies in systematics, phylogenetics, and population genetics of biting midges.
Xiaohong Jiang, Yao Xie, Guojiang Zhang et al.· Mitochondrial DNA. Part A, D...· 0 citations
Abstract Urceola huaitingii (Chun & Tsiang) D. J. Middleton 1994, a member of the Apocynaceae family, is widely distributed across southern and southwestern China and has been traditionally used in folk medicine to treat hemiplegia and paralysis. In this study, we report the first complete chloroplast genome of U. huaitingii and perform phylogenetic analysis with 30 related species within the Apocynaceae. The chloroplast genome of U. huaitingii is 155,182 bp in length and has a GC content of 38.11%. It displays a typical quadripartite structure, consisting of a large single-copy (LSC) region of 85,254 bp, a small single-copy (SSC) region of 18,242 bp, and two inverted repeat (IR) regions of 25,843 bp each. A total of 111 unique genes were annotated, including 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Phylogenetic analysis revealed that U. huaitingii is closely related to the genera Aganosma, Trachelospermum, and Amalocalyx. This study provides the first chloroplast genomic resource for the genus Urceola, laying a foundation for future investigations into its evolutionary relationships. It also contributes to future molecular and phylogenetic studies within the Apocynaceae family.
Xianglan Liang, Guoan Shen, Lichai Yuan et al.· Mitochondrial DNA Part B: Re...· 0 citations
Background and aims
– The genus
Allium
exhibits extensive diversification in the Mediterranean Basin, where insular endemism and polyploidy have played a significant role in species evolution. During taxonomic and biosystematic studies of
A.
sect.
Codonoprasum
, an undescribed species was discovered on the volcanic islands of Milos and Antimilos (Kiklades, Greece). This study aims to determine its taxonomic status and phylogenetic relationships using an integrative approach.
Material and methods
– The new species was investigated using comparative morphology, leaf anatomy, karyological analyses, genome size estimation by flow cytometry, and phylogenetic reconstruction based on nrITS sequence data. These data were compared with those of closely related species, particularly
A. occultum
, as well as other representatives of
A.
sect.
Codonoprasum
from Europe and the Mediterranean region.
Key results
–
Allium erimomeli
is described here as a new species. Karyological and flow cytometric analyses revealed a hexaploid chromosome complement (2
n
= 6
x
= 48) with a mean genome size of 46.2 pg. Phylogenetic reconstruction recovered the species as a strongly supported clade sister to the tetraploid
A. occultum
. Despite their close phylogenetic relationship, the two taxa differ in ploidy level, genome size, and diagnostic morphological characters, primarily relating to the bulb, leaves, and ovary. Additional differentiation is supported by leaf anatomy. Morphological characters were also compared with those of
A. sibthorpianum
and
A. rumelicum
.
Conclusion
– The recognition of
A. erimomeli
as a distinct species emphasizes the significance of polyploidy and insular isolation in the diversification of
A.
sect.
Codonoprasum
in the Aegean region. These findings further enhance our understanding of evolutionary relationships within the section and call for expanded phylogenetic and cytogenetic sampling across the eastern Mediterranean region.
Iasonas Nikolopoulos, K. Tan, Lucie Kobrlová et al.· Plant Ecology and Evolution· 0 citations
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