Mitochondrial DNA. Part B, Resources最新文献

Yangxincai, a "highcalcium vegetable," is a hybrid of Phedimus aizoon L. and Phedimus kamtschaticus (Fisch., 1840), historically misidentified as P. aizoon L. owing to their morphological similarity. Uncertainty regarding its parentage has impeded official nomenclature and caused confusion in research. To clarify its maternal origin, we sequenced and assembled its complete chloroplast genome, 151,666 bp in length with a GC content of 37.73%, comprising LSC 83,128 bp, SSC 16,704 bp, and a pair of IRs (25,917 bp). A total of 128 genes were annotated,including 84 proteincoding, 36 tRNA, and 8 rRNA genes. Phylogenetic analysis of the maternally inherited chloroplast genome confirmed P. aizoon as the maternal parent, and we propose the corrected name Phedimus aizoon × kamtschaticus for this hybrid cultivar.

Pocillopora meandrina Dana, 1846 is a coral species widely distributed in the Indo-Pacific Oceans. Here, we report the first complete mitochondrial genome of P. meandrina from the South China Sea. The mitogenome is 17,422 bp in length, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 2 transfer RNA genes (tRNAs), with a GC content of 30.1%. Eleven PCGs start with ATG, and ten end with TAA. Phylogenetic analysis revealed that P. meandrina is closely related to other Pocillopora species. The study provides valuable molecular data for evolutionary and phylogenetic studies of Pocillopora.

The complete mitochondrial genome of the giant tun shell, Tonna galea (Linnaeus, 1758), was sequenced using a hybrid Illumina and Nanopore approach. The assembled mitochondrial genome is a circular 17,504 bp molecule, encoding the typical 37 genes (13 PCGs, 22 tRNAs, and two rRNAs). Mitogenomic phylogenetic analysis robustly places T. galea as a sister taxon to Tonna dolium (Linnaeus, 1758). Additionally, the analysis strongly supports a close phylogenetic relationship between the families Tonnidae and Bursidae. These findings offer essential genetic insights into the phylogenetic framework of the family Tonnoidea.

The complete chloroplast genome of Solanum lyratum Thunberg was sequenced and analyzed, revealing a quadripartite structure with a total length of 155,870 base pairs. It comprises two regions with inverted repeat (IR) regions of 25,571 bp each, located between a large single-copy (LSC) region (86,319 bp) and a small single-copy (SSC) region (18,409 bp). Comprehensive genome annotation identified 128 functional genomic elements, consisting of 83 protein-coding genes, 37 tRNA sequences, and 8 rRNA sequences, with a guanine-cytosine content of 37.8%. Maximum likelihood (ML) analysis based on 86 conserved protein-coding loci from 38 taxa revealed a robust phylogenetic relationship between S. dulcamara and S. lyratum, with maximum bootstrap support (100%) at the branch node. The genomic data elucidated chloroplast architecture and speciation mechanisms in Solanum, particularly in S. lyratum. These findings provide critical insights into taxonomic classification, phylogenetic investigations, and the development of species-specific molecular markers.

The mitochondrial genome of Palpimanus capensis Simon, 1893 has been sequenced and annotated from ultraconserved elements (UCEs). The species is endemic to South Africa and is a free-living ground-dweller. Contigs were assembled in SPAdes, with a rough draft mitogenome extracted from the resulting contigs that was used as the seed for de novo assembly by NOVOPlasty for the final, circularized genome. The mitogenome was annotated using MITOS2 and by comparing it to other species in the order Araneae. The mitogenome is 14,268 bp, including 22 transfer RNA (tRNA), 13 protein coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, and a control region. This is the first species in the genus Palpimanus and the family Palpimanidae with a sequenced and annotated mitochondrial genome.

Cladopus doianus Koriba 1928, a species within the Cladopus genus, possesses remarkable aerial shoots and an extensive underground root system, making it an exceptional model for investigating the evolutionary aspects of angiosperm morphology. In this study, we employed Illumina sequencing to assemble and annotate the complete chloroplast (cp) genome of C. doianus. The cp genome is 133,017 base pairs in length, containing 107 unique genes: 73 protein-coding genes, 30 tRNA genes, and four rRNA genes. Notably, 17 of these genes are duplicated within the inverted repeat (IR) regions, comprising four rRNA genes, seven tRNA genes, and six protein-coding genes. Additionally, we constructed a phylogenetic tree of selected species within the Podostemaceae family, and the results were consistent with previous studies, indicating that C. doianus is closely related to P. chiangmaiensis. In conclusion, our study presents the first complete chloroplast genome of C. doianus, providing valuable insights for future research on the Podostemaceae family.

We sequenced the first chloroplast (cp) genome of Rhododendron simsii var. putuoense G. Y. Li & Z. H. Chen 2010, an endemic coastal plant species unique to East China, to clarify its phylogenetic relationships. The cp genome is 151,998 bp long with a 35.76% GC content and lacks the typical quadripartite structure.  It contains118 genes: 76 mRNAs, 38 tRNAs, and four ribosomal RNAs. Phylogenetic analysis shows that R. simsii var. putuoense is closely related to R. simsii supporting its recent divergence from this species. This study expands genetic resource for the variety and clarifies its position within Rhododendron.

We present the complete mitochondrial genome of the East Asian "dark" firefly Lucidina vitalisi (Coleoptera: Lampyridae: Lampyrinae). The circular mitogenome measures 14,882 bp and includes the standard set of 37 genes along with a 259-bp control region. Phylogenetic analysis based on the 13 protein-coding genes places L. vitalisi as sister to Lucidina sp., within the Lampyrinae subfamily, distinct from the Luciolinae subfamily. This mitogenome serves as a validated genomic resource for Lucidina, refines its phylogenetic position, and supports future comparative, population, and conservation genetic studies of East Asian fireflies.

Piper bambusifolium Y.C. Tseng 1979, a climbing shrub of the family Piperaceae, has attracted increasing research attention due to its dual medicinal and ornamental value. This study presented the first complete chloroplast genome sequence of P. bambusifolium, spanning 161,476 bp with a GC content of 38.3%. The circular genome exhibited a typical quadripartite structure, consisting two inverted repeats (IRs; 27,058 bp each) that separate a large single-copy (LSC; 89,143 bp) and a small single-copy (SSC; 18,217 bp). The genome encoded 129 genes, including 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis revealed the close relationship between P. bambusifolium and P. hencai within the family Piperaceae. Overall, our study expanded the genomic resources for P. bambusifolium, providing a valuable foundation for further exploration and utilization, and highlights the new insights into phylogenetic relationships within the family Piperaceae.

Viola grayi, a caulescent species in subsection Rostratae, adapted to coastal dunes, with leathery leaves, is here reported with its first sequenced complete chloroplast genome (158,408 bp), comprising a large single-copy (86,662 bp), a small single-copy (17,994 bp), and pair of inverted repeats (26,876 bp each). Phylogenetic analysis of 22 Viola species, based on a 184,817 bp whole-plastome alignment, resolved the genus as monophyletic and placed V. grayi in a clade with V. grypoceras (BP = 100). This plastome provides a valuable genomic resource for future comparative, taxonomic, phylogenetic, and evolutionary studies.