Mitochondrial DNA. Part B, Resources最新文献

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.

Hemidactylus bowringii Gray, 1845, a species of the family Gekkonidae, has garnered attention due to its ecological significance and adaptability to diverse environments. The mitochondrial DNA of H. bowringii was packaged as a compact 17,091 bp circular molecule with an A + T content of 53.8%. It contains 37 typical mitochondrial genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, and 1 non-coding region. We reconstructed a phylogenetic tree based on the mitogenome sequences of 17 species and two outgroups (Sphenomorphus indicus and Calotes versicolor). This newly characterized mitogenome provides a foundational resource for conservation genomics and phylogenetic studies of gekkonid lizards.

Protea cynaroides 'Red Rex' (James Petiver 1698) is a perennial evergreen shrub of the Proteaceae family valued for ornamental and medicinal uses, yet its genomic data remain unexplored. Here, we report the complete chloroplast genome sequence (157,894 bp) of P. cynaroides 'Red Rex'. The genome exhibits a quadripartite structure, including a large single-copy region (86,427 bp), a short single-copy region (18,553 bp), and two inverted repeats (26,457 bp each), with 38.06% GC content. A total of 130 genes were annotated. Phylogenetic analysis confirmed close relationships within Proteaceae, advancing insights into the genetics and evolution of Protea.

Luciogobius parvulus (Snyder, 1909) is distributed in restricted areas of Japan and South Korea. Here, we report the first complete mitochondrial genome of this species. The 16,488 bp mitogenome contains 13 protein-coding genes, 22 tRNAs, and two rRNAs, with no gene rearrangements detected. Four protein-coding genes (COX2, COX3, ND4, and CytB) exhibit incomplete stop codons. Maximum-likelihood analysis of Gobionellinae indicates that two Luciogobius species may require morphological reexamination. Only five of the 17 Luciogobius species currently have complete mitogenomes. These results provide essential genomic data for future phylogenetic and taxonomic studies.

Polylepis rugulosa Bitter is an endangered species native to the central and northern Andes and is one of the woody species that form the highest altitude woodlands in the world. Despite its ecological importance, genomic information for P. rugulosa is scarce, which limits our understanding of its evolutionary relationships and hinders the development of conservation strategies. In this study, we assembled the complete chloroplast genome of P. rugulosa and conducted phylogenetic analyses using 25 chloroplast genomes. The chloroplast genome is composed of 155,163 bp, with a typical quadripartite structure: a large single copy (85,290 bp), a small single copy (18,761 bp), and two inverted repeats (26,556 bp each). A total of 129 genes were identified, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis confirmed the placement of P. rugulosa within the Sanguisorbinae clade (Sanguisorbeae tribe). This is the first report of the complete plastome genome of a Polylepis species, providing valuable genomic data for conservation strategies and for reconstructing the biogeographical history of the genus Polylepis in South America.

The complete mitochondrial genome (mitogenome) of the symmetrical brain coral Pseudodiploria strigosa (Dana, 1846) is sequenced for the first time in this study. The newly assembled mitogenome is 16,906 bp long and encodes 13 protein coding genes (PCGs), 2 tRNA genes (trnM[cat] and trnW[tca]), and 2 ribosomal genes (rrnL and rrnS). A group I intron bisected the PCG nad5. The studied mitogenome also includes two relatively long non-coding regions, one 910 bp long, located between cox3 and cox2 and a second 799 b long, located between cox1 and trnM(cat). Mitochondrial synteny is identical to that previously reported in cofamilial corals. The mitogenome of P. strigosa is AT-rich with nucleotide use as follows: A = 24.84%, C = 13.21%, G = 20.41%, and T = 41.54%. A maximum-likelihood phylomitogenomic analysis that relied on the phylogenetic signal provided by translated PCGs supported the monophyly of the family Faviidae to which P. strigosa belongs. This newly assembled mitochondrial genome will be employed as a reference in studies biomonitoring this and other imperiled corals in the Caribbean basin using environmental DNA.

Bolbitis angustipinna (Hayata) H. Ito is a rare ornamental fern primarily distributed throughout East Asia and Southeast Asia. Its complete chloroplast genome was assembled, and a phylogenetic tree was constructed using 15 fern species. The genome is 152,562 base pairs, with a large single-copy region (82,712 bp), a small single-copy region (21,403 bp), and two inverted repeat regions (24,208 bp). It encodes 115 genes, including 72 protein-coding genes, 35 tRNA genes, and 8 rRNA genes. Phylogenetic analysis shows that B. angustipinna is most closely related to B. deltigera, providing valuable genetic and evolutionary insights.