Mitochondrial DNA. Part B, Resources最新文献

In this study, we report the chloroplast (cp) genome of Dendrobium hainanense. The cp genome was 151,367 bp in length; the overall CG content of the genome was 37.46%. The length of the large single-copy (LSC) region was 83,938 bp, and 15,829 bp in a small single-copy (SSC) region, and a pair of inverted repeats (IRs) of 12,900 bp. One hundred and twenty-seven genes were predicted, including 81 protein-coding genes, 38 genes for tRNA, and eight genes for rRNA. The results of phylogenetic tree showed that Dendrobium hainanense had the closest genetic relationship with Dendrobium parciflorum. This study will be help to understand the genetic diversity of Dendrobium.

Mitochondrial genomes of Scotoplanes clarki and Protelpidia murrayi are presented, each with 13 protein coding genes, two rRNA genes, and 22 tRNA genes. That of Scotoplanes clarki has 15,909 base pairs and that of Protelpidia murrayi is 15,896 base pairs. There is a suspected tandem repeat region of undetermined length in the assemblies of both Scotoplanes clarki and Protelpidia murrayi. The gene order of both mitogenomes is identical to that of other Elasipodida. Phylogenetic analysis revealed that Protelpidia murrayi lies within the Scotoplanes clade, suggesting that Scotoplanes is paraphyletic. Sequencing of the type species, Scotoplanes globosa, is needed to confirm if Protelpidia murrayi should be renamed as Scotoplanes murrayi.

Phellinus pomaceus var. prunastri (Pers.) Pat. 1926 is a famous medicinal fungus that has attracted considerable interest in biotechnology because of its diverse biologically active ingredients. Here, we provide the full mitochondrial genome sequence of P. pomaceus, which spans 122,850 bp and has a GC content of 26.04%. The genome comprises 15 essential protein-coding genes, 26 distinct ORFs, 24 intronic ORFs, 25 tRNAs, and 2 rRNA genes. Bayesian inference (BI) was employed for phylogenetic analysis, revealing the evolutionary relationships among 17 Basidiomycota fungi. The results strongly supported distinct clades and indicated that P. pomaceus is closely related to Fomitiporia mediterranea.

Oxyceros horridus Lour. 1790, valued for ornamental and medicinal properties, has been extensively utilized in traditional medicinal in Vietnam. This study assembled and characterized the first chloroplast of Oxyceros horridus, consisted of 155,333 bp with a GC content of 37.5%. The genome included 130 annotated genes (including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes), exhibited a typical quadripartite structure consistent with those found in other members of the Rubiaceae family. Phylogenetic analysis placed O. horridus in Ixoroideae subfamily, closely related to Fosergia shweliensis and Gardenia tenophylla. This study enriches cp genome data and phylogenetic insights within Rubiaceae.

The Duke of Bedford's vole (Proedromys bedfordi Thomas 1911) is distributed only at the border areas of the Sichuan and Gansu Provinces, China. In this study, the first complete mitochondrial genome of P. bedfordi is generated and characterized. The assembled genome is 16,262 base pairs in length and the base compositions present clearly the A-T bias (60.84%). Its genetic constitution and arrangement are consistent with the taxon of the voles, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 main non-coding regions, D-loop region and O_L region. This mitochondrial genome will be a significant supplement for the genus Proedromys and whole mitogenome phylogenetic analysis provided insights into further evolutionary research of the subfamily Arvicolinae.

The wild raspberry species Rubus sumatranus Miq 1861 is a promising resource for breeding thermotolerant cultivars. Its complete chloroplast genome spans 155,935 base pairs (bp), featuring the classic quadripartite structure: an 18,729 bp small single-copy region, an 85,662 bp large single-copy region, and two 25,772 bp inverted repeats. A total of 130 genes were identified, including 86 protein-coding, 36 tRNA genes, and 8 rRNA genes. A maximum likelihood phylogenetic tree based on chloroplast genomes shows that R. sumatranus, within the subgenus Idaeobatus, is sister to the subgenus Batothamnus. This confirms the polyphyletic nature of the subgenus Idaeobatus. The chloroplast genome assembly of R. sumatranus enhances our understanding of its evolutionary history.

The complete mitochondrial genome sequence of Dendrodoris krusensternii (J. E. Gray, 1850) was determined using next-generation sequencing. The complete mitochondrial genome of D. krusensternii is 14,361 bp long, comprising 13 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs. The nucleotide composition was estimated: 28.7% A, 14.8% C, 19.6% G, and 36.9% T. Phylogenetic analysis was performed using the maximum likelihood method (including 13 PCGs). D. krusensternii is related to the Phyllidiidae (superfamily Phyllidioidea), suggesting a distinct phylogenetic placement within Nudibranchia. This study represents a genomic resource, contributing to molecular studies on the evolution of the Dendrodorididae.

Melothria scabra has gradually become an economically important plant worldwide. The complete chloroplast genome of M. scabra has a length of 156,744 bp, contains a large single-copy (LSC) region (86,387 bp), a small single-copy (SSC) region (18,055 bp), and two inverted repeats (IRs) with the same length of 26,151 bp. In total, 126 genes were detected, including 83 protein-encoding genes, 35 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. For phylogenetic analysis, M. scabra has a closer genetic relationship with Cucumis sativus and Citrullus lanatus. The complete chloroplast genome sequence of M. scabra would promote the germplasm exploration, phylogenetic relationships, and molecular biology researches in Melothria.

The complete chloroplast genome of Syzygium zeylanicum (L.) DC. 1828 has been sequenced and analyzed for the first time. The S. zeylanicum chloroplast genome is 159,445 bp in length, comprised of a large single-copy region (88,034 bp), a small single-copy region (18,455 bp), and a pair of inverted repeat regions (26,478 bp each). The genome encoded 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis indicated that S. zeylanicum is closely related to S. acuminatissimum. This research provides essential genomic data for S. zeylanicum, offering valuable resources for future comparative genomics, phylogenetics, and conservation biology studies.

Hemerocallis cultivar Small orange lamp is a hybrid variety. Its whole chloroplast genome was 156,053 bp in size, consisting of 135 genes in total, including 89 mRNA genes, 38 tRNA genes, and 8 rRNA genes. The chloroplast genome contained a large single copy region (LSC 84,805 bp), a small single copy region (SSC 18,510 bp) and a pair of inverted repeats (IRa and IRb 26,369 bp). The overall GC content was 37.34%. Phylogenetic analysis showed that Hemerocallis lilioasphodelus and H. cultivar Small orange lamp are most closely related. This will provide valuable reference for further research on the genetic information of plants in the Hemerocallis.