Mitochondrial DNA. Part B, Resources最新文献

Crepidium calophyllum is a terrestrial orchid native to tropical forests in southern China and Southeast Asia. Once classified under Malaxis, it has since been reassigned to Crepidium. This study presents the first complete plastid genome (plastome) of C. calophyllum, which is 158,884 bp in length. Its gene content and order are highly conserved compared to other autotrophic species within Malaxidinae. Phylogenomic analyses using both maximum likelihood and Bayesian inference, based on complete plastomes, place C. calophyllum within Crepidium, as sister to Dienia. Interestingly, these analyses also reveal the polyphyly of Malaxis and Liparis, suggesting unresolved taxonomic issues within Malaxidinae.

Suillus is an important group of ectomycorrhizal fungi that often symbiose with Pinaceae. While the genus has 113 recognized species, genomic data remain scarce. Herein, we sequenced and characterized the mitogenome of Suillus collinitus (Fr.) Kuntze 1898. The circular mitogenome is 77,697 bp with low GC content (20.3%), encoding 14 standard protein-coding genes, 2 rRNA genes, 26 tRNA genes, and 6 non-conserved ORFs. Notably, 19 group I introns are identified in five genes. Phylogenetic analysis of mitochondrial proteins clearly places it in Suillaceae (suborder Suillineae, order Boletales), providing key molecular evidence for exploring evolutionary relationships among species in this fungal family.

Salvia yunnanensis C.H. Wright 1896, a species in the Lamiaceae family, is a medicinal plant whose roots are used as herbal medicine under the name "Zidanshen." To provide useful genetic information on this plant, in this study, we assembled another complete plastome of a successfully introduced S. yunnanensis using a combination of next-generation sequencing (NGS) and third-generation sequencing (TGS) data. The plastome is 151,486 bp and comprises a large single-copy (LSC) region of 82,759 bp, a small single-copy (SSC) region of 17,577 bp, and a pair of inverted repeat (IR) regions of 25,575 bp each. It encodes 132 genes, which include 87 protein-coding genes, eight rRNA genes, and 37 tRNA genes. The guanine-cytosine (GC) content of the genome is 38.01%. Phylogenetic analysis revealed that S. yunnanensis was closely related to S. honania. Genome assembly benefits from the strengths of NGS and TGS data, resulting in high-quality assembly. It showed 99.53% similarity to the previously reported plastome (MN341012), with a slight increase in length. However, the gene count and GC content remained unchanged. Phylogenetic analysis of whole plastomes revealed that S. yunnanensis in this study formed a monophyletic clade distinct from Salvia honania but did not group with any publicly available S. yunnanensis plants. This newly sequenced plastome provides a valuable resource for the introduction and domestication of this plant resource in the future.

The Mycenaceae family comprises one of the most taxonomically diverse and ecologically important groups of saprotrophic fungi, yet no mitochondrial genome (mitogenome) has been reported to date. This study reports the first mitogenome of Mycenaceae, sequenced from Mycena pura (Pers.) P. Kumm. 1871. The 107,684 bp circular mitogenome (GC 27.83%) contains 14 conserved protein-coding genes (PCGs), 25 tRNAs, 2 rRNAs, and 11 non-conserved open reading frames (ORFs), with 18 introns (mostly harboring ORFs) identified in seven genes. Phylogenetic analysis based on mitochondrial amino acid sequences validated its Mycenaceae placement, providing crucial genomic resources for future evolutionary studies.

The mitochondrial genome of Grapsus adscensionis (Osbeck, 1765), a rocky shore crab distributed across the Macaronesian archipelagos and the eastern Atlantic, was sequenced and annotated for the first time. The circular mitogenome is 15,553 bp in length and comprises 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and a non-coding control region. It exhibits a strong AT bias, with negative AT- and GC-skews. Gene arrangement and composition are consistent with other brachyuran crabs. These findings provide novel molecular data for the species, representing the third mitogenome published for the genus Grapsus, and contribute to a better understanding of brachyuran evolutionary relationships.

The silver-backed chevrotain (Tragulus versicolor Thomas, 1910) is the only endemic ungulate species in Vietnam and among the most little-known ungulates in the world. The species currently has a very narrow distribution area and is facing many threats of extinction due to habitat loss and illegal hunting. In this study, we describe complete mitochondrial genome of T. versicolor and its taxonomic position within Tragulidae. The circular genome is 16,317 bp in length, comprising 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region, with a GC content of 40.3%. Phylogenetic analysis based on complete mitochondrial genomes using the maximum-likelihood method confirms the monophyly of Tragulidae and the distinct position of T. versicolor within Tragulus. This is the first publicly available mitogenome of T. versicolor (GenBank accession no. PV872897), which provides an essential resource for future studies on evolution, taxonomy, and conservation of this elusive species.

Zehneria japonica (Thunb.) H. Y. Liu is a traditional Chinese medicinal plant. We sequenced and annotated its complete chloroplast genome, which is 157,052 bp in length with 36.99% GC content. It exhibits a typical quadripartite structure, including a large single-copy region of 86,849 bp, a small single-copy region of 17,867 bp, and two inverted repeat regions of 26,168 bp. The genome encodes 131 genes (86 protein-coding, 37 tRNA, and 8 rRNA). Phylogenetic analysis based on chloroplast genomes supports the monophyly of Zehneria species. These results enrich genomic resources and provide a foundation for future phylogenetic and evolutionary studies within Zehneria.

Bibio Geoffroy, 1762 is a species-rich genus within the family Bibionidae. In this study, we present the complete mitochondrial genome of Bibio hordeiphagus Yang and Luo 1988 for the first time. Complete mitochondrial genome of B. hordeiphagus is 15,496 bp in length, comprising 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. The nucleotide composition of mitochondrial genome of B. hordeiphagus was 40.55% of A, 39.02% of T, 8.37% of G, and 12.05% of C. Based on the sequencing and annotating results, we conducted a preliminary phylogenetic analysis of Bibionomorpha. Our findings support the monophyly of both family Bibionidae and genus Bibio, with the family Bibionidae identified as the sister group to Sciaridae and Mycetophilidae. This study encompasses all reliable annotated mitochondrial genome data for Bibionidae and analyzed the higher-level phylogenetic relationships within the Bibionomorpha from the perspective of mitochondrial genome data.

Persicaria hydropiper (L.) Spach and P. pubescens (Blume) Hara (Polygonaceae) are widely used as traditional Chinese medicinal plants. In this study, the complete chloroplast (cp) genomes of P. hydropiper and P. pubescens were sequenced, assembled, and annotated. The cp genome sizes of P. hydropiper and P. pubescens are 159,054 bp and 159,502 bp, respectively. The cp genomes of P. hydropiper and P. pubescens each contain a total of 130 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. Phylogenetic analysis reveals that P. hydropiper is close to P. pubescens and P. japonica, and Persicaria is mostly closely related to Bistorta.

Amynthas susakii (Kobayashi 1936) is an earthworm species endemic to Korea that typically inhabits mountainous forest environments. The specimens were collected from Mount Jiri, South Korea. The complete mitogenome of A. susakii was sequenced, assembled, and annotated. The mitogenome of A. susakii is a circular DNA molecule of 15,115 bp with an A + T content of 67.7%, comprising 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. Phylogenetic analysis showed that A. susakii clustered with other Amynthas species in the well-supported Megascolecidae family.