Mitochondrial DNA. Part B, Resources最新文献

Asparagus densiflorus 'Sprengeri' is an economically important ornamental and medicinal plant within the genus Asparagus. In this study, we sequenced and assembled its complete chloroplast (cp) genome using the Illumina NovaSeq platform. The circular cp genome is 157,116 bp in length with a GC content of 38%, comprising a large single-copy (LSC) region (85,327 bp), a small single-copy (SSC) region (18,677 bp), and two inverted repeat (IR) regions (26,556 bp each). The genome encodes 133 functional genes, including 87 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicates that A. densiflorus 'Sprengeri' is most closely related to A. densiflorus 'Myers' and A. falcatus, suggesting a shared evolutionary lineage. This study will not only shed light on A. densiflorus 'Sprengeri''s evolutionary position but also provide valuable chloroplast genomic information for future studies into the origins and diversification of the genus Asparagus and the Asparagaceae family.

Odoiporus longicollis (Marshall, 1930), a major banana pest in the family Curculionidae, primarily infests banana pseudostems. The mitogenomic analysis of O. longicollis and its phylogenetic relationships enhances the available mitogenomic data of Curculionidae and provides valuable resources for the molecular identification, population monitoring, and management of this species. In this study, the complete mitogenome of O. longicollis (16,294 bp) was sequenced for the first time. The circular genome comprises 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs, with GC contents of 24.81%. Phylogenetic analysis based on 16 Curculionidae mitogenomes offers novel insights into the evolutionary relationships of O. longicollis.

This study reports the first complete mitochondrial genome of Ischiodon scutellaris. The mitochondrial genome is 15,815 bp in length, with an A + T content of 80.7%. The genome contains 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and a control region. All PCGs initiate with ATN (G/C/T), except COX1and ND1(TTG). Three PCGs (COX1, ATP6, ND5) terminate with an incomplete T stop codon. Phylogenetic analysis based on 13 PCG sequences using maximum likelihood revealed that I. scutellaris forms a sister clade with Scaeva affinis and clusters closely with multiple Eupeodes species. This study advances understanding of syrphid mitochondrial genomics and evolutionary relationships.

In this study, the complete mitochondrial genome of Ancylis sativa was sequenced and assembled. The circular genome is 15,262 bp in length and comprises 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes, along with one AT-rich region. The average nucleotide composition is A = 40.95%, T = 38.04%, C = 13.01%, and G = 8.00%, resulting in an A + T content of 78.99%. Phylogenetic analysis indicated that Ancylis sativa was closely related to Ancylis unculana in the subfamily Olethreutinae, which can enhance the evolutionary and phylogeographic study of Ancylis sativa.

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.