Mitochondrial DNA. Part B, Resources最新文献

Hypecoum erectum L., a widespread species in northern Eurasia, is a valuable medicinal plant, but its chloroplast genome has not previously been reported. We determined its complete chloroplast genome using a high-throughput sequencing technique. Its total length was 169,241 bp, consisting of a large single-copy region of 93,301 bp and a small single-copy region of 17,316 bp, separated by a pair of inverted repeat regions of 29,312 bp. A total of 140 genes were annotated, including 91 protein coding genes, 41 tRNA genes, and eight rRNA genes. The phylogenetic analysis shows that H. erectum and H. zhukanum of the subfamily Hypecoideae are monophyletic with the highest support.

The complete mitochondrial genome of Locastra muscosalis (Walker, 1866) was sequenced and characterized in this study, which was the first reported complete mitogenome of the genus Locastra. The mitogenome of L. muscosalis has a total length of 15,177 bp, encompassing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A-T rich region. Phylogenetic analysis revealed that L. muscosalis is closely associated with Orthaga euadrusalis. These data will serve as a valuable foundation for future investigations into the Epipaschiinae and Pyralidae evolutionary history.

The soft-shell clam Mya japonica (Jay, 1857) is a commercially important fishery resource. In this study, we identified the complete mitochondrial genome of M. japonica and performed a phylogenetic analysis to explore its genetic relationship with Mya arenaria. The genome is 21,396 bp in length and contains 13 protein-coding genes (PCGs), 23 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 5 D-Loop control regions. The atp8 gene was annotated in Myidae for the first time. Notably, the genome contains an additional trnM, consistent with M. arenaria. The length of the cox2 gene is 1,947 bp, which is 513 bp longer than that in M. arenaria. Its base composition is 29.14% A, 37.26% T, 10.89% C, and 22.71% G. Phylogenetic analysis based on 12 PCGs and 2 rRNAs indicates that M. japonica and M. arenaria form a sister group. In this study, the identification and phylogenetic analysis of the complete mitochondrial genome of M. japonica provide significant information for future taxonomic and evolutionary research of the genus Mya.

Blechnopsis orientalis (Linnaeus) C. Presl (1753) is a fern used both as food and medicine. It is found primarily in southern China and Southeast Asia, thriving in warm, humid shrublands or sparse forest. The total length of the chloroplast genome is 155,211 bp, including a large single-copy region (LSC, 81,877 bp), a small single-copy region (SSC, 21,500 bp), and two inverted repeat regions (IRs, 25,917 bp). The GC content is 41.3%. A total of 131 genes were annotated, including 88 protein-coding genes, eight rRNA genes, and 35 tRNA genes. The phylogenetic analysis using the maximum-likelihood method showed that B. orientalis and Oceaniopteris gibba were closely related. This study provides genomic resources for phylogenetic genetics and resource exploitation of B. orientalis.

Homoderus mellyi belongs to the Lucanidae family of Coleoptera. The first complete mitogenome of Homoderus is reported in this paper. The genome is 16,807 bp in length and contains the typical 37 genes with 22 transfer RNA genes, 13 protein coding genes, and 2 ribosomal RNA genes. The gene order is conserved across the lineage. The average base composition of the mitogenome is 36.6% for A, 20.8% for C, 11.6% for G, and 31.1% for T. The percentage of GC is 32.3%. The genome organization, nucleotide composition, and codon usage are similar to other beetles. Phylogenetic analysis shows that Lucanidae is monophyletic, and all subfamilies are monophyletic, respectively. The phylogenetic position of H. mellyi is consistent with other research.

Cyanopterus ninghais is an important gregarious ectoparasitoid during the larval stage of Monochamus alternatus, a key vector for pine wilt disease in Asia. In this study, the complete mitochondrial genome of C. ninghais was sequenced and analyzed. The mitochondrial genome of C. ninghais is 15,386 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The nucleotide composition is 41.32% A, 8.29% G, 6.06% C, and 44.33% T. Phylogenetic trees of Braconidae were constructed using 13 PCG sequences via Bayesian inference (BI) and maximum likelihood (ML) analyses to determine their phylogenetic position. Both ML and BI analyses revealed that C. ninghais is closely related to Euurobracon yokahamae, Virgulibracon endoxylaphagus, and Habrobracon hebetor.

Endemic to Taiwan Province, China, Cotoneaster rosiflorus Kun-Cheng Chang & Fu-Yuan Lu 2011 (Rosaceae) holds significant ecological and ornamental importance. Despite its value, research on its molecular data and phylogenetic position has remained limited. In this study, we addressed this gap by sequencing the genome-skimming data, assembling its plastome, and investigating its phylogenetic position. The plastome, spanning 159,449 bp in length, consisted of a large single-copy (87,433 bp), a small single-copy (19,262 bp), and two inverted repeat regions (26,377 bp). We annotated a total of 128 functional genes, including 84 protein-coding genes, 36 transfer genes, and eight ribosomal RNA genes. The phylogenetic results indicated that C. rosiflorus is closely related to C. dammerii, suggesting that C. rosiflorus might have captured its chloroplast from C. dammerii through hybridization and introgression events. This study offered valuable insights for forthcoming phylogenetic and population genetic investigations of Cotoneaster.

Singerocybe alboinfundibuliformis (Seok et al.) Yang, Qin & Takah 2014 is an edible mushroom distributed in several East or Southeast Asian countries. Herein, we report the mitochondrial genome of S. alboinfundibuliformis based on Illumina sequencing data. The overall length of the mitochondrial genome is 64,279 bp, with a GC content of 29.0%. It contains 14 typical protein-coding genes, 27 tRNA genes, two rRNA genes, and 13 intergenic ORFs. Most of these genes (39 out of 56) are transcribed at the forward strand, and few (17 out of 56) are transcribed at the reverse strand. Among these genes, only the rnl gene is invaded by an intron, and all other genes are intron-free. Phylogenetic analysis based on mitochondrial amino acid sequences supports the phylogenetic position of S. alboinfundibuliformis in Clitocybaceae, being close to Lepista sordida (Schumach.) Singer 1951. This study serves as a springboard for future investigation on fungal evolution in Clitocybaceae.

Lemna turionifera is native to North America and northern Asia, with significant potential for industrial wastewater remediation. The complete nucleotide sequence of the L. turionifera chloroplast genome (cpDNA) was determined. The cpDNA is a circular molecule of 166,606 bp and containing a pair of inverted repeats (IRs) measuting 31,663 bp each. These IRs are flanked by a small single-copy region of 13,542 bp and a large single-copy region of 89,738 bp. The chloroplast genome of L. turionifera consisted of 112 unique genes, including 78 protein-encoding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis utilizing cpDNA provided a well-supported resolution of the relationships among subfamilies within the Araceae family. Our findings indicated a close relationship between L. turionifera and a clade consisting of L. minor, L. japonica, and L. gibba. The availability of the complete chloroplast genome sequence of L. turionifera presents valuable data for future phylogenetic investigations within the Lemnaceae family.

Bird's nest fungi involve six different genera, but only one of these genera (i.e. Cyathus) have available mitochondrial genomes (mitogenomes) to date. In this study, we report the first mitogenome in the genus Nidula with Nidula shingbaensis K. Das & R.L. Zhao 2013 as a representative. The mitogenome is a circular molecule of 65,793 bp with a GC content of 26.2%. There are a total of 43 genes, including 14 typical protein-coding genes, 26 tRNA genes, two rRNA genes, and one free-standing intergenic open reading frame (ORF). Three introns (two in cox1 and one in cob) are present in the mitogenome, with each containing an ORF encoding for a LAGLIDADG endonuclease. Phylogenetic analysis based on mitochondrial amino acid sequences confirms the phylogenetic placement of N. shingbaensis in Nidulariaceae in Agaricales. This study serves as a springboard for future investigation on fungal evolution in Nidulariaceae.