Mitochondrial DNA. Part B, Resources最新文献

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.

In this study, we sequenced and analyzed the mitochondrial genome of the Satanas beetle, Dynastes satanas Moser, 1909, which was intercepted by Chinese Customs during an attempted smuggling operation in 2022. The complete mitochondrial genome is 16,973 bp in length (GenBank accession number: OQ998898) and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region of 2285 bp. The gene order of trnQ-trnI-trnM in the mitochondrial genome of Dynastes satanas is consistent with that of other species in the genus Dynastes. All 13 PCGs are initiated by the ATN start codon. Seven genes terminate with the TAA stop codon, one with TAG, and five with a single T. The nucleotide composition of mitochondrial genome of Dynastes satanas was 38.07% of A, 31.49% of T, 20.52% of C, and 9.92% of G. Phylogenetic analysis indicates that Dynastes satanas and Dynastes neptunus (Quensel, 1805) exhibit a considerable genetic distance, suggesting that they should be classified as two distinct subgenera.

The complete mitochondrial genome of Culex hutchinsoni Barraud, 1924 was reported with 15,586 bp long. It contained 37 annotated genes and the control region, which is consistent with other mosquitoes. Most PCGs used typical ATN as start codons, while some special start codons were also used (i.e. TCG for COX1, TTG for ND1, GTG for ND5). Most PCGs terminated with TAA as well as some PCGs (COX1, COX2, COX3, ND3, ND4 and CYTB) terminated with TA-tRNA or T-tRNA. Cx. (Lophoceraomyia) was recovered as the sister group to Cx. (Culex), while Cx. hutchinsoni was recovered within the species group of Cx. pipiens.

Cymodocea rotundata Asch. & Schweinf. 1870 (Cymodoceaceae) is a seagrass found in the tropical and temperate Indo-Pacific coastal waters. Seagrass beds composed of C. rotundata and other seagrasses form ecologically valuable ecosystems. In this study, the complete chloroplast genome of C. rotundata was sequenced and characterized for the first time. It is a circular genome of 158,311 bp in length, consisting of a large single-copy region (88,451 bp), a small single-copy region (18,836 bp), and a pair of inverted repeats (25,512 bp). A total of 130 genes were annotated, including 86 protein-coding genes (PCGs), 36 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Seven PCGs and 6 tRNA genes contain 1 intron, and 3 PCGs contain 2 introns. In addition, 7 PCGs, 7 tRNA genes, and all the rRNA genes are multi-copy genes with 2 copies. Phylogenetic analysis shows that C. rotundata clusters with Syringodium isoetifolium in one clade, both belonging to the family Cymodoceaceae. This study provides new information to support further research on the phylogeny of Cymodoceaceae.

In order to understand the molecular insights within the Terebellida, the complete mitochondrial genome of Loimia arborea was sequenced. The mitochondrial genome is 16,023 bp, with 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding region (D-loop). Notably, two adjacent copies of methionine tRNA genes (trnMs) were detected. The phylogeny of Terebellida was constructed based on 13 PCGs from 13 species, two main clades were strongly supported, i.e., Cirratuliformia (clade A) and Terebelliformia (clade B). And the monophyly of the Terebellidae was restored.

Lilium paradoxum, a herb from southeastern Xizang, China, has its first complete chloroplast genome sequenced using next-generation sequencing. The genome is 151,814 bp, consisting of inverted repeats (IRs; 26,323 bp), small single-copy (SSC; 17,524 bp), and large single-copy regions (LSC; 81,644 bp). It encodes 112 unique genes: 78 protein-coding, 30 tRNA, and 4 rRNA genes. Phylogenetic analysis of 22 genomes shows L. paradoxum is closely related to L. gongshanense, L. apertum, and L. souliei. These findings enhance understanding of Lilium's phylogenetic relationships and evolution, particularly the Nomocharis clade in the Hengduan Mountains.