tRNA Genes Research Articles

CHARACTERIZATION OF THE CHLOROPLAST GENOME OF AQUILARIA CRASSNA PIERRE EX LECOMTE DISTRIBUTED IN VIETNAM USING LONG-READ DATA (OXFORD NANOPORE TECHNOLOGIES)

Aquilaria crassna Pierre ex Lecomte is a critically endangered species that is famous for its fragrance compounds for perfume and incense production. In this study, the complete chloroplast genome of A. crassna was sequenced using a long-read sequencing method of Oxford Nanopore Technologies. The complete chloroplast genome of A. crassna was 174,766 bp in length, which comprised a large single copy region of 87,231 bp, a small single copy region of 3,343 bp, and two inverted repeat regions of 42,096 bp. This genome contained 95 protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes. The analysis ofsmall single repeats revealed 39 mononucleotide and seven dinucleotide repeats, which are located mainly in non-coding regions. Comparative genomic analysis exhibited high conservation of the chloroplast genome within the Aquilaria genus regarding gene content, gene order, and genomic structure. This study provides useful genomic data for further studies examining the genetic population, genetic conservation, molecular markers, and phylogeny of Aquilaria crassna and related species within Thymelaeaceae.

Comparative and phylogenetic analysis of the complete chloroplast genomes of 10 Artemisia selengensis resources based on high-throughput sequencing

BackgroundArtemisia selengensis, classified within the genus Artemisia of the Asteraceae family, is a perennial herb recognized for its dual utility in culinary and medicinal domains. There are few studies on the chloroplast genome of A. selengensis, and the phylogeographic classification is vague, which makes phylogenetic analysis and evolutionary studies very difficult.ResultsThe chloroplast genomes of 10 A. selengensis in this study were highly conserved in terms of gene content, gene order, and gene intron number. The genome lengths ranged from 151,148 to 151,257 bp and were typical of a quadripartite structure with a total GC content of approximately 37.5%. The chloroplast genomes of all species encode 133 genes, including 88 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Due to the contraction and expansion of the inverted repeats (IR), the overlap of ycf1 and ndhF genes occurred at the inverted repeats B (IRB) and short single copy sequence (SSC) boundaries. According to a codon use study, the frequent base in the chloroplast genome of A. selengensis’ third codon position was A/T. The number of SSR repeats was 42–44, most of which were single nucleotide A/T repeats. Sequence alignment analysis of the chloroplast genome showed that variable regions were mainly distributed in single copy regions, nucleotide diversity values of 0 to 0.009 were calculated by sliding window analysis, 8 mutation hotspot regions were detected, and coding regions were more conserved than non-coding regions. Analysis of non-synonymous substitution (Ka) and synonymous substitution (Ks) revealed that accD, rps12, petB, and atpF genes were affected by positive selection and no genes were affected by neutral selection. Based on the findings of the phylogenetic analysis, Artemisia selengensis was sister to the genus Artemisia Chrysanthemum and formed a monophyletic group with other Artemisia genera.ConclusionsIn this research, the present study systematically compared the chloroplast genomic features of A. selengensis and provided important information for the study of the chloroplast genome of A. selengensis and the evolutionary relationships among Asteraceae species.

Evolutionary and phylogenetic insights from the mitochondrial genomic analysis of Diceraeus melacanthus and D. furcatus (Hemiptera: Pentatomidae)

The mitochondrial genomes of D. melacanthus and D. furcatus were sequenced and used to investigate the phylogenetic relationships with 54 species of Pentatomidae. Their mitogenomes are 17,197 and 15,444 bp-long, respectively, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22/21 transfer RNA genes, with conserved gene arrangement. Leu, Lys, and Ser were the most common amino acids in their PCGs. PCGs evolutionary analysis indicated their mitogenomes are under purifying selection, and the most conserved genes are from the cytochrome complex, reinforcing their suitability as markers for molecular taxonomy. We identified 490 mtSSRs in 56 Pentatomidae species, with large variation and a positive correlation between mtSSR number and genome size. Three mtSSRs were identified in each Diceraeus species. Only the mtSSR in the nad6 (D. melacanthus) and nad4 (D. furcatus) appear to have application as molecular markers for species characterization. Phylogenetic analysis confirmed the monophyly of Pentatomidae. However, our analysis challenged the monophyly of Pentatominae and Podopinae. We also detected unexpected relationships among some tribes and genera, highlighting the complexity of the internal taxonomic structure of Pentatomidae. Both Diceraeus species were grouped in the same clade with the remaining Carpocorini analyzed.

Mitochondrial genome complexity in Stemona sessilifolia: nanopore sequencing reveals chloroplast gene transfer and DNA rearrangements.

Mitochondria are semi-autonomous organelles in eukaryotic cells with their own genome. Plant mitogenomes differ from animal mitogenomes in size, structure, and repetitive DNA sequences. Despite larger sizes, plant mitogenomes do not have significantly more genes. They exhibit diverse structures due to variations in size, repetitive DNA, recombination frequencies, low gene densities, and reduced nucleotide substitution rates. In this study, we analyzed the mitochondrial genome of Stemona sessilifolia using Nanopore and Illumina sequencing. De-novo assembly and annotation were conducted using Unicycler, Geseq, tRNAscan-SE and BLASTN, followed by codon usage, repeat sequence, RNA-editing, synteny, and phylogenetic analyses. S. sessilifolia's mitogenome consisted of one linear contig and six circular contigs totaling 724,751bp. It had 39 protein-coding genes, 27 tRNA genes, and 3 rRNA genes. Transfer of chloroplast sequences accounted for 13.14% of the mitogenome. Various analyses provided insights into genetic characteristics, evolutionary dynamics, and phylogenetic placement. Further investigations can explore transferred genes' functions and RNA-editing's role in mitochondrial gene expression in S. sessilifolia.

Comparative Mitogenomics and Phylogenetic Implications for Nine Species of the Subfamily Meconematinae (Orthoptera: Tettigoniidae).

Currently, the subfamily Meconematinae encompasses 1029 species, but whole-mitochondrial-genome assemblies have only been made available for 13. In this study, the whole mitochondrial genomes (mitogenomes) of nine additional species in the subfamily Meconematinae were sequenced. The size ranged from 15,627 bp to 17,461 bp, indicating double-stranded circular structures. The length of the control region was the main cause of the difference in mitochondrial genome length among the nine species. All the mitogenomes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and a control region (CR). The majority strand encoded 23 genes, and the minority strand encoded 14 genes. A phylogenetic analysis reaffirmed the monophyletic status of each subfamily, but the monophysitism of Xizicus, Xiphidiopsis and Phlugiolopsis was not supported.

Sequencing and analysis of the complete mitochondrial genome of Amrasca biguttula biguttula Ishida, 1913 (Hemiptera: Cicadellidae: Typhlocybinae: Empoascini)

The complete mitogenome of the cotton leafhopper, Amrasca biguttula biguttula Ishida, 1913, was sequenced and annotated. The mitogenome is 14,474 bp long and contains 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, as well as a control region. The nucleotide composition of the mitogenome is as follows: A, 39.17%; T, 39.3%; C, 11.13%; and G, 10.39%. The total length of the 13 PCGs is 10,496 bp, which encodes 3503 amino acids. All PCGs start with the ATG codon, except for ATA, ATC, GTG, and ATT. Most of the PCGs stop with TGA, and the remaining with CCT, GAA, GGT, TCA, CCA, CTA, TTA, AAA, ATT, or ATA. The phylogenetic tree shows that A. biguttula biguttula belongs to Empoascini of the subfamily Typhlocybinae, but is different from other species within the subfamily.

The complete mitochondrial genome of enigmatic mycoparasitic fungus Squamanita imbachii

The complete mitochondrial genome of Squamanita imbachii I. Saar, is unveiled in this research for the first time. It covers 76,643 base pairs (bp) and exhibits a guanine-cytosine (GC) content of 23%. The genome includes 14 conserved protein-coding genes, 1 DNA polymerase gene, 2 ribosomal RNA gene (RNS and RNL), 25 transfer RNA (tRNA) genes and 18 open reading frames (ORFs). Phylogenetic analysis, utilizing a mitochondrial gene dataset from 15 taxa across seven families within the Agaricales order, was conducted employing the maximum-likelihood (ML) approach. This analysis identified a close phylogenetic relationship between S. imbachii and Floccularia luteovirens (Alb. & Schwein.) Pouzar 1957, positioning both within the Squamanitaceae family.

Characterization of the complete chloroplast genome sequence of Bassia scoparia (L.) A. J. Scott 1978 (Amaranthaceae) and its phylogenetic analysis

Bassia scoparia, an annual potherb belonging to the family Amaranthaceae, has been widely used in traditional Chinese and Japanese medicine for over 2000 years. Herein, we presented its complete chloroplast. The chloroplast genome sequence was 151,278 bp in length with a 36.6% content of GC. The genome showed the typical quadripartite structure, comprising a pair of inverted repeat (IR) regions (24,353 bp) separated by a large single-copy (LSC) region (84,067 bp) and a small single-copy (SSC) region (18,505 bp). This chloroplast genome harbored 133 predicted genes, including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis indicated that B. scoparia was closely related to B. littorea. This newly sequenced chloroplast genome not only enhances our understanding of the genome of Bassia but also provides valuable insights for the evolutionary study of the family Amaranthaceae.

The first mitochondrial genome of Meroplius fukuharai (Diptera: Sepsidae)

Meroplius fukuharai is an important sanitary and ecological resource insect. We sequenced and annotated the mitogenome of Meroplius fukuharai which is the first representative of the genus Meroplius with nearly complete mitochondrial data. This mitogenome is 14,803 bp long, which consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), and two ribosomal RNA genes. All genes have a conservational arrangement with other published species of Sepsidae. Our results also supported the monophyly of Sepsidae, and the genus Meroplius is more closely related to genus Sepsis, Microsepsis, and Archisepsis.

Complete mitogenome and phylogenetic analysis of Hyalinocerus flavoscutatus Cai and Shen 1998 (Hemiptera: Eurymelinae: Idiocerini)

This study presents the initial sequencing and characterization of the complete mitochondrial genome (mitogenome) of Hyalinocerus flavoscutatus, making the first comprehensive exploration of the mitogenome in the Hyalinocerus. Utilizing next-generation sequencing techniques, we identified a circular DNA molecule spanning 15,307 bp. The mitogenome comprises 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a primary non-coding region. Maximum likelihood phylogenetic evaluation, based on 13 protein-coding genes and two ribosomal RNA genes, robustly supports H. flavoscutatus as the basal group within Idiocerini. This research unveils valuable insights into the mitogenome of H. flavoscutatus and enhances our understanding of phylogenetic placement within the broader context of related tribes.

The complete chloroplast genome sequence of Olea dioica Roxb, 1820 (Oleaceae)

Olea dioica Roxb, 1820 is a very important ethnomedicinal tree because of its medicinal properties and it belongs to the Oleaceae family. It is mainly distributed in evergreen and semi-evergreen forests. However, the chloroplast genome of O. dioica has not yet been reported. In this study, the chloroplast genome sequence of O. dioica was sequenced using next-generation sequencing technologies. The complete chloroplast genome of O. dioica was 155,138 bp in length (GenBank accession no. PP048999), comprising a large single-copy (LSC) region of 86,048 bp, a small single-copy (SSC) region of 17,816 bp, and two inverted repeat (IR) regions 25,637 bp each. The overall GC content was 37.8%. The complete chloroplast genome of O. dioica contains 131 complete genes, which are 88 protein-coding genes, 35 transfer RNA genes, and eight ribosomal RNA genes. A maximum-likelihood (ML) tree of O. dioica and 14 other species in the family Oleaceae suggested that O. dioica showed a close relationship with Olea brachiata.

The complete mitochondrial genome of Anidiocerus bimaculatus Zhang, Li & Qi, 2008 (Hemiptera: Cicadellidae: Eurymelinae: Idiocerini)

In this study, the complete mitochondrial genome of Anidiocerus bimaculatus was sequenced and annotated for the first time, which belongs to the subfamily Eurymelinae. The mitogenome of A. bimaculatus was 15,267 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one non-coding control region. In this mitogenome, all the PCGs are initially encoded by ATT, ATA, ATG, or TTG, and terminated by TAA, or single T. The overall base composition of A. bimaculatus is 43.6% adenines, 36.0% thymines, 9.1% guanines, and 11.3% cytosines. ML phylogenetic analyses confirmed that Idiocerini forms a monophyletic clade and the newly sequenced A. bimaculatus clustered within the Idiocerini clade based on 13 protein-coding genes and two rRNA genes.

The complete mitochondrial genome of Ceresium sinicum ornaticolle Pic, 1907 (Coleoptera: Cerambycidae)

Ceresium sinicum ornaticolle Pic, 1907 (Coleoptera: Cerambycidae) is one of the main pests of pomegranate and citrus trees. In this study, we described the complete mitochondrial genome of C. sinicum ornaticolle. The total length of the mitochondrial genome was 15,817 bp, and the entire content of GC was 27.8%. The genome encoded 2 ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and 22 transfer RNA genes (tRNAs). The phylogenetic tree showed that C. sinicum ornaticolle was clustered with Allotraeus orientalis and Zoodes fulguratus. These results will provide the genetic information for understanding the genetic evolution of C. sinicum ornaticolle and the insights to control cerambycid pests.

The complete mitochondrial genome of Vibrissina turrita (Meigen, 1824) (Diptera, Tachinidae)

In this study, the mitogenome of Vibrissina turrita (Meigen, 1824) (Diptera, Tachinidae) was sequenced based on the next-generation sequencing approach and analyzed here for the first time. The 17,387 bp genome has a high A + T content and consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one noncoding control region. The phylogenetic analysis results support that Exoristinae is monophyletic and V. turrita belongs to the subfamily. This study reveals the systematic classification status of V. turrita and will enrich the genetic data on Tachinidae.

The complete mitochondrial genome of Sigara lateralis (Leach, 1817) (Nepomorpha: Corixidae)

The Sigara lateralis (Leach, 1817) is a small aquatic insect belonging to the family Corixidae. The study aims to reveal the genomic data of the mitochondrial genome of S. lateralis. The length of its circular mitochondrial genome is 15,725 bp long with an A + T bias (75.96%). The mitogenome comprises 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two rRNA genes. The phylogenetic analyses showed that the S. lateralis is the closest to S. septemlineata. These findings will help the conservation of Corixidae from the perspective of genetic evolution.

The complete chloroplast genome of Meconopsis torquata (Papaveraceae), a traditional Tibetan medicine

Meconopsis torquata Prain 1906, a national second-class rare and endangered plant, is reported here for the first time for its complete chloroplast genome. The genome is 153,290 bp in length, comprising a large single-copy region (LSC, 83,918 bp), a small single-copy region (SSC, 17,740 bp), and two inverted repeat sequences (IRa and IRb, each 25,816 bp). The overall GC content is 38.7%, with the IR region having the highest content (43.1%). The genome is annotated with 112 unique genes, including 4 rRNA genes, 29 tRNA genes, and 79 protein-coding genes. Analysis of codon usage bias reveals that codons ending in A/T account for 96.7% of those with a Relative Synonymous Codon Usage (RSCU) value above 1. This predominance of A/T-ending codons might be indicative of M. torquata adaptation to high-altitude environments. Phylogenetic analysis reveals a close kinship between M. torquata and M. pinnatifolia and M. paniculata, indicating that the ancestral groups of these species might have a complex evolutionary history. This study uncovers the genetic characteristics and adaptive evolution of M. torquata, offering a new perspective in understanding the phylogenetic relationships within the genus. The findings not only provide a solid theoretical foundation for the conservation and sustainable use of this rare and endangered species but also offer significant scientific support for the conservation of biodiversity.

The complete chloroplast genome of the first registered Paeonia Itoh hybrid cv. Hexie in China

The first registered Paeonia Itoh hybrid cv. Hexie in China is a naturally occurring intersectional hybrid of Sect. Paeonia and Sect. Moutan. In this study, we sequenced, assembled, and analyzed the complete chloroplast genome of Paeonia Itoh hybrid cv. Hexie. The result showed that the chloroplast genome of Hexie, with a typical circular tetrad structure, is 152,958 bp in length, comprising a large single copy (LSC) region of 84,613 bp, a small single copy (SSC) region of 17,051 bp, and two reverse complementary sequences (IRs) of 25,647 bp. The chloroplast genome encoded 116 genes, including 80 protein-coding genes, 32 tRNA genes, and 4 rRNA genes. Phylogenetic analysis inferred from the shared protein-coding genes showed that the Paeonia Itoh hybrid cv. Hexie had the closest phylogenetic relationship with P. suffruticosa, followed by P. ostii, indicating that P. suffruticosa was its maternal parent. This study provides a molecular resource for phylogenetic and maternal parent studies of Paeonia Itoh hybrid, contributing to a basis for Paeonia Itoh hybrid breeding strategies in the future.

The complete mitochondrial genome of a Biwa goby, Gymnogobius isaza (Tanaka, 1916)

We determined the complete mitochondrial DNA sequence of a Biwa goby, Gymnogobius isaza (Tanaka, 1916) using next-generation sequencing methods. The composition of its mitogenome is the same as that observed in most other vertebrates, comprising of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions. Our molecular phylogenetic analysis confirmed the close phylogenetic relationship between G. isaza and G. petschiliensis. This mitogenome information will be useful for distribution surveys using environmental DNA and the development of conservation strategies for this species.

Phylogenetic analysis of Cyprinus acutidorsalis (Wang, 1979) from the Hainan population using complete mitochondrial genome

Cyprinus acutidorsalis (Wang, 1979) is an endemic fish in China that is sparsely distributed in the Hainan provinces and Guangxi Zhuang Autonomous Region (GZAR). In this study, the complete mitochondrial genome of C. acutidorsalis from the Hainan population from the Wanquan River was sequenced, and its phylogenetic relationship was analyzed. The circular mtDNA was 16,581 bp in length, and the overall base composition was A (32.0%), C (27.5%), T (24.8%), and G (15.70%), with a slight bias toward A + T. The complete mitogenome encoded 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis indicated that the most closely related fish to C. acutidorsalis from the Hainan population was C. acutidorsalis from the Guangxi population. These findings offer basic molecular data and a better understanding of the phylogenetic relationships among the Cyprinus species.

Complete mitochondrial genome of Devario shanensis (Cypriniformes: Danionidae: Danioninae): genome characterization and phylogenetic consideration

In this study, a comprehensive analysis is presented on the complete mitochondrial genome and phylogenetic relationships of Devario shanensis, an endemic species to the Irrawaddy drainage in southwestern China. The complete mitogenome sequence of D. shanensis was sequenced to be 16,860 bp long and encompassed 13 protein-coding genes, 22 tRNA genes, two rRNA genes and a non-coding control region. The overall AT content (61.1%) was much higher than GC content (38.9%). Phylogenetic analyses employing maximum-likelihood and Bayesian inference methods on the complete mitogenomes, including D. shanensis and 13 other species, unveiled a close genomic relationship between D. shanensis and Devario interruptus. This work will contribute to the genetic resource enrichment and phylogenetic researches on genus Devario.