Complete mitochondrial genome of critically endangered catfish Hemibagrus punctatus (Jerdon, 1849) and comparative analysis for insights into the phylogeny of hemibagrids through mitogenomic approach

Molecular Biology Reports, Journal Year: 2024, Volume and Issue: 51(1)

Published: May 1, 2024

Language: Английский

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Phylogenetic relationship analysis of leafhopper subfamily Iassinae (Hemiptera: Cicadellidae) based on low-coverage whole-genome data

Arthropod Systematics & Phylogeny, Journal Year: 2025, Volume and Issue: 83, P. 31 - 41

Published: Feb. 25, 2025

Iassinae, a widely distributed group of herbivorous pest insects, is subfamily Cicadellidae. Previous studies on the phylogeny Iassinae were mostly based morphological characteristics, mitochondrial genomes, and molecular fragments (H3, 28S, 12S), their phylogenetic relationships controversial. To better understand we analyzed among four genera in with use thousands universal single-copy orthologs ultraconserved elements extracted from 25 newly sequenced low-coverage whole genome data. Both marker sets provided consistent results across maximum likelihood coalescent-based species tree approaches. The showed that two Batracomorphus Trocnadella monophyletic groups, Krisna paraphyletic group. For genus Gessius , could not explain whether it or since only one was involved. In this study, relationship stable, all supported sister possess relationship. addition, divergence time began at approximately 49–72 Mya, 33–57 51–78 Mya 17–36 respectively. These will help us to evolutionary Iassinae.

Language: Английский

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Assembly and comparative analysis of the complete mitochondrial genome of Lactuca sativa var. ramosa Hort

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 18, 2025

Lettuce (Lactuca sativa var. ramosa Hort) is an important leaf vegetable that widely cultivates due to its high-quality, short growth cycle, and less diseases. L. Hort belongs Asteraceae family evolutionary relationships with related species of are not completely assessed based on genome sequences. Here, we assembled the whole mitochondrial (mt) Hort, performed a comparative other species. The mt has typical circular structure length 363,324 bp, within GC content accounted for 45.35%. In total 71 genes, comprising 35 protein-coding genes (PCGs), 6 rRNAs, 28 tRNAs, 2 pseudogenes were annotated. Codon preference, RNA-editing sites, repetitive sequences, migrating from chloroplast (cp) genomes investigated in genome. Nucleotide diversity (Pi) showed was relatively conserved. A Bayesian phylogenetic tree closely capitata virosa, which belonged Lactuca genus family. Our findings will provide useful information explore genetic variation, diversity, molecular breeding genus.

Language: Английский

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First report of the complete mitochondrial genome of 3 beetles (Coleoptera: Scarabaeidae) harming Gastrodia elata (Asparagales: Orchidaceae)

Journal of Insect Science, Journal Year: 2024, Volume and Issue: 24(1)

Published: Jan. 1, 2024

Abstract Gastrodia elata Blume, a valuable traditional Chinese medicine with significant clinical and nutritional importance, is fungal heterotrophic orchid. We present the first report of mitochondrial genome structure characteristics 3 Scarabaeidae pests affecting G. elata: Sophrops peronosporus Gu & Zhang, Anomala rufiventris Kollar Redtenbacher, Callistethus plagiicollis Fairmaire. Each mitogenome contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal (rRNAs), control region, no gene rearrangements observed. All 21 tRNAs, except trnS1 that lacks dihydrouridine, had stable cloverleaf secondary structure. Maximum likelihood Bayesian inference analyses based on PCGs produced topologically similar phylogenetic trees, both high nodal support. Larvae these cause substantial damage by gnawing tubers roots elata, leading to reduced yield compromised quality. These findings contribute studies Scarabaeidae, expand knowledge pests, offer reference materials for their identification control.

Language: Английский

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Mitochondrial Genome Characteristics Reveal Evolution of Acanthopsetta nadeshnyi (Jordan and Starks, 1904) and Phylogenetic Relationships

Genes, Journal Year: 2024, Volume and Issue: 15(7), P. 893 - 893

Published: July 8, 2024

In the present study, mitochondrial genomic characteristics of Acanthopsetta nadeshnyi have been reported and depicted phylogenetic relationship among Pleuronectidae. Combined with a comparative analysis 13 PCGs, TN93 model was used to review neutral evolution habitat catalysis mitogenome verify distancing purification selectivity in At same time, species differentiation classification based on data established. This study is expected provide new perspective taxonomic status A. lay foundation for further exploration environmental biological evolutionary mechanisms.

Language: Английский

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Codon usage bias analysis in the mitochondrial genomes of five Rhingia Scopoli (Diptera, Syrphidae, Eristalinae) species

Gene, Journal Year: 2024, Volume and Issue: 917, P. 148466 - 148466

Published: April 12, 2024

Language: Английский

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Characterisation of the complete mitochondrial genomes and phylogenetic analysis of ten Oedipodinae grasshoppers (Orthoptera: Acrididae) from Algeria

Oriental Insects, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 34

Published: June 5, 2024

This study presents the mitogenomes of ten species Oedipodinae grasshoppers belonging to seven different genera in Algeria; nine these were sequenced for first time, providing mitochondrial genomic sequences their respective genera. Mitogenomes obtained using next-generation sequencing and de-novo assembly techniques range length from 15,603 15,766 bp. These are composed double-stranded cyclic molecules encode typical set 37 genes. The AT content, skew GC skew, codon usage nucleotide bias similar across species. All 13 protein-coding genes start with a ATN (G/C/T/A) codon, except COX1 Sphingonotus octofasciatus, which starts CCG. Two ribosomal RNA located on N-strand 22 tRNA folded into clover-leaf structures, trnS (AGN), lacks DHU arm. tRNAs encoded by carry two three times more non-canonical base pairs than J-strand. A+T-rich regions variable terms composition, number repeated units. Moreover, conserved blocks identified all Additionally, phylogenetic relationships reconstructed both ML BI methods based datasets included newly along previously published data. results reveal that subfamilies Oedipodinae, Acridinae, Gomphocerinae Catantopinae paraphyletic strong nodal support. As previous studies, especially show inconsistencies between taxonomy phylogeny suggesting need future large-scale revision.

Language: Английский

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Mitochondrial genomes of Macropsini (Hemiptera: Cicadellidae: Eurymelinae): Structural features, codon usage patterns, and phylogenetic implications

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(9)

Published: Sept. 1, 2024

Abstract Macropsini is a tribe of Eurymelinae in the family Cicadellidae that widely distributed worldwide. Still, its taxonomic status has been unstable, and classification certain clades at genus level controversial. The aim this study to address patterns processes explain structure evolution mitogenomes Macropsini, while contributing resolution systematic issues involving five their genera. To task, 26 species were sequenced characterized, phylogenetic relationships reconstructed. results revealed nucleotide composition mitochondrial genes these was significantly skewed toward A T. Codons ending with T or relative synonymous codon usage more prevalent than those C G. parity plot, neutrality correspondence analysis mutation selective pressure affect patterns. In monophyly Pedionis Macropsis well‐supported. Meanwhile, Oncopsis paraphyletic regarding Pediopsoides . conclusion, research not only contributes valuable data understanding mitogenome but also provides reference for future investigations on patterns, potential adaptive evolution, phylogeny within subfamily Eurymelinae.

Language: Английский

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Description of mitochondrial genomes and phylogenetic analysis of Megophthalminae (Hemiptera: Cicadellidae)

Journal of Insect Science, Journal Year: 2024, Volume and Issue: 24(6)

Published: Nov. 1, 2024

To elucidate phylogenetic relationships within the leafhopper's subfamily Megophthalminae (Hemiptera: Cicadellidae), mitogenomes of 12 species were sequenced and assembled. These added to eight other that are currently available. Mitogenome size ranged from 15,193 bp in Onukigallia onukii (Matsumura, 1912) 15,986 Multinervis guangxiensis (Li Li, 2013), they all contained 37 genes, gene order was similar leafhoppers. Nucleotide composition analysis showed AT content higher than GC, protein-coding genes usually ended with A/T at 3rd codon position. The Ka/Ks ratio CYTB has slowest evolutionary rate, while ND4 is fastest rate. Relative synonymous usage revealed most frequently used UUA (L), followed by CGA (R), least CCG (P). Parity plot neutrality analyses bias mitochondrial influenced natural selection mutation pressure. However, plays a major role, effect pressure small. Effective number codons values 40.15-49.17, which represented relatively low bias. Phylogenetic based on three datasets (AA, 13PCG, 13PCG_2rRNA) using two methods (maximum likelihood Bayesian inference). In obtained topology, clustered into monophyletic group. conclusion, our results clarify structural modules confirm monophyly Cicadellidae.

Language: Английский

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Exploring the mitogenomes of Batracomorphus (Hemiptera: Cicadellidae: Iassinae): new insights from structural diversity and phylogenomic analyses

Insect Systematics and Diversity, Journal Year: 2024, Volume and Issue: 8(4)

Published: July 1, 2024

Abstract Comparisons of mitogenomes are widely used for species identification and to explore the phylogenetic relationship among insect taxa. Batracomorphus is third most diverse distributed genus in Cicadellidae (Hemiptera). However, there have been no analyses genome structure relationships within genus. To compensate paucity genomic information this genus, we sequenced novel complete mitochondrial genomes 11 combined these with 23 previously perform structural comparisons phylogenomic studies. Our results reveal generally conserved mitogenome organization, one case tRNA gene rearrangement, trnI-trnQ reversed trnQ-trnI when compared ancestral arrangement. Analysis ratio nonsynonymous (Ka) synonymous substitutions (Ks) showed ATP8 fastest COI slowest evolving gene. ND2 ND6 highly variable nucleotide diversity, whereas ND1 exhibit lowest diversity. Phylogenetic analysis sequences grouped into a clade subfamily Iassinae. Within Batracomorphus, 3 clades were reconstructed consistent observed indicating that such rearrangements can serve as reliable molecular markers supporting hypotheses. These also correspond clusters recovered by morphometric aedeagal shape, suggesting characters male genitalia traditionally delimitation phylogenetically informative. Molecular divergence time estimates indicate speciation events occurred between Paleogene Neogene. This study provides insight population genetics, biology, phylogeny, morphological evolution leafhopper Iassinae its largest Batracomorphus.

Language: Английский

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