The 206 kbp mitochondrial genome of Phanerochaete carnosa reveals dynamics of introns, accumulation of repeat sequences and plasmid-derived genes

International Journal of Biological Macromolecules, Journal Year: 2020, Volume and Issue: 162, P. 209 - 219

Published: June 18, 2020

Language: Английский

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Codon Usage Bias Analysis of the WRKY Gene Family in Musa acuminata

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 10, 2025

Abstract Codon usage bias (CUB) is a universal phenomenon across all organisms and species, providing valuable insights into codon patterns to understand evolutionary mechanisms. The WRKY transcription factor family plays pivotal role in regulating plant responses various stresses at both physiological biochemical levels. Bananas ( Musa spp.), widely consumed as fruit or staple food, are an important horticulture crop the tropical subtropical regions around world. A total of 151 factors were identified genome acuminata banana cultivar ‘Guijiao 9’, which has been shown be resistant Tropical Race 4 Fusarium wilt banana. codons these factors, selected based on their expression from RNA-Seq data, analysed investigate genes . average GC content MaWRKY was 55.49%, with GC3 62.13%, indicating preference for G/C-ending codons. Among codons, 27 high frequency, 22 ending G C. effective number (ENC) values (34.53–60.79) low adaptation index (CAI) (0.143–0.3) suggested weak CUB that associated gene ENC-plot, PR2-plot, neutrality analysis revealed natural selection mutation pressure contributed observed CUB, being dominant influencing M. 9’. Fourteen optimal C, identified. This provides theoretical foundation further understanding mechanisms identifying key involved resistance biotic stress Analysing evolution can offer genetic growth development, supporting phenotypic hybrids breeding programs.

Language: Английский

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Codon usage bias and nucleotide bias are not influenced by the 5′ flanking but by 3′ and intronic region composition in SCID-associated genes

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: unknown, P. 142182 - 142182

Published: March 1, 2025

Language: Английский

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The mitochondrial genome of the mountain wooly tapir, Tapirus pinchaque and a formal test of the effect of altitude on the adaptive evolution of mitochondrial protein coding genes in odd-toed ungulates

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Sept. 6, 2023

The harsh conditions of high-altitude environments are known to drive the evolution physiological and morphological traits in endothermic animals. These expected result adaptive protein coding genes encoded mitochondrial genomes that vital for oxidative phosphorylation pathway. In this study, we formally tested signatures on Tapirus pinchaque other odd-toed ungulates inhabiting high-elevation environments.The AT-rich genome T. is 16,750 bp long. A phylomitogenomic analysis supports monophyly genus families Perissodactyla. ratio non-synonymous synonymous substitutions demonstrated all undergo purifying selection odd living at high elevations. Over negative background selection, Branch Models suggested cox3 nad6 might be undergoing stronger than genes. Furthermore, Site one four sites nad2 nad5, respectively, could experiencing positive selection. However, these results were supported by Likelihood Ratio Tests but not Bayesian Empirical Bayes posterior probabilities. Additional analyses (in DataMonkey) indicated a relaxation strength nad6, evidence episodic diversifying cob, revealed positive/diversifying two nad1, site each nad4.The an important genomic resource conservation species study contributes understanding environments.

Language: Английский

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Comparative analysis of codon usage of mitochondrial genomes provides evolutionary insights into reptiles

Gene, Journal Year: 2022, Volume and Issue: 851, P. 146999 - 146999

Published: Oct. 26, 2022

Current available information on reptile genomes provides great potential for the study of unique adaptations from a genomic perspective. We compared differences in base composition and codon usage patterns across 400 mitochondrial assessing AT GC skew, frequency, usage, effective number codons, adaptation index. identified poor content genomes, with predominant bias toward Adenine. determined compositional asymmetry between different taxonomic groups, which are inversely correlated to rates rearrangements mitogenome. found that most common codons mitochondrion CTA (L), ATA (M) ACA (T), relates have been birds, meaning these shared sauropsid mitogenomes. Codon clustering analyses revelated based RSCU as well mitogenomes translationally efficient under selection pressure. index revealed highest values turtles indicating higher translational efficiency genes among all reptiles, could be related metabolic (i.e., tolerance anoxic conditions). This was also seen other groups such crocodiles acclimation cold) snakes (phylogenetic origin toxin-secreting oral glands evolutionary redesign cytochrome c oxidase complex genes). discuss our findings context implications provide reptiles.

Language: Английский

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Cryopreservation effect on DNA methylation profile in rainbow trout spermatozoa

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Nov. 3, 2023

Spermatozoa are the cells that most commonly used for cryopreservation of valuable genetic resources in aquaculture. It is known fish spermatozoa transmit to embryo not only their but also epigenetic profile, especially DNA methylation. Therefore, any alteration methylation profile induces risk transmitting alterations offspring. The aim this study was assess effect on rainbow trout spermatozoa. To trigger variable cellular response after freezing-thawing, from mature males were cryopreserved with dimethyl sulfoxide, methanol or glycerol as cryoprotectant. We observed sulfoxide best preserve thawed functions. Methanol slightly preserved all parameters, while failed protect motility and fertilization ability. consequences assessed using Reduced Representation Bisulfite Sequencing (RRBS). Sperm did thoroughly impact methylation, although 335-564 differentially methylated cytosines characterized depending Very few them shared between cryoprotectants, no correlation extent damage found. Our showed altered sperm cryopreservation, may render further analysis progeny very challenging.

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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The systematic codon usage bias has an important effect on genetic adaption in native species

Gene, Journal Year: 2024, Volume and Issue: 926, P. 148627 - 148627

Published: May 31, 2024

Language: Английский

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Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae)

Virus Evolution, Journal Year: 2024, Volume and Issue: 10(1)

Published: Jan. 1, 2024

Abstract Trypanosomatids (Euglenozoa) are a diverse group of unicellular flagellates predominately infecting insects (monoxenous species) or circulating between and vertebrates plants (dixenous species). Monoxenous trypanosomatids harbor wide range RNA viruses belonging to the families Narnaviridae, Totiviridae, Qinviridae, Leishbuviridae, putative tombus-like viruses. Here, we focus on subfamily Blastocrithidiinae, previously unexplored divergent monoxenous comprising two related genera: Obscuromonas Blastocrithidia. Members genus Blastocrithidia employ unique genetic code, in which all three stop codons repurposed encode amino acids, with TAA also used terminate translation. isolates studied here bear families: Mitoviridae. The latter viral is documented trypanosomatid for first time. While other known mitoviruses replicate mitochondria, those appear reside cytoplasm. Although no were detected spp., identified an endogenous element genome B. triatomae indicating its past encounter(s)

Language: Английский

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A comparative analysis of GH18 chitinases and their isoforms from Beauveria bassiana: An in-silico approach

Process Biochemistry, Journal Year: 2020, Volume and Issue: 100, P. 207 - 216

Published: Oct. 21, 2020

Language: Английский

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