Rapid Targeted Assembly of the Proteome Reveals Evolutionary Variation of GC Content in Avian Lice DOI Creative Commons

Avery R. Grant,

Kevin P. Johnson, Edward L. Stanley

et al.

Bioinformatics and Biology Insights, Journal Year: 2024, Volume and Issue: 18

Published: Jan. 1, 2024

Nucleotide base composition plays an influential role in the molecular mechanisms involved gene function, phenotype, and amino acid composition. GC content (proportion of guanine cytosine DNA sequences) shows a high level variation within among species. Many studies measure small number genes, which may not be representative genome-wide variation. One challenge when assembling extensive genomic data sets for these is significant amount resources (monetary computational) associated with processing, many bioinformatic tools have been optimized resource efficiency. Using high-performance computing (HPC) cluster, we manipulated provided to targeted assembly program, automated target restricted method (aTRAM), determine optimum way run program maximize use. our approach, assembled measured all protein-coding genes diverse group parasitic feather lice. Of 499 426 across 57 species, lice were GC-poor (mean = 42.96%) between species (GC range 19.57%-73.33%). We found correlation standard deviation per taxon overall

Language: Английский

Heterochromatin Is Not the Only Place for satDNAs: The High Diversity of satDNAs in the Euchromatin of the Beetle Chrysolina americana (Coleoptera, Chrysomelidae) DOI Open Access
José M. Rico‐Porras, Pablo Mora, Teresa Palomeque

et al.

Genes, Journal Year: 2024, Volume and Issue: 15(4), P. 395 - 395

Published: March 22, 2024

The satellitome of the beetle Chrysolina americana Linneo, 1758 has been characterized through chromosomal analysis, genomic sequencing, and bioinformatics tools. C-banding reveals presence constitutive heterochromatin blocks enriched in A+T content, primarily located pericentromeric regions. Furthermore, a comprehensive analysis unveils extensive diversity satellite DNA families within genome C. americana. Using fluorescence situ hybridization techniques innovative CHRISMAPP approach, we precisely map localization satDNA on assembled chromosomes, providing insights into their organization distribution patterns. Among 165 identified families, only three them exhibit remarkable amplification accumulation, forming large predominantly In contrast, remaining, less abundant are dispersed throughout euchromatic regions, challenging traditional association with heterochromatin. Overall, our findings underscore complexity repetitive elements emphasize need for further exploration to elucidate functional significance evolutionary implications.

Language: Английский

Citations

12
A phylogenetic approach to comparative genomics DOI
Anna E. Dewar, Laurence J. Belcher, Stuart A. West

et al.

Nature Reviews Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Language: Английский

Citations

1
Do the “big four” orders of insects comprise evolutionarily significant higher taxa with coherent patterns of selection on protein-coding genes? DOI Creative Commons

Pierre J Février,

Timothy G. Barraclough

Evolution Letters, Journal Year: 2025, Volume and Issue: unknown

Published: March 6, 2025

Abstract Species are often treated as evolutionarily significant units of diversity that reflect patterns gene flow and selection. In contrast, higher taxa mostly regarded convenient labels for levels in the tree life, which evolutionary history if defined cladistically but assumed to have no real significance ongoing evolution. We test alternative hypothesis some with coherent selection on their constituent species. Specifically, we ask whether big 4 orders holometabolous insects, namely Coleoptera, Diptera, Hymenoptera, Lepidoptera, display divergent, internally conserved acting protein-coding genes. Analyzing orthologous genes from whole genome sequence data multiple species per order, find that, most genes, roughly one fifth codons is within each order differs significantly among orders. The shift associated variation GC content orders, primarily at codon 2nd positions hence due rather than mutational or repair bias. Comparison models assigning different taxonomic (either more lumped divided orders) shows best always specify Hymenoptera Lepidoptera units, whereas Coleoptera especially Diptera better explained by subdividing them further. hypothesise aspect general lifestyle, body plan genetic makeup (or nested clades Diptera) leads across them, constraints differ them. emergence whole-genome broad deep phylogenetic samples will allow this versus evenly dispersed shifts be tested

Language: Английский

Citations

0
Satellitome Analysis of Adalia bipunctata (Coleoptera): Revealing Centromeric Turnover and Potential Chromosome Rearrangements in a Comparative Interspecific Study DOI Open Access
Pablo Mora, José M. Rico‐Porras, Teresa Palomeque

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(17), P. 9214 - 9214

Published: Aug. 25, 2024

Eukaryotic genomes exhibit a dynamic interplay between single-copy sequences and repetitive DNA elements, with satellite (satDNA) representing substantial portion, mainly situated at telomeric centromeric chromosomal regions. We utilized Illumina next-generation sequencing data from

Language: Английский

Citations

1
Whole mitochondrial genome analysis of Aedes aegypti reveal association with Wolbachia infection DOI Creative Commons
Bhavna Gupta,

Melveettil Kishor Sumitha,

G Navaneetha Pandiyan

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 7, 2024

Abstract The mitochondrial genomes (mitogenomes) of nine Aedes aegypti samples from India were analysed along with 34 mitogenomes global retrieved GenBank. mitogenome size Indian ranged 15,730 bp to 16,374 bp. A total 199 genetic variants identified among samples, the majority (90%) occurring in protein-coding genes, followed by rRNA and tRNA genes. Phylogenetic analysis 43 revealed two major clades. similar clustering pattern was observed traditional markers for which extensive data is available, indicating that individual Ae. share common genealogy as reflected complete mitogenome. In addition exploring diversity, we investigated relationship these clades Wolbachia infection. Our -infected predominantly located within one clades, suggesting a potential association between specific lineage This demonstrates extent diversity highlights how this associated infection, maternally inherited endosymbiont. These findings have implications effectiveness -based mosquito control strategies.

Language: Английский

Citations

1
Rapid Targeted Assembly of the Proteome Reveals Evolutionary Variation of GC Content in Avian Lice DOI Creative Commons

Avery R. Grant,

Kevin P. Johnson, Edward L. Stanley

et al.

Bioinformatics and Biology Insights, Journal Year: 2024, Volume and Issue: 18

Published: Jan. 1, 2024

Nucleotide base composition plays an influential role in the molecular mechanisms involved gene function, phenotype, and amino acid composition. GC content (proportion of guanine cytosine DNA sequences) shows a high level variation within among species. Many studies measure small number genes, which may not be representative genome-wide variation. One challenge when assembling extensive genomic data sets for these is significant amount resources (monetary computational) associated with processing, many bioinformatic tools have been optimized resource efficiency. Using high-performance computing (HPC) cluster, we manipulated provided to targeted assembly program, automated target restricted method (aTRAM), determine optimum way run program maximize use. our approach, assembled measured all protein-coding genes diverse group parasitic feather lice. Of 499 426 across 57 species, lice were GC-poor (mean = 42.96%) between species (GC range 19.57%-73.33%). We found correlation standard deviation per taxon overall

Language: Английский

Citations

0