Dynamics of sex-biased gene expression during development in the stick insect Timema californicum

Heredity, Journal Year: 2022, Volume and Issue: 129(2), P. 113 - 122

Published: May 17, 2022

Sexually dimorphic phenotypes are thought to arise primarily from sex-biased gene expression during development. Major changes in developmental strategies, such as the shift hemimetabolous holometabolous development, therefore expected have profound consequences for dynamics of expression. However, no studies previously examined development insects, precluding comparisons between strategies. Here we characterized at three stages a stick insect (Timema californicum): hatchlings, juveniles, and adults. As expected, proportion genes gradually increased mirroring gradual increase phenotypic sexual dimorphism. Sex-biased identified early were generally consistently male- or female-biased later stages, suggesting their importance differentiation. Additionally, compared T. californicum those fly Drosophila melanogaster by reanalyzing publicly available RNA-seq data third instar larval, pupal adult stages. In D. melanogaster, 84% stage (compared only 20% californicum), abruptly when morphological dimorphism is manifested. Our findings consistent with prediction that differ extensively species.

Language: Английский

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PlantTribes2: Tools for comparative gene family analysis in plant genomics

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 31, 2023

Plant genome-scale resources are being generated at an increasing rate as sequencing technologies continue to improve and raw data costs fall; however, the cost of downstream analyses remains large. This has resulted in a considerable range genome assembly annotation qualities across plant genomes due their varying sizes, complexity, technology used for annotation. To effectively work genomes, researchers increasingly rely on comparative genomic approaches that integrate community types. Such efforts have aided process yielded novel insights into evolutionary history gene families, including complex non-model organisms. The essential tools achieve these family analysis genome-scale, but they not well integrated rapid new data, learning curve can be steep. Here we present PlantTribes2, scalable, easily accessible, highly customizable, broadly applicable framework with multiple entry points user provided data. It uses objective classifications annotated protein sequences from existing, high-quality studies. PlantTribes2 transcript models then sort them, either annotations or individual coding sequences, pre-computed orthologous clusters rich functional information. Then, families interest, performs customizable visualizations including, (1) sequence alignment, (2) phylogeny, (3) estimation synonymous non-synonymous substitution rates among homologous (4) inference large-scale duplication events. We give examples applications studies economically important namely transcriptomics weedy Orobanchaceae core orthogroup (CROG) Rosaceae. is freely available use within main public Galaxy instance downloaded GitHub Bioconda. Importantly, readily adapted transcriptomic any kind organism.

Language: Английский

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Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant

eLife, Journal Year: 2024, Volume and Issue: 12

Published: Feb. 14, 2024

Sex-biased genes offer insights into the evolution of sexual dimorphism. genes, especially those with male bias, show elevated evolutionary rates protein sequences driven by positive selection and relaxed purifying in animals. Although rapid sequence sex-biased forces have been investigated animals brown algae, less is known about dioecious angiosperms. In this study, we separately compared expression between female floral buds flowers at anthesis Trichosanthes pilosa (Cucurbitaceae). buds, gene was pervasive, had significantly different roles dimorphism such as physiology. We observed higher for male-biased to female-biased unbiased genes. Male-biased under were mainly associated functions abiotic stress immune responses, suggesting that high are adaptive evolution. Additionally, may contribute accelerated generated duplication. Our findings, first time angiosperms, suggest evident advance our understanding patterns driving plants.

Language: Английский

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Dissecting cricket genomes for the advancement of entomology and entomophagy

Biophysical Reviews, Journal Year: 2022, Volume and Issue: 14(1), P. 75 - 97

Published: Jan. 21, 2022

Significant advances in biophysical methods such as next-generation sequencing technologies have now opened the way to conduct evolutionary and applied research based on genomic information of greatly diverse insects. Crickets belonging Orthoptera (Insecta: Polyneoptera), one most flourishing groups insects, contributed development multiple scientific fields including developmental biology neuroscience been attractive targets ecology for their ecological niches. In addition, crickets recently gained recognition food feed. However, underlying biological basis application toward breeding is currently underrepresented. this review, we summarize progress genomics crickets. First, outline phylogenetic position insects then introduce recent studies cricket transcriptomics a variety fields. Furthermore, present findings from our analysis polyneopteran genomes, with particular focus large genome sizes, chromosome number, repetitive sequences. Finally, how can be beneficial industry discussed. This review expected enhance greater important genomes are basic contribute tackling global security.The online version contains supplementary material available at 10.1007/s12551-021-00924-4.

Language: Английский

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Genomics and genome editing techniques of crickets, an emerging model insect for biology and food science

Current Opinion in Insect Science, Journal Year: 2022, Volume and Issue: 50, P. 100881 - 100881

Published: Feb. 2, 2022

Language: Английский

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oskaracts with the transcription factor Creb to regulate long-term memory in crickets

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(21)

Published: May 16, 2023

Novel genes have the potential to drive evolution of new biological mechanisms, or integrate into preexisting regulatory circuits and contribute regulation older, conserved functions. One such gene, novel insect-specific gene

Language: Английский

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Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster

G3 Genes Genomes Genetics, Journal Year: 2023, Volume and Issue: 13(8)

Published: June 1, 2023

The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed so far used whole-body data and only single crosses, which may have limited their scope detect patterns that are robust across tissues biological replicates. Here, we use allele-specific parental reciprocal hybrid crosses 6 Drosophila melanogaster inbred lines quantify cis- trans-regulatory variation heads gonads both separately 3 replicate crosses. Our results suggest female male heads, as well ovaries, a similar architecture. On the other hand, testes display more different cis-regulatory effects, suggesting sex differences been previously observed largely derive from testis-specific effects. We also examine difference genes levels bias heads. Consistent with idea intersex correlations constrain can lead sexual antagonism, find cis unbiased moderately biased In reduced for male-biased genes, variants acting on these males do not changes ovary expression. Finally, dominance sex- tissue-specific inheritance highly variable although were controlled experimental conditions. This highlights importance using various genetic backgrounds infer generalizable patterns.

Language: Английский

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Transcriptome analysis of sex-biased gene expression in the spotted-wing Drosophila, Drosophila suzukii (Matsumura)

G3 Genes Genomes Genetics, Journal Year: 2022, Volume and Issue: 12(8)

Published: May 19, 2022

Abstract Sexual dimorphism occurs widely throughout insects and has profound influences on evolutionary path. Sex-biased genes are considered to account for most of phenotypic differences between sexes. In order explore the sex-biased potentially associated with sexual development in Drosophila suzukii, a major devastating invasive crop pest, we conducted whole-organism transcriptome profiling gene expression analysis adults both We identified transcripts involved several sex-specific physiological functional processes, including sex determination, reproduction, olfaction, innate immune signals. A total 11,360 differentially expressed were comparison, 1,957 female-biased 4,231 male-biased. The pathway predominantly enriched was related spliceosome, which might reflect alternative splicing mechanism males females. Twenty-two determination 16 sex-related reproduction identified, pattern revealed that majority Additionally, olfactory processes analyzed these may play important roles pheromone odor detection, response. As valuable dataset, our transcriptomic data can significantly contribute fundamental elucidation molecular mechanisms fruit flies, provide candidate useful genetic sexing strains, an tool sterile insect technique applications against this economically species.

Language: Английский

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Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes

BMC Genomics, Journal Year: 2021, Volume and Issue: 22(1)

Published: April 6, 2021

Abstract Background For multicellular organisms, much remains unknown about the dynamics of synonymous codon and amino acid use in highly expressed genes, including whether their varies with expression different tissue types sexes. Moreover, specific codons acids may have translational functions transcribed that largely depend on relationships to tRNA gene copies genome. However, these putative are poorly understood, particularly systems. Results Here, we studied genes from reproductive nervous system tissues (male female gonad, somatic system, brain ventral nerve cord, male accessory glands) cricket Gryllus bimaculatus . We report an optimal codon, defined as preferentially used for each 18 this organism. The were mostly shared among both frequency was highest gonadal genes. Concordant selection, a majority had abundant matching genome, but sometimes obligately required wobble tRNAs. suggest latter comprise mechanism slowing translation transcripts, cell-cycle Non-optimal codons, those least commonly intriguingly often tRNAs, elevated subset specialized (gametic apoptosis genes), suggesting promotes upregulation particular mRNAs. In terms acids, found evidence frequency, copy number, biosynthetic costs (size/complexity) all interdependently evolved insect model, potentially optimization. Conclusions Collectively, results model whereby optimal, wobble, non-optimal abundances, well use, been influenced by adaptation various functional roles within cricket. effects two sexes discussed.

Language: Английский

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Gene Protein Sequence Evolution Can Predict the Rapid Divergence of Ovariole Numbers in the Drosophila melanogaster Subgroup

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(7)

Published: June 7, 2024

Ovaries play key roles in fitness and evolution: they are essential female reproductive structures that develop house the eggs sexually reproducing animals. In Drosophila, mature ovary contains multiple tubular egg-producing known as ovarioles. Ovarioles arise from somatic cellular larval called terminal filaments (TFs), formed by TF cells subsequently enclosed sheath (SH) cells. As many other insects, ovariole number per varies extensively Drosophila. At present, however, there is a striking gap of information on genetic mechanisms evolutionary forces shape well-documented rapid interspecies divergence numbers. To address this gap, here we studied genes associated with Drosophila melanogaster or functions based recent experimental transcriptional datasets ovaries, including TFs SH cells, assessed their rates patterns molecular evolution five closely related species subgroup exhibit species-specific differences From comprehensive analyses protein sequence (dN/dS), branch-site positive selection, expression specificity (tau), phylogenetic regressions (phylogenetic generalized least squares), report evidence 42 showed signs playing basis change number. These included signaling upd2 Ilp5 extracellular matrix vkg Col4a1, whose dN/dS predicted numbers among species. Together, propose model whereby set ovariole-involved gene proteins have an enhanced evolvability, adaptive evolution, facilitating shifts

Language: Английский

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