PlantTribes2: tools for comparative gene family analysis in plant genomics DOI Open Access
Eric Wafula, Huiting Zhang,

Gregory Von Kuster

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Nov. 18, 2022

Abstract 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

oskaracts with the transcription factor Creb to regulate long-term memory in crickets DOI Creative Commons
Arpita Kulkarni, Ben Ewen‐Campen, Kanta Terao

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Oct. 25, 2022

Abstract Novel genes have the potential to drive evolution of new biological mechanisms, or integrate into pre-existing regulatory circuits and contribute regulation older, conserved functions. One such gene, novel insect-specific gene oskar , was first identified based on its role in establishing Drosophila melanogaster germ line. We previously showed that this likely arose through an unusual domain transfer event involving bacterial endosymbionts, played a somatic before evolving well-known line function. Here, we provide empirical support for hypothesis form evidence neural . show is expressed adult stem cells hemimetabolous insect, cricket Gryllus bimaculatus In these cells, called neuroblasts, required together with ancient animal transcription factor Creb regulate long-term (but not short-term) olfactory memory. positively regulates which plays memory across animals, turn may be direct target Creb. Together previous reports nervous system development function crickets flies, our results are consistent ’s original been insect system. Moreover, co-localization functional cooperation pluripotency piwi facilitated later co-option holometabolous insects.

Language: Английский

Citations

0
PlantTribes2: tools for comparative gene family analysis in plant genomics DOI Open Access
Eric Wafula, Huiting Zhang,

Gregory Von Kuster

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Nov. 18, 2022

Abstract 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

Citations

0