New Zealand Tree and Giant Wētā (Orthoptera) Transcriptomics Reveal Divergent Selection Patterns in Metabolic Loci
(2019) In Genome Biology and Evolution 11(4). p.1293-1306- Abstract
Exposure to low temperatures requires an organism to overcome physiological challenges. New Zealand wētā belonging to the genera Hemideina and Deinacrida are found across a wide range of thermal environments and therefore subject to varying selective pressures. Here we assess the selection pressures across the wētā phylogeny, with a particular emphasis on identifying genes under positive or diversifying selection. We used RNA-seq to generate transcriptomes for all 18 Deinacrida and Hemideina species. A total of 755 orthologous genes were identified using a bidirectional best-hit approach, with the resulting gene set encompassing a diverse range of functional classes. Analysis of ortholog ratios of synonymous to nonsynonymous amino acid... (More)
Exposure to low temperatures requires an organism to overcome physiological challenges. New Zealand wētā belonging to the genera Hemideina and Deinacrida are found across a wide range of thermal environments and therefore subject to varying selective pressures. Here we assess the selection pressures across the wētā phylogeny, with a particular emphasis on identifying genes under positive or diversifying selection. We used RNA-seq to generate transcriptomes for all 18 Deinacrida and Hemideina species. A total of 755 orthologous genes were identified using a bidirectional best-hit approach, with the resulting gene set encompassing a diverse range of functional classes. Analysis of ortholog ratios of synonymous to nonsynonymous amino acid changes found 83 genes that are under positive selection for at least one codon. A wide variety of Gene Ontology terms, enzymes, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways are represented among these genes. In particular, enzymes involved in oxidative phosphorylation, melanin synthesis, and free-radical scavenging are represented, consistent with physiological and metabolic changes that are associated with adaptation to alpine environments. Structural alignment of the transcripts with the most codons under positive selection revealed that the majority of sites are surface residues, and therefore have the potential to influence the thermostability of the enzyme, with the exception of prophenoloxidase where two residues near the active site are under selection. These proteins provide interesting candidates for further analysis of protein evolution.
(Less)
- author
- Twort, Victoria G. LU ; Newcomb, Richard D. and Buckley, Thomas R.
- organization
- publishing date
- 2019
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- diversifying selection, metabolic rate, molecular evolution, transcriptome
- in
- Genome Biology and Evolution
- volume
- 11
- issue
- 4
- pages
- 14 pages
- publisher
- Oxford University Press
- external identifiers
-
- scopus:85065345504
- pmid:30957857
- ISSN
- 1759-6653
- DOI
- 10.1093/gbe/evz070
- language
- English
- LU publication?
- yes
- id
- 9585b779-0f60-4a1b-8cdf-f97a8b6583fe
- date added to LUP
- 2019-05-21 15:01:34
- date last changed
- 2024-04-16 06:50:00
@article{9585b779-0f60-4a1b-8cdf-f97a8b6583fe,
abstract = {{<p>Exposure to low temperatures requires an organism to overcome physiological challenges. New Zealand wētā belonging to the genera Hemideina and Deinacrida are found across a wide range of thermal environments and therefore subject to varying selective pressures. Here we assess the selection pressures across the wētā phylogeny, with a particular emphasis on identifying genes under positive or diversifying selection. We used RNA-seq to generate transcriptomes for all 18 Deinacrida and Hemideina species. A total of 755 orthologous genes were identified using a bidirectional best-hit approach, with the resulting gene set encompassing a diverse range of functional classes. Analysis of ortholog ratios of synonymous to nonsynonymous amino acid changes found 83 genes that are under positive selection for at least one codon. A wide variety of Gene Ontology terms, enzymes, and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways are represented among these genes. In particular, enzymes involved in oxidative phosphorylation, melanin synthesis, and free-radical scavenging are represented, consistent with physiological and metabolic changes that are associated with adaptation to alpine environments. Structural alignment of the transcripts with the most codons under positive selection revealed that the majority of sites are surface residues, and therefore have the potential to influence the thermostability of the enzyme, with the exception of prophenoloxidase where two residues near the active site are under selection. These proteins provide interesting candidates for further analysis of protein evolution.</p>}},
author = {{Twort, Victoria G. and Newcomb, Richard D. and Buckley, Thomas R.}},
issn = {{1759-6653}},
keywords = {{diversifying selection; metabolic rate; molecular evolution; transcriptome}},
language = {{eng}},
number = {{4}},
pages = {{1293--1306}},
publisher = {{Oxford University Press}},
series = {{Genome Biology and Evolution}},
title = {{New Zealand Tree and Giant Wētā (Orthoptera) Transcriptomics Reveal Divergent Selection Patterns in Metabolic Loci}},
url = {{http://dx.doi.org/10.1093/gbe/evz070}},
doi = {{10.1093/gbe/evz070}},
volume = {{11}},
year = {{2019}},
}