Gene duplication leads to paralogy, which complicates the de novo assembly of genotyping-by-sequencing (GBS) data. The issue of paralogous genes is exacerbated in plants, because they are particularly prone to gene duplication events. Paralogs are normally filtered from GBS data before undertaking population genomics or phylogenetic analyses. However, gene duplication plays an important role in the functional diversification of genes and it can also lead to the formation of postzygotic barriers. Using populations and closely related species of a tropical mountain shrub, we examine 1) the genomic differentiation produced by putative orthologs, and 2) the distribution of recent gene duplication among lineages and geography. We find high differentiation among populations from isolated mountain peaks and species-level differentiation within what is morphologically described as a single species. The inferred distribution of paralogs among populations is congruent with taxonomy and shows that GBS could be used to examine recent gene duplication as a source of genomic differentiation of nonmodel species.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224332 | PMC |
| http://dx.doi.org/10.1093/gbe/evu205 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Plant AT-rich protein and zinc-binding protein (PLATZ) family in Dendrobium huoshanense: identification, evolution and expression analysis.
BMC Plant Biol
December 2024
Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, College of Clinical Medicine of Henan, University of Science and Technology, Luoyang, 471003, China.
PLATZ (plant A/T-rich protein and zinc-binding protein) transcription factors are essential for plant growth, development, and responses to abiotic stress. The regulatory role of PLATZ genes in the environmental adaptation of D. huoshanense is inadequately comprehended.
View Article and Find Full Text PDFConvergent evolution of type I antifreeze proteins from four different progenitors in response to global cooling.
BMC Mol Cell Biol
December 2024
Department of Biomedical and Molecular Sciences, Queen's University, Botterell Hall, 18 Stuart Street, Kingston, K7L 3N6, Canada.
Alanine-rich, alpha-helical type I antifreeze proteins (AFPs) in fishes are thought to have arisen independently in the last 30 Ma on at least four occasions. This hypothesis has recently been proven for flounder and sculpin AFPs, which both originated by gene duplication and divergence followed by substantial gene copy number expansion. Here, we examined the origins of the cunner (wrasse) and snailfish (liparid) AFPs.
View Article and Find Full Text PDFGone with the Species: From Gene Loss to Gene Extinction.
Front Biosci (Schol Ed)
December 2024
Department of Biological Sciences, Virtual University of Pakistan, 55150 Lahore, Punjab, Pakistan.
Background: Vertebrae protein-coding genes exhibit remarkable diversity and are organized into many gene families. These gene families have emerged through various gene duplication events, the most prominent being the two rounds of whole-genome duplication (WGD). The current research project analyzed a unique class of genes called "singletons".
View Article and Find Full Text PDFIdentification and characterization of playing a positive role in the abiotic stress resistance of Chinese chestnut via an integrated strategy.
Front Plant Sci
December 2024
Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China.
Chinese chestnut ( Blume) is an important economic forest tree species and mainly cultivated in mountainous areas and wastelands, subjecting it to various abiotic stresses. The protein phosphatase 2C (PP2C) genes contributes largely to stress responses in plants. However, the characteristics and functions of genes in remain unknown.
View Article and Find Full Text PDFIdentification and analysis of major latex protein () family genes in responsive to infection by RNA-seq approaches.
Front Plant Sci
December 2024
College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou, China.
Roses () are among the most cherished ornamental plants globally, yet they are highly susceptible to infections by , the causative agent of gray mold disease. Here we inoculated the resistant rose variety 'Yellow Leisure Liness' with to investigate its resistance mechanisms against gray mold disease. Through transcriptome sequencing, we identified 578 differentially expressed genes (DEGs) that were significantly upregulated at 24, 48, and 72 hours post-inoculation, with these genes significantly enriched for three defense response-related GO terms.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!