Back to Search
Start Over
Distribution, expression and methylation analysis of positively selected genes provides insights into the evolution in Brassica rapa
- Source :
- PLoS ONE, Vol 16, Iss 10, p e0256120 (2021), PLoS ONE
- Publication Year :
- 2021
- Publisher :
- Public Library of Science (PLoS), 2021.
-
Abstract
- It is believed that positive selection is one of the major evolutionary forces underlying organism phenotypic diversification. Nevertheless, the characteristics of positively selected genes (PSGs), have not been well investigated. In this study, we performed a genome-wide analysis of orthologous genes between Brassica rapa (B. rapa) and Brassica oleracea (B. oleracea), and identified 468 putative PSGs. Our data show that, (1) PSGs are enriched in plant hormone signal transduction pathway and the transcription factor family; (2) PSGs are significantly lower expressed than randomly selected non-PSGs; (3) PSGs with tissue specificity are significantly higher expressed in the callus and reproductive tissues (flower and silique) than in vegetable tissues (root, stem and leaf); (4) the proportion of PSGs is positively correlated with the number of retained triplication gene copies, but the expression level of PSGs decay with the increasing of triplication gene copies; (5) the CG and CHG methylation levels of PSGs are significantly higher in introns and UTRs than in the promoter and exon regions; (6) the percent of transposable element is in proportion to the methylation level, and DNA methylation (especially in the CG content) has the tendency to reduce the expression of PSGs. This study provides insights into the characteristics, evolution, function, expression and methylation of PSGs in B. rapa.
- Subjects :
- Evolutionary Genetics
Adaptation, Biological
Gene Expression
Plant Science
Biochemistry
Exon
Gene Expression Regulation, Plant
Gene expression
Genetics
Base Composition
DNA methylation
Multidisciplinary
Plant Anatomy
Brassica rapa
Eukaryota
Genomics
Methylation
Plants
Phenotype
Chromatin
Nucleic acids
Medicine
Epigenetics
DNA modification
Chromatin modification
Genome, Plant
Research Article
Chromosome biology
Signal Transduction
Transposable element
Cell biology
Science
Flowers
Brassica
Biology
Genome Complexity
Evolution, Molecular
Selection, Genetic
Gene
Evolutionary Biology
Biology and life sciences
Organisms
Computational Biology
DNA
Genome Analysis
Genome Annotation
Introns
DNA Transposable Elements
Sequence Alignment
Subjects
Details
- ISSN :
- 19326203
- Volume :
- 16
- Database :
- OpenAIRE
- Journal :
- PLOS ONE
- Accession number :
- edsair.doi.dedup.....44db3d1335ed895e69d4d25151205cfc