A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice

Abstract

Background Copy number variations (CNVs) are an important type of structural variations in the genome that usually affect gene expression levels by gene dosage effect. Understanding CNVs as part of genome evolution may provide insights into the genetic basis of important agricultural traits and contribute to the crop breeding in the future. While available methods to detect CNVs utilizing next-generation sequencing technology have helped shed light on prevalence and effects of CNVs, the complexity of crop genomes poses a major challenge and requires development of additional tools. Results Here, we generated genomic and transcriptomic data of 93 rice (Oryza sativa L.) accessions and developed a comprehensive pipeline to call CNVs in this large-scale dataset. We analyzed the correlation between CNVs and gene expression levels and found that approximately 13% of the identified genes showed a significant correlation between their expression levels and copy numbers. Further analysis showed that about 36% of duplicate pairs were involved in pseudogenetic events while only 5% of them showed functional differentiation. Moreover, the offspring copy mainly contributed to the expression levels and seemed more likely to become a pseudogene, whereas the parent copy tended to maintain the function of ancestral gene. Conclusion We provide a high-accuracy CNV dataset that will contribute to functional genomics studies and molecular breeding in rice. We also showed that gene dosage effect of CNVs in rice is not exponential or linear. Our work demonstrates that the evolution of duplicated genes is asymmetric in both expression levels and gene fates, shedding a new insight into the evolution of duplicated genes.

In-Depth Sequence Analysis of Bread Wheat VRN1 Genes

“…In plants, similar observations were recently made. In Oryza sativa, 4.5% of analyzed genes showed a negative correlation, 82.32% showed no significant correlations, and only 13.7% of genes showed a significant positive correlation with copy number [57].…”

Copy Number Variation among Resistance Genes Analogues in Brassica napus

“…Since CNVs are ubiquitous and encompass more nucleotides per genome than the total number of SNPs [ 21 , 30 ], more attention has recently been paid to their role. There are a growing number of investigations in plant species such as maize [ 31 , 32 , 33 ], Arabidopsis [ 28 , 34 , 35 ], rice [ 36 , 37 ], wheat [ 38 , 39 ], barley [ 40 , 41 , 42 ], banana [ 43 ], tomato [ 44 ], and soybean [ 45 , 46 ], suggesting that genes affected by CNVs are associated with agronomically important traits.…”

Identification of Genetic Loci for Sugarcane Leaf Angle at Different Developmental Stages by Genome-Wide Association Study

“…The raw reads filtered out those corresponding to adapter sequences, those with more than a 10% N content, and those <10 bases and selected those with more than a 50% quality value. All sequencing data were aligned to the Saccharum spontaneum reference genome (Zhang et al, 2018) by BWA software (fast and accurate short read alignment with the Burrows-Wheeler transform; Giannoulatou et al, 2014), and PCR duplicates reads were further removed by SAMtools (v1.3.167, the Sequence Alignment/Map format and SAMtools; Zhao et al, 2020). SNPs were identified among 216 samples by the HaplotypeCaller module of GATK (v3.868) in GVCF mode (The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data; Bernhardsson et al, 2020).…”