Abstract
BackgroundBoth selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species.ResultsWe identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves’ transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including “Terpenoid backbone biosynthesis”, “Valine, leucine and isoleucine biosynthesis”, “Butanoate metabolism”, “C5-Branched dibasic acid metabolism” “Pantothenate and CoA biosynthesis”. We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species.ConclusionSome important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.
Highlights
Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists
According to the age and outcomes of cytogenetics and karyotype, Whole genome duplication (WGD) events can be classified into two kinds, one is the recent or new polyploidization event, which results in “autopolyploids” and emerge from the fusion of gametes produced by non-meiosis, or hybridization of normal meiosis gametes of same species individuals, or “allopolyploids” produced from inter-specific hybridization [18]
Summary of protein coding unigenes From 45,535 assembled unigenes in rabbiteye blueberry (T1), 42,914 in southern highbush blueberry (T2) and 43,630 in northern highbush blueberry (T3) species, we identified 30,143, 29,922 and 28,891 protein coding unigenes according to the annotation of Nr, Swiss-Prot, GO and KEGG databases, and by using program ESTScan in three blueberry species, respectively (Table 1)
Summary
Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. About 47–70% of angiosperm species are estimated as polyploid and approximately 25% of vascular plants have undergone recent polyploidization [19, 20], and this WGD event could be detected by karyotyping and flow cytometry method [21]. Another is the ancient polyploidization event, which happened in earlier geological ages. In spite of subsequent diploidization (massive gene loss and structural rearrangements) or fractionation events occur and made the polyploidy return to a diploid state, the footprint of ancient WGD would still be detected in genome sequence in the form of blocks of duplicated genes [24, 25]
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