Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset

Abstract

Background: 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. 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. Results: We 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. Conclusion: Some 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.

Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum

“…Our analysis agreed with results from a comparative genomics study in Rhododendron williamsianum and related species in the Ericaceae family that found two shared WGDs (the γ-triplication and Ac-β events) among cranberry (the Vm-α event found here), Camellia sinensis , and Rhododendron ( Soza et al, 2019 ). In relation to the evolutionary history of Vaccinium species, our molecular dating-based estimation for the divergence of cranberry- V. microcarpum ancestor and blueberry (10.4 Mya) agreed with a recent study ( Wang et al, 2020 ) dating the most recent polyploidization event in tetraploid blueberry (approximately 9 Mya) little after divergence.…”

Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism

“…3 B ). Thus, 39.0% of the genes in the P. veris genome are present in two or more copies, similarly to other Ericales known to have experienced both the Ad -β and more recent WGDs ( Larson et al 2020 ; Wang et al 2020 ; supplementary fig. S16 , Supplementary Material online ).…”

Comprehensive Analysis of the SBP Family in Blueberry and Their Regulatory Mechanism Controlling Chlorophyll Accumulation

“…Noticeably, the VcSBP genes in the same group in the phylogenetic tree showed relatively low identity (8–48%) except the two segmental duplication pairs ( VcSPB7a and VcSBP7b , VcSBP14b , and VcSBP14c , Figures 1C , 2A ), suggesting that most VcSBP s might be single-copy genes with functional specificity. However, it was estimated that at least three rounds of whole-genome duplication occurred during the evolution of blueberry species ( Wang et al, 2020 ), which are supposed to facilitate the generation of multiple copy genes. It can be explained by at least two reasons: (1) it is still possible that the number of VcSBP genes might have been underestimated since the identification of SBP genes was conducted on the basis of available transcriptome data; (2) VcSBP s might belong to the duplication-resistant genes, which generally return to single-copy status through the duplication-resistant system or genetic drift after suffering duplication events ( Wang et al, 2020 ).…”