Abstract
Brassica oleracea comprises various economically important vegetables and presents extremely diverse morphological variations. They provide a rich source of nutrition for human health and have been used as a model system for studying polyploidization. Transposable elements (TEs) account for nearly 40% of the B. oleracea genome and contribute greatly to genetic diversity and genome evolution. Although the proliferation of TEs has led to a large expansion of the B. oleracea genome, little is known about the population dynamics and evolutionary activity of TEs. A comprehensive mobilome profile of 45,737 TE loci was obtained from resequencing data from 121 diverse accessions across nine B. oleracea morphotypes. Approximately 70% (32,195) of the loci showed insertion polymorphisms between or within morphotypes. In particular, up to 1221 loci were differentially fixed among morphotypes. Further analysis revealed that the distribution of the population frequency of TE loci was highly variable across different TE superfamilies and families, implying a diverse expansion history during host genome evolution. These findings provide better insight into the evolutionary dynamics and genetic diversity of B. oleracea genomes and will potentially serve as a valuable resource for molecular markers and association studies between TE-based genomic variations and morphotype-specific phenotypic differentiation.
Highlights
Brassica oleracea (2n = 18, CC) is one of the most diverse species within Brassiceae, which encompasses a wide range of economically important vegetables such as cabbage, kohlrabi, cauliflower, and broccoli[1]
The next-generation sequencing (NGS) reads of each accession were compared against the flanking sequence library to detect chimeric reads spanning breakpoints; the unmatched portions of these reads were aligned to the corresponding Transposable elements (TEs) to determine the presence or absence of TE insertions in individual accessions (Supplementary Fig. S1 and “Methods” section)
A comprehensive mobilome profile for B. oleracea TEs account for a large proportion of the B. oleracea genome; most of the work on this topic has focused on single families or a few families[32,33,34,35] or has been conducted only within reference genomes[8,10,11]
Summary
Brassica oleracea (2n = 18, CC) is one of the most diverse species within Brassiceae, which encompasses a wide range of economically important vegetables such as cabbage, kohlrabi, cauliflower, and broccoli[1]. In addition to its phenotypic diversity and important nutritional value, B. oleracea is a model species for studying the evolution of polyploidy because it has experienced multiple rounds of whole-genome duplication (WGD) events[3,4] and one whole-genome. 40% of the genome is estimated to consist of TEs in B. oleracea[8,9]. TEs are a powerful driver of genome evolution in Brassica[10,11,12,13]. The comparison of nucleotide substitution rates demonstrated the evolutionary asymmetry of the B. oleracea and B. rapa genomes and indicated that TEs are likely be responsible for this progress[10]. Recent studies have revealed that the biased distribution of TEs among the three
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