Characterization of B-Genome Specific High Copy hAT MITE Families in Brassica nigra Genome.

Sampath Perumal,Stephen J Robinson,Sateesh Kagale,Lily Tang,Brian James,Isobel A P Parkin,Tae-Jin Yang

doi:10.3389/fpls.2020.01104

Abstract

Miniature inverted-repeat transposable elements (MITEs) are non-autonomous class II transposons which have been shown to influence genome evolution. Brassica nigra L. (B-genome) is one of three Brassica diploids cultivated primarily as an oil crop, which harbors novel alleles important for breeding. Two new high copy hAT MITE families (BniHAT-1 and BniHAT-2) from the B-genome were characterized and their prevalence assessed in the genomes of the related diploids, rapa L. (A) and Brassica oleracea L. (C). Both novel MITE families were present at high copy numbers in the B-genome with 434 and 331 copies of BniHAT-1 and BniHAT-2, respectively. Yet less than 20 elements were identified in the genome assemblies of the A, and C -genomes, supporting B-genome specific proliferation of these MITE families. Although apparently randomly distributed across the genome, 68 and 70% of the B-genome MITEs were present within 2 kb flanking regions of annotated genes suggesting they might influence gene expression and/or function. In addition, MITE derived microRNAs and transcription factor binding sites suggested a putative role in gene regulation. Age of insertion analysis revealed that the major proliferation of these elements occurred during 2–3 million years ago. Additionally, site-specific polymorphism analyses showed that 44% MITEs were undergoing active amplification into the B-genome. Overall, this study provides a comprehensive analysis of two high copy MITE families, which were specifically amplified in the B-genome, suggesting a potential role in shaping the Brassica B-genome.

Highlights

Transposable elements (TEs) constitute a major fraction of most eukaryotic genomes; for instance more than 85 and 71% of the Triticum aestivum and Aedes albopictus genome, respectively were occupied by TEs (Lee and Kim, 2014; Chen et al, 2015; Appels et al, 2018)
Mining of Miniature inverted-repeat transposable elements (MITEs) families using MITE Digger and MITE FinderII identified 170 candidate MITE families accounting for approximately 1.2% (6.3 mega bases (Mb)) of the Bgenome (Table S4)
Comparative analysis of the relative copy number of the 170 MITE families from the three Brassica diploid genomes (A, B, C-genomes) revealed two MITE elements with high copy numbers in the B-genome compared to the A and Cgenomes (Table 1)

Summary

Introduction

Transposable elements (TEs) constitute a major fraction of most eukaryotic genomes; for instance more than 85 and 71% of the Triticum aestivum and Aedes albopictus genome, respectively were occupied by TEs (Lee and Kim, 2014; Chen et al, 2015; Appels et al, 2018). Miniature inverted-repeat transposable elements (MITEs) are non-autonomous class II DNA transposons, usually small (< 1000 bp) in size, AT-rich, and ubiquitously present in almost all plant genomes (Pritham, 2009; Bennetzen and Wang, 2014; Sampath and Yang, 2014). Some MITE families, such as the stowaway MITE superfamily may have originated through cross mobilization facilitated by distantly related TEs such as Marinar like elements (Feschotte et al, 2005; Macko-Podgórni et al, 2019). Regardless of their size and origin and their requirement for transacting transposases, MITEs tend to be present in high copy numbers. Though studies have suggested that MITEs are formed through usurping the endogenous gap repair mechanism, it is still unclear how MITE copy numbers increase (Naito et al, 2009)

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Discussion

Conclusion