A Global Landscape of Miniature Inverted-Repeat Transposable Elements in the Carrot Genome

Abstract

Miniature inverted-repeat transposable elements (MITEs) are the most abundant group of Class II mobile elements in plant genomes. Their presence in genic regions may alter gene structure and expression, providing a new source of functional diversity. Owing to their small size and lack of coding capacity, the identification of MITEs has been demanding. However, the increasing availability of reference genomes and bioinformatic tools provides better means for the genome-wide identification and analysis of MITEs and for the elucidation of their contribution to the evolution of plant genomes. We mined MITEs in the carrot reference genome DH1 using MITE-hunter and developed a curated carrot MITE repository comprising 428 families. Of the 31,025 MITE copies spanning 10.34 Mbp of the carrot genome, 54% were positioned in genic regions. Stowaways and Tourists were frequently present in the vicinity of genes, while Mutator-like MITEs were relatively more enriched in introns. hAT-like MITEs were relatively more frequently associated with transcribed regions, including untranslated regions (UTRs). Some carrot MITE families were shared with other Apiaceae species. We showed that hAT-like MITEs were involved in the formation of new splice variants of insertion-harboring genes. Thus, carrot MITEs contributed to the accretion of new diversity by altering transcripts and possibly affecting the regulation of many genes.

Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots

“…De novo identification of carrot repetitive DNA was carried out with RepeatModeler (v.2.0.1) ( http://www.repeatmasker.org/RepeatModeler/ ). The annotation of the consensus sequences was performed using a curated database of carrot LTR retrotransposons, Helitrons and MITE 61 , carrot satellite repeats 15 and dicot plant repeats from RepBase (v.23.05) 62 and DANTE (v.1.1.0) 63 – 65 . Masking was performed using RepeatMasker (v.4.1.0; http://www.repeatmasker.org ) (see the Supplementary Note for the parameter and filtering settings).…”

Genome-wide characterization of Mariner-like transposons and their derived MITEs in the Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae)

“…In order to compare the genes and transcripts with the reference annotation and reports statistics, we conducted an optional step using gffcompare ( http://ccb.jhu.edu/software/stringtie/gff.shtml or http://github.com/gpertea/gffcompare ). Finally, StringTie estimate transcript abundances and create table counts for Ballgown, which is an R package, used to calculate the normalized FPKM (fragments per kilobase of exon per million reads mapped) values and genes with FPKM > 1 ( Macko-Podgórni et al 2021 ).…”

Detection of Transposon Gene in Lurik Peanuts (Arachis hypogaea var. lurik L.) with AhMITEs Analysis

“…Miniature Inverted-Repeat Transposable Elements (MITEs) are a group of non-autonomous, widely distributed Class II transposons with high abundance in the plant genome [15]. The MITEs group comprised short DNA fragments (125 -500 bp) with terminal inverted repeats (TIR; 10-15 bp), high AT content, and high copy number.…”