Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome

BMC Plant Biology
Yohannes Gedamu GebreAndrea Zuccolo

Abstract

Eragrostis tef is an allotetraploid (2n = 4 × = 40) annual, C4 grass with an estimated nuclear genome size of 730 Mbp. It is widely grown in Ethiopia, where it provides basic nutrition for more than half of the population. Although a draft assembly of the E. tef genome was made available in 2014, characterization of the repetitive portion of the E. tef genome has not been a subject of a detailed analysis. Repetitive sequences constitute most of the DNA in eukaryotic genomes. Transposable elements are usually the most abundant repetitive component in plant genomes. They contribute to genome size variation, cause mutations, can result in chromosomal rearrangements, and influence gene regulation. An extensive and in depth characterization of the repetitive component is essential in understanding the evolution and function of the genome. Using new paired-end sequence data and a de novo repeat identification strategy, we identified the most repetitive elements in the E. tef genome. Putative repeat sequences were annotated based on similarity to known repeat groups in other grasses. Altogether we identified 1,389 medium/highly repetitive sequences that collectively represent about 27 % of the teff genome. Phylogenetic analyses of the...Continue Reading

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Citations

Mar 1, 2017·The Plant Journal : for Cell and Molecular Biology·Rimjhim Roy ChoudhuryChristian Parisod
Oct 26, 2016·Molecular Genetics and Genomics : MGG·Aung Kyaw LwinAndrea Zuccolo
Apr 16, 2018·Journal of Plant Physiology·Federico MartinelliZerihun Tadele
Dec 9, 2020·Plant Science : an International Journal of Experimental Plant Biology·Delphine GiraudArmel Salmon
Oct 9, 2021·Frontiers in Genetics·María Laura GonzálezJuan Domingo Urdampilleta

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Datasets Mentioned

BETA
SRR1463355
PRJNA294641

Methods Mentioned

BETA
gypsy
whole genome shotgun
electrophoresis
PCR
chip

Software Mentioned

Blast
Atlantys
EMBOSS
RepArk
RepeatScout
hit
MiSeq
TblastN
distmat
CAP3

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