Reference Genome for the Highly Transformable Setaria viridis ME034V.

G3 : Genes - Genomes - Genetics
P. M. ThielenJennifer H. Wisecaver

Abstract

Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S. viridis accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited its utility. We present a 397 Mb highly contiguous de novo assembly of ME034V using ultra-long nanopore sequencing technology (read N50 = 41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for S. viridis Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis accessions. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in Setaria, i...Continue Reading

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Citations

Dec 22, 2020·Molecular Plant·Chu-Yu Ye, Longjiang Fan
Mar 5, 2021·Frontiers in Plant Science·Chuanmei ZhuElizabeth A Kellogg

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Datasets Mentioned

BETA
PRJNA560942
SRR1587768
CP050795

Methods Mentioned

BETA
genetic modification
transgenic
Illumina sequencing
RNA-Seq
PCR
gypsy
flow cytometry

Software Mentioned

MUMmer package
MAKER
hypergeom
Interproscan
Jellyfish
SAMtools
MuDR
PlantiSMASH
bedtools genomecov
xmatchview

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