Feb 7, 2014

Genome assembly and annotation for red clover (Trifolium pratense; Fabaceae)

American Journal of Botany
Jan IstvánekJana Řepková

Abstract

Red clover (Trifolium pratense) is an important forage plant from the legume family with great importance in agronomy and livestock nourishment. Nevertheless, assembling its medium-sized genome presents a challenge, given current hardware and software possibilities. Next-generation sequencing technologies enable us to generate large amounts of sequence data at low cost. In this study, the genome assembly and red clover genome features are presented. First, assembly software was assessed using data sets from a closely related species to find the best possible combination of assembler plus error correction program to assemble the red clover genome. The newly sequenced genome was characterized by repetitive content, number of protein-coding and nonprotein-coding genes, and gene families and functions. Genome features were also compared with those of other sequenced plant species. Abyss with Echo correction was used for de novo assembly of the red clover genome. The presented assembly comprises ∼314.6 Mbp. In contrast to leguminous species with comparable genome sizes, the genome of T. pratense contains a larger repetitive portion and more abundant retrotransposons and DNA transposons. Overall, 47 398 protein-coding genes were anno...Continue Reading

Mentioned in this Paper

Genes, Plant
Nodule
Genome
Genome Assembly Sequence
Retrotransposons
Genome Mapping
Genomics
Massively-Parallel Sequencing
Sequence Determinations, DNA
Trifolium pratense, flower essence

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