Development of a goosegrass (Eleusine indica) draft genome and application to weed science research

Abstract

BACKGROUND Genomes are vital to the study of genomics, population genetics, and evolution of species. To date, only one genome (Echinochloa crus‐galli) for C4 annual weedy grass species has been sequenced. Research was conducted to develop a draft genome of goosegrass (Eleusine indica; 2n = 2x = 18), one of the most common and troublesome weeds in the world. RESULTS A draft assembly of an approximately 492 Mb whole‐genome sequence of goosegrass was obtained by de novo assembly of paired‐end and mate‐paired reads generated by Illumina sequencing of total genomic DNA. The genome was assembled into 24,072 scaffolds with N50 = 233,459 bp. More than 99% of transcriptome sequences were mapped to the goosegrass draft genome, and 95% of the commonly conserved plant genes were present. The assembled genome contains 25,467 unique protein‐coding genes. Genes associated with herbicide resistance were obtained and variant calling allowed the detection of 754,409 single nucleotide polymorphisms. In addition, we also report 115,417 simple sequence repeats which can be deployed in population genetics and phylogenetic analysis. CONCLUSION This is the first report of genome sequence of goosegrass. Our assembly was able to identify all major herbicide‐resistance related genes and develop a useful tool for other genomic and evolutionary analysis. © 2019 Society of Chemical Industry

A novel mutation A212T in chloroplast Protoporphyrinogen oxidase (PPO1) confers resistance to PPO inhibitor Oxadiazon in Eleusine indica

“…The RNA‐Seq dataset of the S biotype was acquired from the NCBI‐SRA database under the accession number SRR 1560465 . Similarly, a previously published draft genome assembly of the S biotype was downloaded from the NCBI as accession number SAMN09001275 . Raw RNA‐Seq reads R1, R2 and S were assembled using the following pipeline.…”

“…24 Similarly, a previously published draft genome assembly of the S biotype was downloaded from the NCBI as accession number SAMN09001275. 25 Raw RNA-Seq reads R1, R2 and S were assembled using the following pipeline. Adaptor contamination and unqualified reads were removed via Trimmomatic-0.32, then the trimmed reads were quality checked with FastQC and de novo assembly with Trinity 2014-2104-13pl.…”

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

“…Eleusine indica genome (NCBI Accession: QEPD01000000) [66], was compared to the Eleusine coracana DDJB DRA Accession: DRA005897 [12] genome using SynMap CoGe [67,68] with quota align [69] 3/31/2020). This approach first categorized E. coracana genes by the identity of their matching syntenic E. indica gene.…”

Detection of subgenome bias using an anchored syntenic approach in Eleusine coracana (finger millet)

“…Eleusine indica genome (NCBI Accession: QEPD01000000) [71], was compared to the Eleusine coracana DDBJ DRA Accession: DRA005897 [16] genome using SynMap CoGe [72,73] with quota align [74] set to limit 2 E. coracana to 1 E. indica, minimum number of aligned gene pairs was at 5, Ka\Ks values were calculated CoGe version of codeml [75] with a maximum value of 3 and a minimum value of 0. A vs B genome calls were made from raw downloaded CoGe output using with dc_ks_bagofgenes.py (https://github.com/NDHall/coge_tools/blob/master/dc_tools/dc_ks_bagofgenes.py last accessed: 3/31/2020).…”