Draft genome sequence of Sclerospora graminicola, the pearl millet downy mildew pathogenGenome sequence of pearl millet downy mildew pathogen

Authors Organisations
  • S. Chandra Nayaka (Author)
    University of Mysore
  • H. Shekar Shetty(Author)
    University of Mysore
  • C. Tara Satyavathib(Author)
  • Rattan Yadav(Author)
  • P. B. Kavi Kishor(Author)
    Osmania University
  • M. Nagaraju(Author)
    Osmania University
  • T. A. Anoop(Author)
    AgriGenome Labs Pvt. Ltd
  • M. Milner Kumar(Author)
    AgriGenome Labs Pvt. Ltd
  • Boney Kuriakose(Author)
    AgriGenome Labs Pvt. Ltd
  • Navajeet Chakravartty(Author)
    AgriGenome Labs Pvt. Ltd
  • A. V. S. K. Mohan Katta(Author)
    AgriGenome Labs Pvt. Ltd
  • V. B. Reddy Lachagan(Author)
    AgriGenome Labs Pvt. Ltd
  • Om Vir Singh(Author)
  • Pranav Pankaj Sahu(Author)
  • Swati Puranik(Author)
  • Rakesh Srivastava(Author)
    International Crops Research Institute for the Semi-Arid Tropics
  • Pankaj Kaushal(Author)
    ICAR-National Institute of Biotic Stress Management
Type Article
Original languageEnglish
Pages (from-to)18-20
Number of pages3
JournalBiotechnology Reports
Volume16
Early online date24 Aug 2017
DOI
Publication statusPublished - 01 Dec 2017
Show download statistics
View graph of relations
Citation formats

Abstract

Sclerospora graminicola pathogen is one of the most important biotic production constraints of pearl millet worldwide. We report a de novo whole genome assembly and analysis of pathotype 1. The draft genome assembly contained 299,901,251 bp with 65,404 genes.

Pearl millet [Pennisetum glaucum (L.) R. Br.], is an important crop of the semi-arid and arid regions of the world. It is capable of growing in harsh and marginal environments with highest degree of tolerance to drought and heat among cereals (1).

Downy mildew is the most devastating disease of pearl millet caused by Sclerospora graminicola (sacc. Schroet), particularly on genetically uniform hybrids. Estimated annual grain yield loss due to downy mildew is approximately 10–80 % (2-7). Pathotype 1 has been reported to be the highly virulent pathotype of Sclerospora graminicola in India (8). We report a de novo whole genome assembly and analysis of Sclerospora graminicola pathotype 1 from India.
A susceptible pearl millet genotype Tift 23D2B1P1-P5 was used for obtaining single-zoospore isolates from the original oosporic sample. The library for whole genome sequencing was prepared according to the instructions by NEB ultra DNA library kit for Illumina (New England Biolabs, USA). The libraries were normalised, pooled and sequenced on Illumina HiSeq 2500 (Illumina Inc., San Diego, CA, USA) platform at 2 x100 bp length. Mate pair (MP) libraries were prepared using the Nextera mate pair library preparation kit (Illumina Inc., USA). 1 μg of Genomic DNA was subject to tagmentation and was followed by strand displacement. Size selection tagmented/strand displaced DNA was carried out using AmpureXP beads. The libraries were validated using an Agilent Bioanalyser using DNA HS chip. The libraries were normalised, pooled and sequenced on Illumina MiSeq (Illumina Inc., USA) platform at 2 x300 bp length.
The whole genome sequencing was performed by sequencing of 7.38 Gb with 73,889,924 paired end reads from paired end library, and 1.15 Gb with 3,851,788 reads from mate pair library generated from Illumina HiSeq2500 and Illumina MiSeq, respectively. The sequences were assembled using various assemblers like ABySS, MaSuRCA, Velvet, SOAPdenovo2, and ALLPATHS-LG. The assembly generated by MaSuRCA (9) algorithm was observed superior over other algorithms and hence used for scaffolding using SSPACE. Assembled draft genome sequence of S. graminicola pathotype 1 was 299,901,251 bp long, with a 47.2 % GC content consisting of 26,786 scaffolds with N50 of 17,909 bp with longest scaffold size of 238,843 bp. The overall coverage was 40X. The draft genome sequence was used for gene prediction using AUGUSTUS. The completeness of the assembly was investigated using CEGMA and revealed 92.74% proteins completely present and 95.56% proteins partially present, while BUSCO fungal dataset indicated 64.9% complete, 12.4% fragmented, 22.7% missing out of 290 BUSCO groups. A total of 52,285 predicted genes were annotated using BLASTX and 38,120 genes were observed with significant BLASTX match. Repetitive element analysis in the assembly revealed 8,196 simple repeats, 1,058 low complexity repeats and 5,562 dinucleotide to hexanucleotide microsatellite repeats.

Keywords

  • Sclerospora graminicola, Pathotype 1, pearl millet, downy mildew, whole genome sequence