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

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 ?g 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.publishersversionPeer reviewe

Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace (Oryza sativa ssp. indica cv. Purpleputtu)

Purpleputtu (Oryza sativa ssp. indica cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait, associated domestication and de-domestication processes during its coevolution with present day cultivars. Along-with genome level allelic variations in the entire gene repertoire associated with the purple, red coloration of grain and other plant parts. Comparative genomic analysis using ‘a panel of 108 rice lines’ revealed a total of 3,200,951 variants including 67,774 unique variations in Purpleputtu (PP) genome. Multiple sequence alignment uncovered a 14 bp deletion in Rc (Red colored, a transcription factor of bHLH class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in Rc gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of Rc locus revealed a distinct clade showing proximity to the progenitor species Oryza rufipogon and O. nivara. In addition, PP genome exhibits a well conserved 4.5 Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique when SNPs compared to 3,023 lines of rice (SNP-Seek database). The results indicate that PP genome is rich in allelic diversity and can serve as an excellent resource for rice breeding for a variety of agronomically important traits such as disease resistance, enhanced nutritional values, stress tolerance, and protection from harmful UV-B rays

Identification and localization of the NBS-LRR genes in pea

International audienc

Genotyping of Tomato Cultivars and Hybrids using ddRAD

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera and includes annual and perennial plants from diverse habitats. ddRAD-seq is one of the most cost-effective methods in next generation sequencing (NGS) for generating robust genotyping data which permits high throughput simultaneous discovery and genotyping of sequence polymorphism either with or without an existing reference genome. Advantage of ddRAD technique was investigated by performing data analysis of sequence obtained through low pass whole genome sequencing and ddRAD protocol. Here we present a high-quality reduced represented genome sequence of domesticated tomato with the aim of understanding genetic variations in cultivated tomato; single nucleotide polymorphism (SNP) markers covering the whole genome of eight cultivars and four F1 hybrids were developed through Genotyping-By-Sequencing. We have sequenced twelve tomato varieties using Illumina HiSeq 4000, next generation sequencing platform. The raw data was subjected to preprocessing and aligned with reference tomato genome downloaded from ensembl release 36. The SNPs/INDELs were identified for each of the tomato varieties. A total of 30746 SNPs and 913 INDELs were identified. We investigated for homozygous polymorphic markers between PKM-1 and Arka Abha and found 745 markers which can be used as markers for fingerprinting.The homozygous polymorphic markers will be utilized for genetic mapping and trait association in a mapping population

Gene associated SNP discovery in fine quality Indian Gossypium barbadense cotton through whole genome resequencing

262-272The present study deals with the resequencing of cultivars, Suvin and BCS-23-18-7 belonging to Gossypium barbadense which are distinctly differing in fiber qualities and seed cotton yield using Illumina Hiseq2500 sequencer. A total of 2,604,107 single nucleotide polymorphism (SNP) and 592,364 insertion and deletions (INDELs) were identified when compared with G. barbadense reference genome. Among the 14,075 preferentially expressed genes of agronomically important traits of cotton, we have identified 33,637 markers in the genic regions. Comparing between the variants of Suvin and BCS-23-18-7, among the 4,929 preferentially expressed genes in fiber, only 1,128 genes have 2,453 variants and of these 1,512 variants are non-synonymous types, leading to change at the protein level. In order to validate the presence of these markers in the expressed genes could tag the expression and/or phenotypic variation bought by alleles of Suvin/BCS- 23-18-7, among 51 fiber elongation genes, ten genes that had high effect SNPs were utilized for real-time PCR, which showed an extended period of expression up to 15 days post-anthesis (DPA) in Suvin. Hence, utilization of such markers for the construction of SNP array / linkage maps would provide greater value to quantitative trait loci (QTL) mapping instead of random genomic markers

Genome-wide comparative analysis of three local aromatic rice lines revealed novel markers

Rice is the primary source of dietary energy for half of the World population, and 90% of them are present in developing countries in Asia. We have sequenced three local rice varieties Chenga, Tulai-panji, Kalonunia and compared with Oryza sativa cv. Nipponbare, Oryza sativa cv. 93-11 and Oryza sativa cv.Kasalath. 30X paired end 2 X 100 bp reads were generated for each of the 3 samples on Illumina HiSeq 4000, next generation sequencing platform. The raw data was subjected to pre-processing and aligned with reference genomes individually. The SNPs/INDELs were identified for each of the 3 local rice varieties with the each reference genome. A total of 0.15, 0.34 and 0.57 million SNPs and 10863, 11435 and 21841 INDELs were identified in Chenga, compared to Oryza sativa cv. Nipponbare, Oryza sativa cv. 93-11 and Oryza sativa cv.Kasalath, respectively. In Tulai-panji, 0.23, 0.76 and 0.71 SNPs as well as 12854, 18987 and 22901 INDELs were identified when compared to MSU7, 93-11 and Kasalath assemblies respectively. Analysis of Kalonunia data revealed 0.24, 0.58 and 0.54 SNPs and 10775, 14281 and 16657 INDELs against 3 reference genomes as above. We investigated for homozygous polymorphic markers between Chenga (Non aromatic) and Tulai-panji (Aromatic), and found 38,471 SNPs at read depth of 10. Similarly, comparative analysis between Chenga (Non aromatic) and Kalonunia (Aromatic) 130,376 homozygous polymorphic markers which can be explored for mapping novel alleles associated with aroma

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Not AvailableCultivation of the castor crop is hindered by various factors and one of the approaches for genetic improvement of the crop is through exploitation of biotechnological tools. Response of castor tissues to in vitro culture is poor which necessitated this study on understanding the molecular basis of organogenesis in cultured tissues of castor, through de novo transcriptome analysis and by comparing with jatropha and sunflower having good regeneration ability. Transcriptome profiling analysis was carried out with hypocotyl explants from castor, jatropha and cotyledons from sunflower cultured on MS media supplemented with different concentrations of hormones. Differentially expressed genes during dedifferentiation and organogenic differentiation stages of callus included components of auxin and cytokinin signaling, secondary metabolite synthesis, genes encoding transcription factors, receptor kinases and protein kinases. In castor, many genes involved in auxin biosynthesis and homeostasis like WAT1, vacuolar transporter genes, transcription factors like short root like protein were down-regulated while genes like DELLA were up-regulated accounting for regeneration recalcitrance. Validation of 62 DEGs through qRTPCR showed a consensus of 77.4% of the genes expressed. Overall study provides set of genes involved in the process of organogenesis in three oilseed crops which forms a basis for understanding and improving the efficiency of plant regeneration and genetic transformation in castorNot Availabl

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

Sclerospora graminicola pathogen is the most important biotic production constraints of pearl millet in India, Africa and other parts of the world. We report a de novo whole genome assembly and analysis of pathotype 1, one of the most virulent pathotypes of S. graminicola from India. The draft genome assembly contained 299,901,251bp with 65,404 genes. This study may help understand the evolutionary pattern of pathogen and aid elucidation of effector evolution for devising effective durable resistance breeding strategies in pearl millet