Consortium Research Platform on Genomics

• Chr. level genome assembly of the cultivated Guar Resequencing completed for 67 genotypes.
• A high-density SNP linkage map has been developed in Guar and QTLs have been mapped for important architectural and yield traits.
• Deep RNA seq and small RNA data was generated from seed development stages and genes/MiRs involved in gum bio-synthesis pathway were identified
• Black Gram genome is now in a good assembly.
• Draft genomes of 3 wild Pigeonpea has been developed for bio-prospecting of genes.
• Total of 15 publications, highest in Plant Biotechnology Journal (13.26).

Structural genomics

• High quality, whole genome assembly generated

• Hilsa shad, Tenualosa ilisha
• Indian Major carp, Catla catla.
• Indian Major carp, Cirrhinus mrigala
• Indian White Shrimp, Penaeus indicus.
• Flathead grey mullet, Mugil cephalus.
• Mangrove red snapper, Lutjanus argentimaculatus.

• Initiated: Macrobrachium rosenbergii and Labeo fimbriatus

Functional genomics

• Hilsa shad, Tenualosa ilisha: Differential expressing genes in various salinity levels, and identified with hub genes highly associated with salinity tolerance with osmoregulatory function.
• Indian Major Carp, Catla catla: Differential expressing genes at different developmental stages identified, for identification of important growth-related genes at specific growth stage.
• Isoform-level full-length transcript resource developed for Penaeus indicus, Mugil cephalus and Lutjanus argentimaculatus. The transcript resource has great value in genome annotation and aids researchers to derive meaningful results in functional studies..

Databases developed on

• Gene associated SSRs in Hilsa Shad developed: Transcriptome from five tissues and identified associated SSR in annotated and unannotated transcripts https://www.nbfgr.res.in:802/
• A database of SNP variations developed for two shrimp species, Penaeus vannamei and Penaeus indicus and presented them as a searchable user-friendly, web tool, the dbVAST. The database contains 28,895 and 15,554 SNP variations in 4,573 and 3,965 unique genes of Penaeus vannamei and Penaeus indicus, respectively

Software Missing Regions Finder (MRF)

• developed for performing comparative genomics studies in viruses like, white spot syndrome virus where the genomes are length-varying, highly similar and suffer from inconsistent annotation nomenclature. The MRF can be accessed online as a web tool http://14.139.181.163/mrf or can be downloaded https://github.com/vinayciba/MRF.

Brinjal shoot and fruit borer, Leucinodes orbonalis (Lepidoptera: Crambidae)

• De novo genome sequencing by short (Illumina Hiseq) and long read (PacBio RS II) sequencing. The genome size of 488 Mb has been assembled into 5898 scaffolds with scaffold N50 of 1.4 Mb. The genome has 35.4% repeat content and 30879 protein coding genes.
• Genome annotation and mined 72 putative CYP genes, 94 carboxylesterases, 33 Glutathione S transferases, 83 ABC transporters, 34 odorant binding protein genes, 1 pheromone binding protein gene and 28 odorant receptors. Identified CYP324F1, a novel CYP gene from the genome, its role in degradation of insecticides and plant toxic metabolites.

Cotton leafhopper, Amrasca biguttula biguttula (Hemipetra: Cicadellidae)

• De novo genome sequencing revealed the genome size of 1135 Mb assembled into 18122 contigs with contigs N50 of 89Kb. The genome has 25.5% repeat content and 23176 protein coding genes.Genome annotation and mined 24 ABC transporters, 37 cytochrome P450 monooxygenases, 16 carboxylesterases and nine glutathione S-transferase genes and verified their involvement in insecticide resistance through quantitative PCR
• Stage specific transcriptome sequencing, assembly and annotation.

Chilli broad mite, Polyphagotarsonemus latus (Acari: Tarsonemidae)

• De novo genome sequencing revealed the genome size of 49.1 Mb (Third smallest arthropod genome sequenced so far) assembled into 2 contigs with the smallest contigs size of 18.2 Mb. The genome has 2.5 Mb repeat content and 9,286 protein coding genes.
• Identified 54 ABC transporters, 46 cytochrome P450 monooxygenases (CYP), 15 carboxylesterases and 18 glutathione S-transferase genes. Identified 37 CYP genes that are new to science and not reported from any other living organisms.

Green lacewing predator, Chrysoperla zastrowi sillemi (Neuroptera: Chrysopidae)

• De novo genome sequencing revealed the 598 Mb genome assembled into 894 scaffolds with N50 size of 30.4 Mb. Six pseudochromosomes occupied 84% of the genome sequence and the size ranged from 29.36 Mb to170.05 Mb.The genome contains 14,495 protein coding genes and 342.5 Mb of repeat content. The scaffold containing mitochondrial genome is 16,048 bp in size.
• Stage specific transcriptome sequencing, assembly and annotation.
• Expression profiling of genes related to insecticide resistance.



Green lacewing predator, Chrysoperla zastrowi sillemi (Neuroptera: Chrysopidae)

• De novo genome sequencing revealed the genome size of 627 Mb assembly into 56 scaffolds with N50 of 14 Mb size. The genome has 41.86% repeats and codes 12,235 genes.

Whole Genome Sequencing of Fusarium udum F-02845: the first de novo draft WGS in the world. The draft genome was sequenced Genome size in Mb -56.38; Isolation Source-Pigeonpea; Traits- Cause wilt disease in pigeon pea

Whole genome sequencing of Plant growth promoting bacteria:Nine plant growth promoting bacteria were isolated from vegetable leaves and soils of different regions of India and their Whole genome sequencing were done.

• P. aeruginosa PF1RG: Genome size in Mb -6.23; Isolation Source-Ridge gourd leaf; Traits- Cold tolerant P, K solubilizer
• P. plecoglossicida PF2CP: Genome size in Mb - 5.89; Isolation Source- Cow pea leaf; Traits- Cold tolerant PSB
• P. aeruginosa PF3CP: Genome size in Mb - 6.2; Isolation Source- Cow pea root; Traits-Cold tolerant KSB
• P. plecoglossicida PF4CP: Genome size in Mb - 5.89; Isolation Source- Cow pea leaf; Traits-Cold tolerant KSB
• Paenibacillus xylanexedens SK6B7: Genome size in Mb - 7.10; Isolation Source- Soil;Sikkim (Yumthang); Traits- Cold tolerant P, K solubilizer
• Pseudochrobactrum asaccharolyticum SK7B18: Genome size in Mb-4.14; Isolation Source- Soil;Sikkim (Yumthang); Traits- Cold tolerant PSB
• Bacillus subtilis SK6B4: Genome size in Mb-4.15; Isolation Source- Soil;Sikkim (Yumthang); Traits- Cold tolerant KSB
• Bacillus subtilis subsp. subtilis SK7B5: Genome size in Mb-4.2; Isolation Source- Soil;Sikkim (Yumthang); Traits- Cold tolerant PSB
• Bacillus subtilis subsp. subtilis SK7B5: Genome size in Mb-6.3; Isolation Source- Rhizosphere of chickpea; Traits- Sulphur oxidizing bacteria

Whole genome sequencing of extremophilic bacteria: Two extremophilic bacteria were isolated from salt crystal samples collected from Kushmaur, Mau, India and their Whole genome sequencing was done.

• Marinococcus halophilus ANJ206: Genome size in Mb- 3.4; Isolation Source- Salt crystal; Traits- High salinity tolerance (25% NaCl w/v)
• Natrialba taiwanensis ANJ208: Genome size in Mb- 4.4; Isolation Source- Salt crystal; Traits- Halophilic (needs 30% NaCl for growth)

Whole genome sequencing of extremo-tolerant plant growth promoting bacteria: Whole genome sequencing of highly salinity tolerant bacteria Chromohalobacter salexigens ANJ207 strain; isolated from vaporized water salt crystals and can tolerate up to 30% NaCl c; possesses PGP traits such as solubilization of phosphorus, potassium and zinc minerals, production HCN and siderophore which are retained at 5-10% salinity.

• Genome size in Mb-3.66; Isolation Source- Vaporized salt crystal; Traits- Solubilise P, K and produce siderophore production under saline conditions

Transcriptome analysis and differential gene expression profile of extreme-tolerant bacteria Chromohalobacter salexigens ANJ207: De Novo Transcriptome response of Chromohalobacter salexigens assembly was performed of Chromohalobacter salexigens in three different conditions, low salinity (5.0% NaCl), optimal salinity (10.0% NaCl) and high salinity (25.0% NaCl) grown in each condition

Whole genome sequencing of

• • Elite PGP bacteria: Bacillus subtilis RC-25 and Pseudomonas koreensis P2
• Cold tolerant PGP bacteria: Paenibacillus polymyxa SK21271-13, Metasolibacillus fluoroglycofenilyticus SK21272-13, Bacillus velezensis SK2127-23, Bacillus wudalianchiensis SK2127-5, Paenibacillus maysiensis SK2127-7, Bacillus aryabhattai SK2119-83, Bacillus wudalianchiensis SK2127-88, Bacillus wudalianchiensis SKS2119-92, Bacillus wudalianchiensis Sikkism2119-43, Priestia megaterium Sikkism212230, Microbacterium phyllosphaerae Sikkim2127_15, Proteus hauseri strain (137), Brachybacterium paraconglomeratum Sk6-B-6), Bacillus pumilus sikkim2127_10, Stenotrophomonas maltophilia (9), Serratia nematodiphila (139) , Proteus terrae (105), Brevibacterium sediminis (2), Serratia marcescens Sikkim2102_105) and Brevibacterium sediminis (1)

Magnaporthe Genome: The genomes of four fungal blast pathogen Magnaporthe strains sequenced, revealed genome sizes ranging from 40.0 to 50.0 Mb.: those infecting rice (Magnaporthe oryzae RMg_Dl), pearl millet (Magnaporthe grisea PMg_Dl), Indian Goosegrass (Magnaporthe grisea GgMg-Dl), and Napier grass (Magnaporthe grisea GnMg-Dl).

Tilletia Genome:The genomes of Bipolaris strains infecting wheat (Bipolaris sorokiniana, causing spot blotch), rice (Bipolaris oryzae, causing brown spot), and maize (Bipolaris maydis, causing maydis leaf blight) sequenced: sizes ranged from 34.0 to 35.0 Mb.

Bipolaris Genome:The genomes of Bipolaris strains infecting wheat (Bipolaris sorokiniana, causing spot blotch), rice (Bipolaris oryzae, causing brown spot), and maize (Bipolaris maydis, causing maydis leaf blight) sequenced: sizes ranged from 34.0 to 35.0 Mb.

RalstoniaGenome:The genome of Ralstonia pseudosolanacearum CaRs_Mep, responsible for bacterial wilt in crops, sequenced: this high-GC content genome (67.09%) is 5.6 Mb in length

Genome-assisted pathogenomics tools:Genome-assisted genotyping tools, such as Multilocus Sequence Typing (MLST), and sensitive detection methods, like Loop-Mediated Isothermal Amplification (LAMP), were developed for bunt and blast pathogens. Additionally, three novel miRNAs that play a pivotal role in blast resistance were identified in rice.

Genomics assisted Diagnostic Tools: Loop Mediated Isothermal Amplification (LAMP) based Magna-Tracker and Bunt-Trackers were developed for diagnosing blast and bunt disease in rice and wheat respectively.

• A database CbLncRNAdb has been developed for LncRNAs in cluster bean (Cyamopsis tetragonoloba) and made available at http://cabgrid.res.in/cblncrnadb.
• Nine training programs were organized on various areas of genomics, proteomics and metagenomics and around 600 personnel were trained.
• The transcriptome data from three tissues: flower, shoot and leaf has been assembled and lncRNAs have been predicted from guar transcriptome. Four novel endogenous Target Mimic (eTM) lncRNAs were identified from the interaction between putative lncRNAs and miRNAs.
• SNPs were identified from leaf tissues of three different cultivars: RGC1066, RGC-936 and M-83 of cluster bean.
• Genome-Wide Association Study (GWAS) and genomic selection was done on SNP genotyping data of 1762 river buffaloes for three traits: fat, protein and milk yield.
• Secretome prediction of Bipolaris sorokiniana genome was done.