Consortium Research Platform on Genomics

Goat (Capra Hircus)

• First High Density SNP chip for goat developed with >601,000 SNP markers. validated on 480 animals of 15 goat breeds from different Agro- ecological region of the country.
• Identified highly connected, differentially expressed genes associated with triacylglycerol biosynthesis pathway in Barbari and muscle fibre contraction in Changthangi goats.
• Gene expression profiling of skin biopsies of Changthangi and Barbari goats revealed transcriptional regulator genes for hair follicle keratin synthesis viz., GPRC5D, PADI3, HOXC13, FOXN1, LEF1 and ELF5 showed higher transcabundance in Pashmina producing goats
• Investigation into the dynamics of gene expression with progression of age in Bandur sheep skeletal muscles led to the identification of highly connected genes associated with growth, proliferation and adipogenesis in lambs

Buffalo and Cattle

• Designed a medium density SNP array (98000 SNPs) based on country wide diverse buffaloes (Bubalus bubalis)
• Designed a High density SNP array (6.75 Lakh SNPs) for selection in Murrah buffaloes
• Milk somatic cell derived transcriptomic comparison of early, mid and late lactation in Murrah buffalo revealed a discernible shift from metabolism in early stage to metabolism and immune response in mid stage, and an increase in immune response functions in late lactation. Candidate genes and pathways involved in the different stages of lactation in buffalo were also identified.
• Gene expression profiles of Sahiwal cattle and Murrah buffalo milk somatic cells at the mid lactation stage delineated the enrichment of genes for various host defense peptides such as lysozyme, defensin β and granzymes in buffaloes. These results lend support to more robust immune mechanisms in buffaloes, possibly explaining lower susceptibility to mammary infections as compared to cattle.
• Milk somatic cell derived transcriptomic comparison of early, mid and late lactation in Murrah buffalo revealed a discernible shift from metabolism in early stage to metabolism and immune response in mid stage, and an increase in immune response functions in late lactation. Candidate genes and pathways involved in the different stages of lactation in buffalo were also identified.

Hilsa shad Tenualos ailisha

• High-quality draft genome assembly of Tenualos ailisha, Seven novel gene variants, in addition to claudin gene (CLDZ), identified
• 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:

• Draft genome assembly of an Indian Major carp Catla catla (97.12% BUSCO completeness), Repertoire of immune related genes, identified with novel Immune variants/genes in catla
• Differential expressing genes at different developmental stages identified, for identification of important growth related genes at specific growth stage.

Indian Major carp Cirhinus mrigala

• Draft genome assembly contained 1.05 Gb length and N50 of 20.56 Mb and genome completeness of 99.70%.

Indian white prawn Penaeus indicus

• Draft genome of P. indicus assembled (1.93 GB of ~2.4 GB)
• Transcriptome assembly of P. indicus
• Novel Isoform Sequencing Based Full-Length Transcriptome Resource generated

Flathead Grey Mullet Mugil cephalus

• Whole genome assembly of Mugil cephalus has been completed. At the scaffold level, the assembly is 644Mb in length in 583 scaffolds with an N50 of 28.32Mb and 27,269 protein coding genes. The genome completeness for M. cephalus assembly was assessed to be 96% complete
• An isoform-level, full-length transcriptome resource generated for grey mullet based on the PacBio Iso-Sequencing using nine different adult tissues and five different developmental stages.

Draft genomes assemblies of two insect pests

• Broad mite: Polyphagonotarsonemus latus (Tarsonemidae: Acari)
• Co Green lacewing predator, Chrysoperla zastrowi sillemi (Hi-C scaffolded assembly)

Stage specific transcriptome assemblies

• Broad mite: Polyphagonotarsonemus latus (Tarsonemidae: Acari)

Genome mining and comparative analysis

• Mined the genome and transcriptome of broad mite and validated economically important genes through qRTPCR. Twenty four novel CYP genes identified.
• Genome mining of brinjal shoot and fruit borer, Lucinodes orbonalis was undertaken to identify the genes encoding odorant binding protein and pheromone binding proteins. Identification of pheromone binding proteins from adult males were done by differential gene expression analysis of male vs female antennal transcriptome. Gene silencing via RNAi is being employed for the further validation

Draft genome assemblies of Agriculturally Important Microorganisms

• Fusarium udum(58.38 Mb) NAIMCC 2845: Pigeon pea wilt pathogn: first report.
• Bacteria and archea from salt crystals Marinococcus halophilus (3.5 mb) and Natrialba taiwanensis (4.4 mb)
• Pseudomonas azotoformans (6.43Mb): a sulphursolublizer/oxidizer bacteria.
• Pseudomonas koreensis: a cold adaptive and potential P-solublizer, isolated from Sela Lake Arunachal Pradesh.
• Pseudomonas aeruginosa (2 strains) and P. plecoglossicida (2 strains) for comparative studies with P. koreensis.
• Chromohalobacter salexigens ANJ 207 (3.66 Mb) isolated from vaporized water salt crystal, capable to grow up to 30% NaCl and having PGP traits.
• Bacillus subtilisRC25 (3.98 Mb) isolated from chickpea rhizospheric soil

Developed Molecular markers having applications

• Microsatellite markers (SSR) were mined in P. koreensis P2
• SIX genes (Secretion in xylem) based markers for Fusarium
• Effectors genes, of transposable elements, long terminal repeats (LTR) from Fusarium udum

Functional genomics

• The gene expression profiling of gene involved in phosphate solubilization pathway in P. koreensis P2
• Differential genes expression analysis of C. salexigens ANJ 207 for changes in the salt stress

Magnaporthe Genome: Genomes of four strains of fungal blast pathogen Magnaporthe 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) were sequenced by adopting short and long-read sequencing technologies, and published. The high-throughput hybrid assembly revealed genome sizes in the range of 40.0-50.0 Mb

Tilletia Genome:Genomes of two bunt pathogens, namely Tilletia indica and Tilletia caries infecting wheat, were sequenced by adopting a hybrid approach and published. The genome size ranged from 33.0-39.0 Mb

Bipolaris Genome:Genomes of Bipolaris infecting wheat (Bipolaris sorokiniana causing spot blotch) and rice (Bipolaris oryzae causing a brown spot) were sequenced using short and long-read sequencing platforms. The genome sizes were in the range of 34.0-35.0 Mb.

RalstoniaGenome:Genome of Ralstonia pseudosolanacearum CaRs_Mep causing bacterial wilt in crops was sequenced using Illumina HiSeq. The high-GC content (67.09%) genome is 5.6 Mb in length

Genome-assisted pathogenomics tools:Genome-assisted genotyping tools (Multilocus Sequence Typing) and sensitive detection methods (Loop-mediated isothermal amplification-LAMP) for bunt and blast were developed. Three novel miRNAs playing a pivotal role in blast resistance were identified in rice