ICAR-CARI, Izatnagar in Collaboration with ILRI Reports De Novo Chromosome-Scale Genome Assembly of India’s Red Junglefowl

In a significant advancement for avian genomics, indigenous poultry conservation and genetic resource characterization, scientists at ICAR–Central Avian Research Institute, Izatnagar, in collaboration with the International Livestock Research Institute, have successfully generated a de novo chromosome-scale genome assembly of India’s Red Junglefowl (Gallus gallus murghi).

The study successfully generated a platinum-quality genome assembly of approximately 1.12 Gb, achieving 99.2% genome completeness and covering all 40 chromosomes of the chicken genome. The chromosome-level assembly comprises 38 autosomes, including 9 macrochromosomes, 19 microchromosomes and 10 dot chromosomes, together with the Z and W sex chromosomes. The assembly demonstrated exceptional continuity and completeness, with a contig N50 of 36.55 Mb and scaffold N50 of 91.4 Mb, highlighting the high quality and chromosome-scale continuity of the genome.

The chromosome-scale platinum genome assembly of Indian RJF provides an important genomic reference for understanding the genetic diversity and evolutionary history of this ancestral poultry species. It will also support the identification of genomic signatures of purity and admixture, strengthening conservation of RJF.

The full dataset has been deposited and released under NCBI BioProject ID PRJNA1301553. Iso-Seq transcriptome sequencing showed spliced alignment achieved a 97.97% overall mapping rate, with 631,795 of 644,869 reads successfully mapped, while BUSCO analysis against aves_odb10 confirmed 91.5% transcriptomic completeness.

StringTie reference gene models supported the characterization of isoforms across 593,622 loci using SQANTI3, while consensus filtering using CPAT, CPC2 and RNAsamba identified 234,683 putative lncRNAs. Protein-coding transcripts were functionally annotated using eggNOG-mapper across GO, KEGG and COG categories.

Additionally, de novo repeat discovery using RepeatModeler and RepeatMasker identified and soft-masked 15.57% (166.8 Mb) of the genome, providing a robust foundation for downstream transcriptomic and functional genomic analyses.

(Source: ICAR-Central Avian Research Institute, Izatnagar)