Scientists at the ICAR-Central Avian Research Institute (CARI), Izatnagar, working with the International Livestock Research Institute (ILRI), have generated a de novo chromosome-scale genome assembly of India's red junglefowl, Gallus gallus murghi, an advance the institute describes as significant for avian genomics, indigenous poultry conservation and the characterisation of genetic resources.
The platinum-quality assembly is about 1.12 Gb, reaches 99.2% genome completeness and covers all 40 chromosomes of the chicken genome: 38 autosomes, nine macrochromosomes, 19 microchromosomes and ten dot chromosomes, together with the Z and W sex chromosomes. A contig N50 of 36.55 Mb and a scaffold N50 of 91.4 Mb show its continuity at chromosome scale.
The reference is meant to help understand the genetic diversity and evolutionary history of this ancestral poultry species and to identify genomic signatures of purity and admixture, strengthening conservation of the red junglefowl. The full dataset has been deposited and released under NCBI BioProject PRJNA1301553.
Iso-Seq transcriptome sequencing achieved a 97.97% overall mapping rate, with 631,795 of 644,869 reads mapped, and BUSCO analysis against aves_odb10 confirmed 91.5% transcriptomic completeness; StringTie gene models supported the characterisation of isoforms across 593,622 loci using SQANTI3, and consensus filtering with CPAT, CPC2 and RNAsamba identified 234,683 putative long non-coding RNAs, with protein-coding transcripts annotated through eggNOG-mapper.
De novo repeat discovery with RepeatModeler and RepeatMasker identified and soft-masked 15.57% of the genome, 166.8 Mb, giving, the institute says, a robust foundation for transcriptomic and functional genomic work on the bird from which domestic chickens descend.
Source: ICAR
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