ICAR- NRC Guwahati completes Genome Sequencing of indigenous and exotic breeds of pigs.
Whole genome sequencing of two indigenous breeds of pigs, namely Ghungroo (INDIA_PIG_2100_GHOONGROO_09001) and Mali (INDIA_PIG_1900_MALI_09009), and assembly was successfully completed up to the chromosome level. The research work was carried out at ICAR-National Research Centre on Pig, Rani, Guwahati.
Along with the indigenous breeds, genome sequencing of two exotic breeds of pigs (Hampshire and Large White Yorkshire, LWY) upto chromosome level, for which scaffold-level assemblies were only available, was also completed.
The mean size of the genome is about 2.55GB and contains about 40 per cent of repetitive elements, with minor differences between various pig genomes. The analysis of repeated elements in genome shows a distribution among class I retrotransposons (long interspersed nuclear elements (LINEs, 17.3 per cent) short interspersed nuclear elements (SINEs, 3.3 per cent) and long terminal repeat elements (LTRs, 6.8 per cent). The porcine genome contains about 25000 genes with 1580 common single nucleotide variations in indigenous pig breeds as compared to 4100 in exotic animals.
Various classes of variants were identified through a genome-level comparison of Ghungroo, Hampshire, Mali and LWY genomes with the reference assembly Sscrofa11.1. Analysis revealed more than 100800 structural variants in the genomes of four breeds, with 46687 deletions, 352 duplications, and 53825 insertions. Unique variants of heat shock protein genes identified in indigenous Mali and Ghungroo genome provides insights into adaptability of indigenous animals. The assembled genome will serve as a resource for further understanding the porcine genome and promote application in functional genomics.
