Abstract
Pashmina goats produce the world's finest and the most costly animal fiber (Pashmina) with an average fineness of 11–13 microns and have more evolved mechanisms than any known goat breed around the globe. Despite the repute of Pashmina goat for producing the finest and most sought-after animal fiber, meager information is available in the public domain about Pashmina genomics and transcriptomics. Here we present a 2.94 GB genome sequence from a male Changthangi white Pashmina goat. We generated 294.8 GB (>100X coverage) of the whole-genome sequence using the Illumina HiSeq 2500 sequencer. All cleaned reads were mapped to the goat reference genome (2,922,813,246 bp) which covers 97.84% of the genome. The Unaligned reads were used for de novo assembly resulting in a total of 882 MB non-reference contigs. De novo assembly analysis presented in this study provides important insight into the adaptation of Pashmina goats to cold stress and helps enhance our understanding of this complex phenomenon. A comparison of the Pashmina goat genome with a wild goat genome revealed a total of 2,823 high impact single nucleotide variations and small insertions and deletions, which may be associated with the evolution of Pashmina goats. The Pashmina goat genome sequence provided in this study may improve our understanding of complex traits found in Pashmina goats, such as annual fiber cycling, defense mechanism against hypoxic, survival secret in extremely cold conditions, and adaptation to a sparse diet. In addition, the genes identified from de novo assembly could be utilized in differentiating Pashmina fiber from other fibers to avoid falsification at marketing practices.
Highlights
The domestic goat (Capra hircus) is an Asian animal distributed across all ecologies ranging from cold arid to hot humid
We systematically identified a comprehensive list of Long non-coding RNAs (lncRNAs) (Supplementary Table 5) identified from the Pashmina goat genome and their role in regulating different biological processes
Recent studies suggest the role of lncRNAs in modulating immunity; in our study, we identified three major classes of immune regulatory lncRNAs. (1) HOX antisense intergenic RNA myeloid 1 (HOTAIRM1) is known to be associated with granulocytes, and is a key regulator in myeloid transcriptional regulation, by modulating HOXA expression in cis-configuration (Mumtaz et al, 2017)
Summary
The domestic goat (Capra hircus) is an Asian animal distributed across all ecologies ranging from cold arid to hot humid. It serves as an important source of meat, milk, skin, fiber, and manure. An important breed of extremely cold Temperate Himalayan region of India is Changthangi Pashmina goat which produces world’s most sought-after natural animal fiber, Pashmina (Bhat B. et al, 2019). The guard hair develops from primary hair follicles (PHFs) and Pashmina from secondary hair follicles (SHF) (Ansari-Renani et al, 2011) These goats survive in extreme climatic conditions [+35oC (short summer) and −40oC (long winter)] at an altitude of 4,000–5,500 m above mean sea level (AMSL) under cold and hypoxic conditions. The growth of a double hair coat in Pashmina goats may be one of the mechanisms of protection from cold, and the result of the response triggered by the thermoregulatory center of the brain
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