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Screening and identification of hair follicle initiation and development related gene in the fetal period of Inner Mongolian Cashmere Goat

ABSTRACT: Cashmere is an important economic product in Cashmere goat farming. The value of cashmere fleece is thought to be determined by the numbers and density of HFs. In recent years, molecular mechanisms that govern HF cyclic regeneration have been revealed in Cashmere goat breeds, but molecular mechanisms that govern HF initiation, growth and development process in the fetal period is relatively scarce. At present, life science has entered into the Post-Genome Era, the transcriptome and proteomics are important contents of functional genomics research, and also provide useful ways for further study on functional mechanism of hair follicle growth and development. In our study, skin samples at 10 different fetal periods were collected from the lateral body of each Cashmere goat. The RNA-seq and ITRAQ at three specific developmental stages: 45- , 55- and 65-day-old fetuses (E45, E55 and E65) were carried out in the present study according to the preliminary results, the results of sequencing were verified by qPCR and Western blotting (WB) respectively. In order to enhance our understanding of the molecular regulation mechanism and provides research foundation for cashmere HF initiation and development, we carried out omics conjoint analysis

ORGANISM(S): Capra Hircus

SUBMITTER: Yanjun Zhang

PROVIDER: PXD035366 | iProX | Thu Jul 14 00:00:00 BST 2022

REPOSITORIES: iProX

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Project description:The domestic goat, Capra hircus (2n=60), is one of the most important domestic livestock species in the world. Here we report its high quality reference genome generated by combining Illumina short reads sequencing and a new automated and high throughput whole genome mapping system based on the optical mapping technology which was used to generate extremely long super-scaffolds. The N50 size of contigs, scaffolds, and super-scaffolds for the sequence assembly reported herein are 18.7 kb, 3.06 Mb, and 18.2 Mb, respectively. Almost 95% of the supper-scaffolds are anchored on chromosomes based on conserved syntenic information with cattle. The assembly is strongly supported by the RH map of goat chromosome 1. We annotated 22,175 protein-coding genes, most of which are recovered by RNA-seq data of ten tissues. Rapidly evolving genes and gene families are enriched in metabolism and immune systems, consistent with the fact that the goat is one of the most adaptable and geographically widespread livestock species. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat revealed 51 genes that were significantly differentially expressed between the two types of hair follicles. This study not only provides a high quality reference genome for an important livestock species, but also shows that the new automated optical mapping technology can be used in a de novo assembly of large genomes. Corresponding whole genome sequencing is available in NCBI BioProject PRJNA158393. We have sequenced a 3-year-old female Yunnan black goat and constructed a reference sequence for this breed. In order to improve quality of gene models, RNA samples of ten tissues (Bladder, Brain, Heart, Kidney, Liver, Lung, Lymph, Muscle, Ovarian, Spleen) were extracted from the same goat which was sequenced. To investigate the genic basis underlying the development of cashmere fibers using the goat reference genome assembly and annotated genes, we extracted RNA samples of primary hair follicle and secondary hair follicle from three Inner Mongolia cashmere goats and conducted transcriptome sequencing and DGE analysis. This submission represents RNA-Seq component of study.

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Screening and identification of hair follicle initiation and development related gene in the fetal period of Inner Mongolian Cashmere Goat

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