Despite that goat is one of the best nonmodel systems for villus growth studies and hair biology, limited gene resources associated with skin or hair follicles are available. In the present study, using Illumina/Solexa sequencing technology, we de novo assembled 130 million mRNA-Seq reads into a total of 49,115 contigs. Searching public databases revealed that about 45% of the total contigs can be annotated as known proteins, indicating that some of the assembled contigs may have previously uncharacterized functions. Functional classification by KOG and GO showed that activities associated with metabolism are predominant in goat skin during anagen phase. Many signaling pathways was also created based on the mapping of assembled contigs to the KEGG pathway database, some of which have been previously demonstrated to have diverse roles in hair follicle and hair shaft formation. Furthermore, gene expression profiling of three skin types identified ~6,300 transcript-derived contigs that are differentially expressed. These genes mainly enriched in the functional cluster associated with cell cycle and cell division. The large contig catalogue as well as the genes which were differentially expressed in different skin types provide valuable candidates for further characterization of gene functions. 1. Introduction Inner Mongolia Cashmere Goat (Capra hircus, IMCG) is a diploid ( ) mammal that belongs to the family of Bovidae. It plays an important role in the world animal fiber industry because it can produce high quality underhair (cashmere is the commercial name) and is one of the world’s largest breeding groups. Cashmere produced by IMCG, which is of a small diameter (14–18？μm) and is soft to touch, is grown from the secondary hair follicle (HF) of the body skin [1, 2]. Fiber diameter and length determine both the quality and the amount of cashmere produced by an animal. The longer the length and the smaller the diameter of the cashmere fibers, the higher the price becomes. IMCGs exhibit seasonal rhythm and annual cycle of cashmere growth that are controlled by daylength. During the period from the summer solstice to midwinter, when the length of day is reduced, cashmere fiber has a high growth speed; in contrast, it becomes low during the period from midwinter to the next summer solstice [3, 4]. This photoperiodic characteristic of cashmere fiber growth is convenient for cashmere harvest and formulating a management strategy of cashmere production. During the past decades, many mammalian genomic and transcript sequences have become available, including Homo
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