title: RNA-Sequencing for profiling goat milk transcriptome in colostrum and mature milk.
abstract: BACKGROUND
  In this work we aimed at sequencing and assembling the goat milk transcriptome corresponding at colostrum and 120 days of lactation. To reconstruct transcripts we used both the genome as reference, and a de novo assembly approach. Additionally, we aimed at identifying the differentially expressed genes (DEGs) between the two lactation stages and at analyzing the expression of genes involved in oligosaccharides metabolism.
  
  
  RESULTS
  A total of 44,635 different transcripts, organized in 33,757 tentative genes, were obtained using the goat genome as reference. A significant sequence similarity match was found for 40,353 transcripts (90%) against the NCBI NT and for 35,701 (80%) against the NR databases. 68% and 69% of the de novo assembled transcripts, in colostrum and 120 days of lactation samples respectively, have a significant match with the merged transcriptome obtained using Cufflinks/Cuffmerge. CSN2, PAEP, CSN1S2, CSN3, LALBA, TPT1, FTH1, M-SAA3, SPP1, GLYCAM1, EEF1A1, CTSD, FASN, RPS29, CSN1S1, KRT19 and CHEK1 were found between the top fifteen highly expressed genes. 418 loci were differentially expressed between lactation stages, among which 207 and 122 were significantly up- and down-regulated in colostrum, respectively. Functional annotation and pathway enrichment analysis showed that in goat colostrum somatic cells predominate biological processes involved in glycolysis, carbohydrate metabolism, defense response, cytokine activity, regulation of cell proliferation and cell death, vasculature development, while in mature milk, biological process associated with positive regulation of lymphocyte activation and anatomical structure morphogenesis are enriched. The analysis of 144 different oligosaccharide metabolism-related genes showed that most of these (64%) were more expressed in colostrum than in mature milk, with eight expressed at very high levels (SLCA3, GMSD, NME2, SLC2A1, B4GALT1, B3GNT2, NANS, HEXB).
  
  
  CONCLUSIONS
  To our knowledge, this is the first study comparing goat transcriptome of two lactation stages: colostrum and 120 days. Our findings suggest putative differences of expression between stages and can be envisioned as a base for further research in the topic. Moreover because a higher expression of genes involved in immune defense response, carbohydrate metabolism and related to oligosaccharide metabolism was identified in colostrum we here corroborate the potential of goat milk as a natural source of lactose-derived oligosaccharides and for the development of functional foods.
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Animal production research centre, Via Salaria 31, 00015, Monterotondo, Rome, Italy. alessandra.crisa@crea.gov.it.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Crisà
authors.affiliation: Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 6, 40126, Bologna, Italy.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Ferrè
authors.affiliation: Applications and Innovation Department, CINECA, SCAI SuperComputing, Via dei Tizii 6, 00185, Rome, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Chillemi
authors.affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA) - Animal production research centre, Via Salaria 31, 00015, Monterotondo, Rome, Italy.
authors.forename: Bianca
authors.initials: B
authors.lastname: Moioli
mesh_terms: D000818:Animals; D003126:Colostrum / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling; D006041:Goats / Q000235:genetics*; D007774:Lactation; D008892:Milk / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
keywords: Colostrum; Goat milk; Lactation; Milk somatic cells; Oligosaccharides; RNA-seq; Transcriptomic profile