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goat transcriptome

Jianping Li, HaiE Qu, Huaizhi Jiang, Zhihui Zhao, Qiaoling Zhang
Compare the microRNA (miRNA) trancriptomes of goat and sheep skin using Solexa sequencing to understand the development of skin and hair follicles (HFs). miRNA expression patterns vary in the two small RNA libraries from goat (G library) and sheep (S library) telogen skin samples. Analysis of the size distribution of 25.32 million clean reads revealed that most are 21-23 nucleotides. A total of 1910 known miRNAs and 2261 novel mature miRNAs were identified in this study. Among them, 107 novel miRNAs and 1246 known miRNAs were differentially expressed in the two libraries; 10 of the known miRNAs were identified using stem-loop quantitative real-time PCR...
October 18, 2016: DNA and Cell Biology
Xiao-Yang Ji, Jian-Xun Wang, Bin Liu, Zhu-Qing Zheng, Shao-Yin Fu, Getinet Mekuriaw Tarekegn, Xue Bai, Yong-Sheng Bai, Heng Li, Wen-Guang Zhang
BACKGROUND: The fleece of cashmere goats contains two distinct populations of fibers, a short and fine non-medullated insulating cashmere fiber and a long and coarse medullated guard hair. The former is produced by secondary follicles (SFs) and the later by primary follicles (PFs). Evidence suggests that the induction of PFs and SFs may require different signaling pathways. The regulation of BMP2/4 signaling by noggin and Edar signaling via Downless genes are essential for the induction of SFs and PFs, respectively...
2016: PloS One
Weizhong Li, R Alexander Richter, Yunsup Jung, Qiyun Zhu, Robert W Li
BACKGROUND: Remarkable advances in Next Generation Sequencing (NGS) technologies, bioinformatics algorithms and computational technologies have significantly accelerated genomic research. However, complicated NGS data analysis still remains as a major bottleneck. RNA-seq, as one of the major area in the NGS field, also confronts great challenges in data analysis. RESULTS: To address the challenges in RNA-seq data analysis, we developed a web portal that offers three integrated workflows that can perform end-to-end compute and analysis, including sequence quality control, read-mapping, transcriptome assembly, reconstruction and quantification, and differential analysis...
September 27, 2016: BMC Genomics
L J Wang, X W Sun, F Y Guo, Y J Zhao, Z H Zhang, Z Q Zhao
Transcriptome analysis of Inner Mongolia Cashmere goat and Dazu black goat generated 38,772,947 and 38,771,668 clean pair end reads, respectively, which were assembled into 72,422 and 80,069 unigenes by Trinity, respectively. For Inner Mongolia Cashmere goat, 26,051 and 10,100 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups, respectively. A total of 32,772 unigenes can comment to SWISS-Prot database, and the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) mapped 24,420 unigenes...
September 20, 2016: Reproduction in Domestic Animals, Zuchthygiene
Hui Wang, Huaiping Shi, Jun Luo, Yongqing Yi, Dawei Yao, Xueying Zhang, Gongzhen Ma, Juan J Loor
MicroRNAs (miRNAs) are noncoding RNA molecules that regulate gene expression at the post-transcriptional level to cause translational repression or degradation of targets. The profiles of miRNAs across stages of lactation in small ruminant species such as dairy goats is unknown. A small RNA library was constructed using tissue samples from mammary gland of Saanen dairy goats harvested at mid-lactation followed by sequencing via Solexa technology. A total of 796 conserved miRNAs, 263 new miRNAs and 821 pre-miRNAs were uncovered...
July 22, 2016: Journal of Cellular Physiology
Zekun Bao, Jian Lin, Lulu Ye, Qiang Zhang, Jianquan Chen, Qian Yang, Qinghua Yu
Mammary gland development during puberty and reconstruction during pregnancy and lactation is under the control of circulating endocrine hormones, such as growth hormone, which are released from the pituitary. In this study, we explored the influence of overexpression of growth hormone in the mammary gland on breast development and milk production in goats. Using transcriptome sequencing, we found that the number of highly expressed genes was greater in GH transgenic goats than non-transgenic goats. Furthermore, KEGG pathway analysis showed that the majority of the genes belonged to the MAPK signaling pathway and the ECM-receptor interaction pathway...
2016: Frontiers in Physiology
G X E, Y J Zhao, R S Na, Y F Huang
Deep RNA sequencing (RNA-seq) provides a practical and inexpensive alternative for exploring genomic data in non-model organisms. The functional annotation of non-model mammalian genomes, such as that of goats, is still poor compared to that of humans and mice. In the current study, we performed a whole transcriptome analysis of an intestinal mucous membrane lymph node to comprehensively characterize the transcript catalogue of this tissue in a goat. Using an Illumina HiSeq 4000 sequencing platform, 9.692 GB of raw reads were acquired...
2016: Genetics and Molecular Research: GMR
Ye Gao, Xiaolong Wang, Hailong Yan, Jie Zeng, Sen Ma, Yiyuan Niu, Guangxian Zhou, Yu Jiang, Yulin Chen
Cashmere goat skin contains two types of hair follicles (HF): primary hair follicles (PHF) and secondary hair follicles (SHF). Although multiple genetic determinants associated with HF formation have been identified, the molecules that determine the independent morphogenesis of HF in cashmere goats remain elusive. The growth and development of SHF directly influence the quantity and quality of cashmere production. Here, we report the transcriptome profiling analysis of nine skin samples from cashmere goats using 60- and 120-day-old embryos (E60 and E120, respectively), as well as newborns (NB), through RNA-sequencing (RNA-seq)...
2016: PloS One
Xiangyang Miao, Qingmiao Luo, Xiaoyu Qin
The goats are widely kept as livestock throughout the world. Two excellent domestic breeds in China, the Laiwu Black and Jining Grey goats, have different fecundities and prolificacies. Although the goat genome sequences have been resolved recently, little is known about the gene regulations at the transcriptional level in goat. To understand the molecular and genetic mechanisms related to the fecundities and prolificacies, we performed genome-wide sequencing of the mRNAs from two breeds of goat using the next-generation RNA-Seq technology and used functional annotation to identify pathways of interest...
May 10, 2016: Gene
Y X Fan, R B Wu, X Qiao, Y J Zhang, R J Wang, R Su, J H Wu, Y Dong, J Q Li
Previous molecular genetic studies of the goat hair life cycle have focused primarily on a limited number of genes and proteins. To identify additional genes that may play important roles in hair follicle cycle regulation, Illumina sequencing technology was used to catalog differential gene expression profiles in the hair growth cycle (anagen to catagen) of goat, comparing the primary hair follicle with the secondary hair follicle. There were 13,769 and 12,240 unigenes assembled from the reads obtained from primary hair follicle and secondary hair follicle, respectively...
2015: Genetics and Molecular Research: GMR
Xing Huang, Lin Chen, Yingdong Yang, Xiaobin Gu, Yu Wang, Weimin Lai, Xuerong Peng, Guangyou Yang
BACKGROUND: The larval stage of Taenia multiceps, also known as coenurus, is the causative agent of coenurosis, which results in severe health problems in sheep, goats, cattle and other animals that negatively impact on animal husbandry. There is no reliable method to identify coenurus infected goats in the early period of infection. METHODS: We identified a full-length cDNA that encodes acidic ribosomal protein P2 from the transcriptome of T. multiceps (TmP2). Following cloning, sequencing and structural analyses were performed using bioinformatics tools...
2015: Parasites & Vectors
Y H Wang, C L Zhang, M Plath, X T Fang, X Y Lan, Y Zhou, H Chen
Domestic goats are important meat production animals; however, data from transcriptional profiling of skeletal muscle tissue in goat have thus far been scarce. We used comparative transcriptional profiling based on RNA sequencing of longissimus thoracis muscle tissue obtained from fetal goat muscle tissue (27 512 850 clean cDNA reads) and 6-month-old goat muscle tissue (27 582 908 reads) to identify genes that are differentially expressed, novel transcript units and alternative splicing events. Gene annotation revealed that 15 960 and 14 981 genes were expressed in the fetal and juvenile libraries respectively...
December 2015: Animal Genetics
Jiang Wei, Fan Yixing, Qiao Xian, Zhang Yanjun, Liu Zhihong, Zhao Yanhong, Wang Ruijun, Wang Zhixin, Zhang Wenguang, Su Rui, Li Jinquan
Recently, transcriptome sequencing technology has achieved significant progresses in gene network regulation of important economic traits in animals. As the derivative of mammalian skin, hair follicle is capable of self-renew. Its proliferation and differentiation result in hair formation. Researches have revealed that many growth factors and receptors coordinate genes and environment, as well as play an extremely important role during hair growth. In this review, we summarize the progresses that transcriptome sequencing technologies have achieved in researches of hair follicle development and renegeration in a variety of species, such as humans, mice, goats...
June 2015: Yi Chuan, Hereditas
Lele Wang, Yanjun Zhang, Meng Zhao, Ruijun Wang, Rui Su, Jinquan Li
The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing...
September 2015: Asian-Australasian Journal of Animal Sciences
Vijayata Choudhary, Sweta Garg, Reetika Chourasia, J J Hasnani, P V Patel, Tejas M Shah, Vaibhav D Bhatt, Amitbikram Mohapatra, Damer P Blake, Chaitanya G Joshi
Rumen flukes are parasitic trematodes (Platyhelminthes: Digenea) of major socioeconomic importance in many countries. Key representatives, such as Paramphistomum cervi, can cause "Rumen fluke disease" or paramphistomosis and undermine economic animal productivity and welfare. P. cervi is primarily a problem in sheep, goat and buffalo production as a consequence of reduced weight gain and milk production, clinical disease or death. Recent technological advances in genomics and bioinformatics now provide unique opportunities for the identification and pre-validation of drug targets and vaccines through improved understanding of the biology of pathogens such as P...
October 1, 2015: Gene
Qianzi Tang, Wenyao Huang, Jiuqiang Guan, Long Jin, Tiandong Che, Yuhua Fu, Yaodong Hu, Shilin Tian, Dawei Wang, Zhi Jiang, Xuewei Li, Mingzhou Li
Domestic goats are distributed in a wide range of habitats and have acclimated to their local environmental conditions. To investigate the gene expression changes of goats that are induced by high altitude stress, we performed RNA-seq on 27 samples from the three hypoxia-sensitive tissues (heart, lung, and skeletal muscle) in three indigenous populations from distinct altitudes (600 m, 2000 m, and 3000 m). We generated 129Gb of high-quality sequencing data (~4Gb per sample) and catalogued the expression profiles of 12,421 annotated hircine genes in each sample...
August 10, 2015: Gene
Alfredo Pauciullo, Georg Erhardt
In the present paper, we report for the first time the characterization of llama (Lama glama) caseins at transcriptomic and genetic level. A total of 288 casein clones transcripts were analysed from two lactating llamas. The most represented mRNA populations were those correctly assembled (85.07%) and they encoded for mature proteins of 215, 217, 187 and 162 amino acids respectively for the CSN1S1, CSN2, CSN1S2 and CSN3 genes. The exonic subdivision evidenced a structure made of 21, 9, 17 and 6 exons for the αs1-, β-, αs2- and κ-casein genes respectively...
2015: PloS One
Yuxuan Song, Xiaopeng An, Lei Zhang, Mingzhe Fu, Jiayin Peng, Peng Han, Jingxing Hou, Zhanqin Zhou, Bingyun Cao
BACKGROUND: MicroRNAs (miRNAs) are short, highly conserved small noncoding RNAs that had fundamental roles in post-transcriptional gene expression, and they are crucial for proper control of biological processes and known to participate in embryo implantation. However, miRNA expression profiles in the pre-receptive and receptive phases of the goat endometrium during embryo implantation are unknown. RESULTS: A total of 1,069 and 847 miRNAs were expressed in receptive (R) and pre-receptive (P) goat endometrium, and 632 miRNAs were co-expressed in both phases...
2015: PloS One
Jian Lin, Ze Kun Bao, Qiang Zhang, Wei Wei Hu, Qing Hua Yu, Qian Yang
Mammary glands are organs for milk production in female mammals. Growth hormone (GH) is known to affect the growth and development of the mammary gland, as well as to increase milk production in dairy goats. This study performed a comprehensive expression profiling of genes expressed in the mammary gland of early involution GH transgenic (n=4) and non-transgenic goats (n=4) by RNA sequencing. RNA was extracted from mammary gland tissues collected at day 3 of involution. Gene expression analysis was conducted by Illumina RNA sequencing and sequence reads were assembled and analyzed using TopHat...
July 10, 2015: Gene
Siddappa Manjunath, Gandham Ravi Kumar, Bishnu Prasad Mishra, Bina Mishra, Aditya Prasad Sahoo, Chaitanya G Joshi, Ashok K Tiwari, Kaushal Kishore Rajak, Sarath Chandra Janga
Peste des petits ruminants (PPR), is an acute transboundary viral disease of economic importance, affecting goats and sheep. Mass vaccination programs around the world resulted in the decline of PPR outbreaks. Sungri 96 is a live attenuated vaccine, widely used in Northern India against PPR. This vaccine virus, isolated from goat works efficiently both in sheep and goat. Global gene expression changes under PPR vaccine virus infection are not yet well defined. Therefore, in this study we investigated the host-vaccine virus interactions by infecting the peripheral blood mononuclear cells isolated from goat with PPRV (Sungri 96 vaccine virus), to quantify the global changes in the transcriptomic signature by RNA-sequencing...
2015: Veterinary Research
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