Fukuan Du1,2, Yan Li2, Zhixin Wen1, Ruguo Chen1 and Pao Xu2*
...developed SSR markers by transcriptome, which could be used to genetic research. In this study, we performed transcriptome sequencing of six libraries from hepatopancreas samples in E. sinensis. After removing low-quality reads, short reads and reads belonging to mitochondria, a total of 278,260,960 clean reads corresponding to mRNAs were obtained, these reads covered a total of 34,780,598,273 bases. A total of 48,657 SSR lo...
Sung Kwon Park1a, Jin Young Jeong2a, Eun Seok Cho3, Yong Dae Jeong3 and Chang Seok Park4*
...is study was to identify transcriptomes with RNA sequencing (RNA-seq) in peripheral blood mononucleated cell (PBMC) of piglets, Large White x Landrace crossbreds, infected with live strain PED virus (PEDV). Several gene ontology (GO) and differentially expressed gene (DEG) are also identified by RNA-seq. The analyzed transcriptome provides the 1805 DEGs and gene networks involving cellular processes. Between vaccinated and u...
Yi-qiang Ouyang1, Zhen-xin Liang1, Shi-wen Huang2, Ying Zhang3, Shao-shi Luo1, Jin-ning Liang1, Jia-fu Li1, Yu He4 and Song-chao Guo1,*
...anges in the hippocampal transcriptome induced by injection of the three AD agents. These results open the door to new small-animal studies of AD that complement and extend studies in rodents and primates.
...
Guang-Xin E1, Yong-Ju Zhao1, Yue-Hui Ma2, Ming-Xing Chu2, Jia-Hua Zhang1, Zhong-Quan Zhao1, Hui-Jiang Gao2, Huai-Zhi Jiang3, Di Liu4, Li Liu5, Yan-Bin Zhu6, Wang-Dui Basang6, Luo-Bu Danjiu7, Tian-Wu An8, Xiao-Lin Luo8, Shi-Cheng He7 and Yong-Fu Huang1,*
...ogy to provide the first transcriptome dataset for differentially expressed genes in mixed pools of dominant and nondominant follicles of goats. These data will contribute to research on the molecular mechanisms of dominant follicle selection in goats. In this study, 90276370 and 115579236 clear reads in dominant and nondominant follicles of goat were generated through Illumina paired-end sequencing, and their mapping rate was 84.99% and 84.47%, respectively. ...
RuiHua Zhang, YongFang Jia, TingTing Liang, QianWen Yang, QiYan Du and ZhongJie Chang*
...>SoxD sequences from transcriptome sequencing data of carp: CcSox5, CcSox6 and CcSox13 (Cyprinus carpio SoxD).These genes were verified by sequencing, blast and homology alignment. CcSoxD have two to four exons and encode a 780, 784 and 602 amino acid protein, respectively. Chromosome synteny analyses revealed that CcSox5 and CcSox13 weretightly linked with the etnk gene, which was conserved in all sp...
Guifen Liu1,2, Xiaomu Liu1,2, Khuram Shahzad3, Wei You1,2, Juan J. Loor3,* and Fachun Wan1,2,4,*
...erefore, we analyzed the transcriptome changes within adipose tissue in beef cattle at different stages of growth. Microarray analysis of data at 12 vs 18 months, 12 vs 24 months, 12 vs 30 months, 18 vs 24 months, 18 vs 30 months and 24 vs 30 months uncovered a total of 10625 differentially expressed genes (P ≤ 0.05; no fold change). The dynamic impact approach (DIA) bioinformatics tool was used to uncover the most-affected biological pathways among the DEG...
Jingen Xu1, Yang Liu2, Erhui Jin1, Youfang Gu1, Qin Zhang3 and Shenghe Li1,*
...fferences, so we studied transcriptome profiles in spleens of Yorkshire pigs with different peripheral blood T lymphocyte subsets. The results showed that 2050 differentially expressed transcripts were identified, with 1554 up-regulated and 496 up-regulated in high and low T lymphocyte groups, respectively. Among differentially expressed genes, IL1B, IL17F, IL6R, CXCL2, CCL20 and CCL25 were selected based on their immunological functions and C...
Binbin Shan, Yan Liu, Changping Yang, Shengnan Liu and Dianrong Sun*
..., we generated the whole transcriptome of Penaeus penicillatus from four combined tissues (eyestalk, muscle, intestinal and viscus) using High-seq sequencing technology. A total of 65,703,216 high-quality clean reads were generated to produce 27,850 non-redundant transcripts with a mean length of 918 nt using Trinity and Tgicl software. For homological alignment, 13,083 unigenes had significant hits in Nr database. And then, 10,467 unigenes were annotat...
Fukuan Du1,2, Yongkai Tang1, Juhua Yu1, Shengyan Su1, Fan Yu1, Jianlin Li1, Hongxia Li1, Meiyao Wang1 and Pao Xu1,2,*
..., we sequenced the brain transcriptome of C. nasus using Illumina Hiseq 4000 platform. We obtained 123,764 unigenes with an average length of 1092 bp and a total of 115,169 putative Simple Sequence Repeats (SSRs). Among them, 37 SSRs were selected for the validation experiments. All of the loci were found to be polymorphic and showed bi-allelic in 60 individuals of C. nasus. These SSR markers should not only be useful for population conservation,...
Songhao Zhang1, Yiwen Gong1, Jian Xu1, Mou Hu2, Peng Xu3 and Yanliang Jiang1,2,4,*
... approach of comparative transcriptome analysis via high throughput sequencing, and examined transcriptome profiles of purse red carp by comparing with Yellow River carp, of which the skin color and body shape are quite similar to wild carp. A total of 434 million reads was generated, resulted in 203,590 assembled contigs, which was used as the reference sequences. Comparing the skin and blood transc...
Lei Wang1, Lu Yang2, Lei Luo1, Yaqi Gao1*, Jian Gao1 and Ping Liu1
...d 142.65 Gb of data from transcriptome sequencing and recovered 70,397 unigenes through a de novo assembly. In total, 2089, 2420, and 6286 differentially expressed genes were gained from comparing groups of male adults, female adults, and pupa of A. cinerarius, respectively. In addition, 27715 SSR markers were obtained and the SNP site was identified. The results revealed the differences between A. cinerarius in southern and northern Xinji...
Yue Qin Song, Hui Zhong Sun* and Jun Feng Dong
...female and male antennal transcriptomes of Yemma signatus adults, a total of 66 candidate Y. signatus olfactory receptor genes (YsigORs), including one olfactory co-receptor (Orco), were identified in this study. All the sequences were further validated by cloning and sequencing. Tissue expression profiles of all YsigOR genes in the antennae of females and males were analyzed using real-time quantitative PCR (RT-qPCR). The result showed that some...
Hong Hu1, 2, Li Qian1, Yuanlang Wang1, Chaodong Wu1, Xiaodong Zhang1, Yueyun Ding 1*, Li Wang1, Xudong Wu1, Wei Zhang1, Dengtao Li1, Jian Ding1, Min Yang1 and Zongjun Yin1*
...rkshire (lean) pigs. The transcriptome profiling of backfat between Anqingliubai and Yorkshire pigs was carried out by RNA-sequencing technology. The sum of clean reads were 288.3 and 365.3 million which was obtained from the RNA sequencing data in the Anqingliubai and Yorkshire pigs, respectively. Most reads were located in exonic region, while less reads were located in intergenic and intronic regions. There were 2601 upregulated genes, but 284 downregulated...
Fan Sigang1, Guo Yihui1* and Xu Youhou2
Shuang Yang1,2, Huiting Zhao3, Xuewen Zhang2, Kai Xu1, Lina Guo1, Yali Du1 and Yusuo Jiang1,*
...ucidated. In this study, transcriptome sequencing was conducted on the antennae of male and female greater wax moths to assess the differential expression patterns of chemosensory genes and better understand the underlying olfactory mechanism. In the results, a total of 121 chemosensory gene transcripts were identified, including 37 odorant-binding proteins, 35 chemosensory proteins, 33 olfactory receptors, 14 ionotropic receptors and 2 sensory neuron membrane...
Guan-bao Ning1, Sheng Niu1, Yue-jian Li1,2, Xiao-xiao Lu1,3, Shi-xiong Yang1, Ali-Raza Jahejo1, Ding Zhang1, Wei-fang Hao4, Wen-wei Gao1, Yu-jun Zhao1, Jian-hui Li1, Fang Yan1, Rong-kun Gao1, Yu-hai Bi1,5, Wen-xia Tian1* and Ling-xia Han6*
...ythrocytes of chicken by transcriptome analysis. Twenty specific pathogen-free (SPF) chickens were divided into two groups as control and treatment. The chickens of treatment group were inoculated with MDV, and blood samples of two groups were obtained at 14 and 22 days post-infection (dpi) for RNA extraction. Transcriptome analysis was performed to explore the immune responses of chicken erythrocytes to MDV infection at 14 ...
Hui-Ming Li1, Bi-Ze Yang1, Xue-Jun Jin1,2, Lin-Miao Li1, Hai-Ying Jiang1,
Xiu-Juan Zhang1 and Jin-Ping Chen1*
...solated from full-length transcriptome and they were used for assessing of parent-offspring relationship for M. javanica. All SSR markers were highly polymorphic with a mean of 6 alleles per locus, ranged from 2 to 10 alleles. The average polymorphism information content (PIC) was 0.62. The observed (HO) and expected average heterozygosity (HE) value was 0.56 and 0.67 tested in 39 individual samples. For parentage tes...
Guo-dong Zhao1,2*, He-ying Qian1,2, Yi-ling Zhang1,2, Gang Li1, 2, Jian Tang1, 2 and An-ying Xu1,2*
...s study, high-throughput transcriptome sequencing was performed to investigate the gene expression differences between two silkworm strains with different susceptibility after exposure to fenvalerate. The results showed that a total of 2363 differentially expressed genes were detected in the Lan5 DGE library and 1611 were detected in the Mysore DGE library, respectively. The possible functions of all DEGs were determined using the gene ontology (GO) classifica...
Jinzhao He1, Pengfei Feng2, Junqi Qin2, Yun Teng1, Xu Luo2*, Zigui Chen1*, Huawei Ma2* and Dayan Zhou1
...ed. Besides, comparative transcriptome analysis was used to screen the candidate genes linked to the skin color differentiation of pearl white red tilapia. Among them, the body color of Guam red tilapia changed when the water temperature dropped to 16-14°C, and continued to drop to about 11°C, it was discolored in a large area reaching above 90%. According to the differential analysis: Tyrosine Kinase STYK1, HSP70, HSP30 and Transcription factor Sp6 ex...
Dong-Min Hou1, Ting Jia2, Hui-Juan Wang1, Zheng-Kun Wang1 and Wan-Long Zhu1*
...d. In the present study, transcriptome sequencing of BAT in Tupaia belangeri between control and cold acclimation group were carried out by Illumina novaseq 6000 platform. Then the pathways and key genes related to lipid metabolism and energy metabolism were screened out by bioinformatics analysis. The results showed that there were significant differences in the expression of 2879 genes in cold acclimation group compared with that of control group, 1181 were ...
Yue Guo1,2*, Hui Zhang1, Chun Sheng Wang1 and Hong Chang Zhou1
...essed.In this study, the transcriptome of adult female Angiostrongylus cantonensis was analyzed and successfully annotated. Metabolism and parasitism related genes were highly expressed at adult female A. cantonensis....
Jie Wang1, Di Fang1, Jianqing Zhao1, Fei Huang2, Bo Liu2, Weikun Tao2, Baoshan Cui2 and Qinghua Gao1,2,3*
...Over the past few years, transcriptome sequencing has been applied to livestock and poultry, helping to select and investigate candidate genes associated with important traits. Yet, so far, only a few studies have reported differences in single-cell transcriptome between bovine embryos of different genders. In this study, we performed transcriptome analysis of cattle embryos based on a sin...
Wei Fang1,2,3, Jiawei Hong1,2,3,4, Zhengyi Fu1,2,3, Jing Hu1,2,3, Gang Yu1,2,3, Zhenhua Ma1,2,3* and Humin Zong5*
...platform to sequence the transcriptome of E. fuscoguttatus, the transcriptome data clustered by TGICL to obtain Unigene, and bioinformatics methods were then adopted to perform functional annotation classification, metabolic pathways and SSR feature analysis. The results showed that a total of 42.40 Gb data were obtained from transcriptome sequencing, and 38,817 Unigenes were obtained afte...
Zhengfei Wang1*, Chenchen Shen1,2, Yiping Zhang1, Dan Tang1,3, Yaqi Luo1, Yaotong Zhai1, Yayun Guan1, Yue Wang1 and Xinyu Wang1
...conducted the antennules transcriptome of Procambarus clarkii and identified 26 olfactory-related genes, including nine ionotropic receptors, two ionotropic glutamate receptors, ten variant ionotropic glutamate receptors, four cytochrome P450s, and one carboxylesterase. Our study suggested that ionotropic receptors were the main odorant receptors in Procambarus clarkii. Additionally, the key genes that are responsible for olfactory transduction in Procambarus ...
Hong Chen1,2, Jiawei Liu1,2, Chuan Lin1,2, Hao Lv1,2, Jiyun Zhang1,2, Xiaodong Jia1,2, Qinghua Gao1,2 and Chunmei Han1,2*
...top pruning damage using transcriptome sequencing technology. A damage repair model was constructed by top pruning treatment on the left antlers of three 10-month-old Tarim red deer, and RNA-seq analysis was performed on the Illumina platform to compare the transcriptome sequencing results of the left regenerated antlers with the right healthy antlers. Among a total of 56 differentially expressed genes (DEGs) that were scree...
