51
|
Characterization of Embryonic Skin Transcriptome in Anser cygnoides at Three Feather Follicles Developmental Stages. G3-GENES GENOMES GENETICS 2020; 10:443-454. [PMID: 31792007 PMCID: PMC7003092 DOI: 10.1534/g3.119.400875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In order to enrich the Anser cygnoides genome and identify the gene expression profiles of primary and secondary feather follicles development, de novo transcriptome assembly of skin tissues was established by analyzing three developmental stages at embryonic day 14, 18, and 28 (E14, E18, E28). Sequencing output generated 436,730,608 clean reads from nine libraries and de novo assembled into 56,301 unigenes. There were 2,298, 9,423 and 12,559 unigenes showing differential expression in three stages respectively. Furthermore, differentially expressed genes (DEGs) were functionally classified according to genes ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and series-cluster analysis. Relevant specific GO terms such as epithelium development, regulation of keratinocyte proliferation, morphogenesis of an epithelium were identified. In all, 15,144 DEGs were clustered into eight profiles with distinct expression patterns and 2,424 DEGs were assigned to 198 KEGG pathways. Skin development related pathways (mitogen-activated protein kinase signaling pathway, extra-cellular matrix -receptor interaction, Wingless-type signaling pathway) and genes (delta like canonical Notch ligand 1, fibroblast growth factor 2, Snail family transcriptional repressor 2, bone morphogenetic protein 6, polo like kinase 1) were identified, and eight DEGs were selected to verify the reliability of transcriptome results by real-time quantitative PCR. The findings of this study will provide the key insights into the complicated molecular mechanism and breeding techniques underlying the developmental characteristics of skin and feather follicles in Anser cygnoides.
Collapse
|
52
|
Zhao Q, Chen J, Zhang X, Xu Z, Lin Z, Li H, Lin W, Xie Q. Genome-Wide Association Analysis Reveals Key Genes Responsible for Egg Production of Lion Head Goose. Front Genet 2020; 10:1391. [PMID: 32047514 PMCID: PMC6997537 DOI: 10.3389/fgene.2019.01391] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/19/2019] [Indexed: 11/13/2022] Open
Abstract
The lion head goose is one of the most important agricultural resources in China; however, its breeding process is relatively slow. In the present study, a genome-wide association study was performed for the genetic selection of egg production characters in lion head geese. We detected 30 single-nucleotide polymorphisms located in or near 30 genes that might be associated with egg production character, and quantitative real-time polymerase chain reaction was used to verify their expression level in lion head geese. The results showed that the expression levels of CRTC1 (encoding CREB-regulated transcription coactivator 1), FAAH2 (encoding fatty acid amide hydrolase 2), GPC3 (encoding glypican 3), and SERPINC1 (encoding serpin family C member 1) in high egg production population were significantly lower than those in the low egg production populations (*P < 0.05). The expression levels of CLPB (encoding caseinolytic peptidase B protein homolog), GNA12 (encoding guanine nucleotide-binding protein subunit alpha-12), and ZMAT5 (encoding zinc finger, matrin type 5) in the high egg production population were significantly higher than those in the low egg production populations (*P < 0.05). The expression of BMP4 (encoding bone morphogenetic protein 4), FRMPD3 (encoding FERM and PDZ domain containing 3), LIF (encoding leukemia inhibitory factor), and NFYC (encoding nuclear transcription factor Y subunit gamma) in the high egg production population were very significantly lower than those in the low egg production population (**P < 0.01). Our findings provide an insight into the economic traits of lion head goose. These candidate genes might be valuable for future breeding improvement.
Collapse
Affiliation(s)
- Qiqi Zhao
- College of Animal Science, South China Agricultural University and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Junpeng Chen
- Shantou Baisha Research Institute of Original Species of Poultry and Stock, Shantou, China
| | - Xinheng Zhang
- College of Animal Science, South China Agricultural University and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Zhouyi Xu
- College of Animal Science, South China Agricultural University and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Zhenping Lin
- Shantou Baisha Research Institute of Original Species of Poultry and Stock, Shantou, China
| | - Hongxin Li
- College of Animal Science, South China Agricultural University and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Wencheng Lin
- College of Animal Science, South China Agricultural University and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University and Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou, China
- Key Laboratory of Animal Health Aquaculture and Environmental Control, Guangzhou, China
| |
Collapse
|
53
|
Liu X, Li P, He C, Qu X, Guo S. Comparison of overfed Xupu and Landes geese in performance, fatty acid composition, enzymes and gene expression related to lipid metabolism. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:1957-1964. [PMID: 32054153 PMCID: PMC7649397 DOI: 10.5713/ajas.19.0842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/10/2020] [Indexed: 11/27/2022]
Abstract
Objective The aim of this study was to compare overfeeding performance, fatty acid composition, blood chemistry, enzymes and genes expression overfed Xupu and Landes geese. Methods Sixty male Xupu geese (80 d) and Landes geese (80 d) were selected. After a period of one-week of pre-overfeeding, Xupu and Landes geese were overfed three meals of 550 and 350 g/d, respectively, of a high-carbohydrate diet in the first week of the overfeeding period. The next week, geese were given four meals of 1,200 and 850 g/d, respectively, over 8 to 14 d. Finally, geese were given five meals of 1,600 and 1,350 g/d, respectively, for the last two weeks. Results After overfeeding for 28 d: Compared with Landes geese, Xupu geese liver weight and liver-to-body weight ratio decreased (p<0.05), while final weight, slaughter weight, total weight gain, abdominal fat weight, and feed-to-liver weight ratio increased (p<0.05). The levels of elaidic acid (C18:1t9), oleic acid (C18:1n-9), eicosenoic acid, and arachidonic acid in the liver of Xupu geese significantly increased (p<0.05), and the levels of myristic acid and stearic acid significantly decreased (p<0.05), while methyleicosanoate acid significantly increased (p<0.05). Xupu geese had higher plasma concentrations of triglyceride and very low density lipoprotein cholesterol (p<0.05), and decreased activities of alanine aminotransferase, aspartate aminotransferase, and lipase (LPS) (p<0.05). Landes geese had higher LPS activity (p<0.05), but lower cholinesterase activity (p<0.05) when compared with Xupu geese. The mRNA expression levels of fatty acid dehydrogenase (FADS) gene, elongase of long-chain fatty acid 1 (ELOVL1) gene, ELOVL5, and acyl-Co A: cholesterol acyltransferase 2 (ACAT2) gene were significantly upregulated (p<0.05) in Landes goose when compared with Xupu geese. Conclusion This study demonstrates that the liver production performance of Landes geese was better than that of Xupu geese to some extent, which may be closely related to LPS activity, as well as the expression of FADS, ELOVL1, ELOVL5, and ACAT2.
Collapse
Affiliation(s)
- Xu Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China.,Hunan Engineering Research Center of Poultry Production Safety, Hunan 410128, China.,Hunan Co-Innovation Center of Animal Production Safety, Changsha, Hunan 410128, China
| | - Peng Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China.,Hunan Engineering Research Center of Poultry Production Safety, Hunan 410128, China.,Hunan Co-Innovation Center of Animal Production Safety, Changsha, Hunan 410128, China
| | - Changqing He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China.,Hunan Engineering Research Center of Poultry Production Safety, Hunan 410128, China.,Hunan Co-Innovation Center of Animal Production Safety, Changsha, Hunan 410128, China
| | - Xiangyong Qu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China.,Hunan Engineering Research Center of Poultry Production Safety, Hunan 410128, China.,Hunan Co-Innovation Center of Animal Production Safety, Changsha, Hunan 410128, China
| | - Songchang Guo
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China.,Hunan Engineering Research Center of Poultry Production Safety, Hunan 410128, China.,Hunan Co-Innovation Center of Animal Production Safety, Changsha, Hunan 410128, China
| |
Collapse
|
54
|
Li X, Zheng Z, Pan J, Jiang D, Tian Y, Huang Y. Influences of melatonin and endotoxin lipopolysaccharide on goose productive performance and gut microbiota. Br Poult Sci 2019; 61:217-224. [DOI: 10.1080/00071668.2019.1687851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- X. Li
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, P. R. China
| | - Z. Zheng
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, P. R. China
| | - J. Pan
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, P. R. China
| | - D. Jiang
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, P. R. China
| | - Y. Tian
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, P. R. China
| | - Y. Huang
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, P. R. China
| |
Collapse
|
55
|
Zhou C, Tu H, Yu H, Zheng S, Dai B, Price M, Wu Y, Yang N, Yue B, Meng Y. The Draft Genome of the Endangered Sichuan Partridge ( Arborophila rufipectus) with Evolutionary Implications. Genes (Basel) 2019; 10:E677. [PMID: 31491910 PMCID: PMC6770966 DOI: 10.3390/genes10090677] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 12/17/2022] Open
Abstract
The Sichuan partridge (Arborophila rufipectus, Phasianidae, Galliformes) is distributed in south-west China, and classified as endangered grade. To examine the evolution and genomic features of Sichuan partridge, we de novo assembled the Sichuan partridge reference genome. The final draft assembly consisted of approximately 1.09 Gb, and had a scaffold N50 of 4.57 Mb. About 1.94 million heterozygous single-nucleotide polymorphisms (SNPs) were detected, 17,519 protein-coding genes were predicted, and 9.29% of the genome was identified as repetitive elements. A total of 56 olfactory receptor (OR) genes were found in Sichuan partridge, and conserved motifs were detected. Comparisons between the Sichuan partridge genome and chicken genome revealed a conserved genome structure, and phylogenetic analysis demonstrated that Arborophila possessed a basal phylogenetic position within Phasianidae. Gene Ontology (GO) enrichment analysis of positively selected genes (PSGs) in Sichuan partridge showed over-represented GO functions related to environmental adaptation, such as energy metabolism and behavior. Pairwise sequentially Markovian coalescent analysis revealed the recent demographic trajectory for the Sichuan partridge. Our data and findings provide valuable genomic resources not only for studying the evolutionary adaptation, but also for facilitating the long-term conservation and genetic diversity for this endangered species.
Collapse
Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China.
| | - Hongmei Tu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China.
| | - Haoran Yu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China.
| | - Shuai Zheng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China.
| | - Bo Dai
- College of Life Sciences, Leshan Normal University, Leshan 614004, China.
| | - Megan Price
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China.
| | - Yongjie Wu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China.
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610064, China.
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China.
| | - Yang Meng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China.
| |
Collapse
|
56
|
Temperature affects liver and muscle metabolism in photostimulated migratory redheaded buntings (Emberiza bruniceps). J Comp Physiol B 2019; 189:623-635. [DOI: 10.1007/s00360-019-01229-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 08/07/2019] [Indexed: 10/26/2022]
|
57
|
Ren J, Sun C, Chen L, Hu J, Huang X, Liu X, Lu L. Exploring differentially expressed key genes related to development of follicle by RNA-seq in Peking ducks (Anas Platyrhynchos). PLoS One 2019; 14:e0209061. [PMID: 31237879 PMCID: PMC6592512 DOI: 10.1371/journal.pone.0209061] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 06/04/2019] [Indexed: 01/10/2023] Open
Abstract
Duck follicles enter different reproductive phases throughout life, and follicle gene expression patterns differ according to these phases. In particular, differentially expressed genes and related to development of follicle (mRNAs) play an important role to explore the key genes in this process; however, the expression profiles of these genes remain unclear. In this study, transcriptome sequencing was used to investigate the expression levels of duck ovarian genes, and comparative transcriptional analysis was carried out to identify differential genes, and cluster them into groups and function identification. The results showed differential expression of 593 coding genes between young and laying ducks, and of 518 coding genes between laying and old ducks. In further GO analysis, 35 genes from the comparison between old ducks and laying ducks have significant been changed involved in hormones related to follicle development. They include up-regulated genes StAR, CYP17, EPOX, 3β-HSD, CYP1B1 CYP19A1 and down-regulated genes SR-B1 in laying ducks hormone synthesis than old ducks. Among which EPOX is a key gene for time special highly expression during egg laying stage, and other key regulatory genes' highly expression showed in young and laying stage, and lower expression showing with follicular development stopping. Therefore, EPOX is a key regulator for duck follicle development in laying period, its expression level increase 100 times higher than in youth and decrease 98% than stop laying period in duck life cycle.
Collapse
Affiliation(s)
- Jindong Ren
- School of Life Science, Taizhou University, Taizhou, Zhejiang, People’s Republic of China
| | - Changsen Sun
- School of Life Science, Taizhou University, Taizhou, Zhejiang, People’s Republic of China
| | - Li Chen
- Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, People’s Republic of China
| | - Jianhong Hu
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, Shaanxi, People’s Republic of China
| | - Xuetao Huang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, People’s Republic of China
| | - Xiaolin Liu
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, Shaanxi, People’s Republic of China
| | - Lizhi Lu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, People’s Republic of China
| |
Collapse
|
58
|
Wang G, Jin L, Li Y, Tang Q, Hu S, Xu H, Gill CA, Li M, Wang J. Transcriptomic analysis between Normal and high-intake feeding geese provides insight into adipose deposition and susceptibility to fatty liver in migratory birds. BMC Genomics 2019; 20:372. [PMID: 31088359 PMCID: PMC6518675 DOI: 10.1186/s12864-019-5765-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/03/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Dysregulation of adipogenesis causes metabolic diseases, like obesity and fatty liver. Migratory birds such as geese have a high tolerance of massive energy intake and exhibit little pathological development. Domesticated goose breeds, derivatives of the wild greyleg goose (Anser anser) or swan goose (Anser cygnoides), have high tolerance of energy intake resembling their ancestor species. Thus, goose is potentially a model species to study mechanisms associated with adipogenesis. RESULTS Phenotypically, goose liver exhibited higher fat accumulation than adipose tissues during fattening (liver increased by 3.35 fold than 1.65 fold in adipose), showing a priority of fat accumulation in liver. We found the number of differentially expressed genes in liver (13.97%) was nearly twice the number of that in adipose (6.60%). These differentially expressed genes in liver function in several important lipid metabolism pathways, immune response, regulation of cancer, while in adipose, terms closely related to protein binding, gluconeogenesis were enriched. Typically, genes like MDH2 and SCD, which have key roles in glycolysis and fatty acids metabolism, had higher fold change in liver than in adipose tissues. Three hundred two differentially expressed long noncoding RNAs involved in regulation of metabolism in liver were also identified. For example, lncRNA XLOC_292762, which was 5.7 kb downstream of FERMT2, a gene involved phosphatidylinositol-3,4,5-trisphosphate binding, was significantly down-regulated after the high-intake feeding period. Further investigation of documented obesity-related orthologous genes in goose suggested that understanding the evolutionary split from mammals in adipogenesis will make goose fatty liver a better resource for future research. CONCLUSIONS Our research reveals that goose uses liver as the major tissue to regulate a distinct lipid synthesis and degradation flux and the dynamic expression network analyses showed numerous layers of positive responses to both massive energy intake and possible pathological development. Our results offer insights into goose adipogenesis and provide a new perspective for research in human metabolic dysregulation.
Collapse
Affiliation(s)
- Guosong Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, People's Republic of China.,Department of Animal Science, Texas A&M University, College Station, TX, 77843, USA
| | - Long Jin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, People's Republic of China
| | - Yan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, People's Republic of China
| | - Qianzi Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, People's Republic of China
| | - Silu Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, People's Republic of China
| | - Hengyong Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, People's Republic of China
| | - Clare A Gill
- Department of Animal Science, Texas A&M University, College Station, TX, 77843, USA
| | - Mingzhou Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, People's Republic of China.
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, People's Republic of China.
| |
Collapse
|
59
|
Hérault F, Houée-Bigot M, Baéza E, Bouchez O, Esquerré D, Klopp C, Diot C. RNA-seq analysis of hepatic gene expression of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed. BMC Genomics 2019; 20:13. [PMID: 30616512 PMCID: PMC6323773 DOI: 10.1186/s12864-018-5415-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/26/2018] [Indexed: 01/07/2023] Open
Abstract
Background Duck species are known to have different susceptibility to fatty liver production in response to overfeeding. In order to better describe mechanisms involved in the development of hepatic steatosis and differences between species, transcriptome analyses were conducted on RNAs extracted from the livers of Pekin and Muscovy duck species and of their reciprocal hybrids, Mule and Hinny ducks fed ad libitum or overfed to identify differentially expressed genes and associated functions. Results After extraction from the liver of ducks from the four genetic types, RNAs were sequenced and sequencing data were analyzed. Hierarchic clustering and principal component analyses of genes expression levels indicated that differences between individuals lie primarily in feeding effect, differences between genetic types being less important. However, Muscovy ducks fed ad libitum and overfed were clustered together. Interestingly, Hinny and Mule hybrid ducks could not be differentiated from each other, according to feeding. Many genes with expression differences between overfed and ad libitum fed ducks were identified in each genetic type. Functional annotation analyses of these differentially expressed genes highlighted some expected functions (carbohydrate and lipid metabolisms) but also some unexpected ones (cell proliferation and immunity). Conclusions These analyses evidence differences in response to overfeeding between different genetic types and help to better characterize functions involved in hepatic steatosis in ducks. Electronic supplementary material The online version of this article (10.1186/s12864-018-5415-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Frédéric Hérault
- PEGASE, INRA, Agrocampus Ouest, 16 Le Clos, 35590, Saint-Gilles, France
| | | | | | - Olivier Bouchez
- GENPhySE, INRA, ENVT, ENSAT, 31326, Castanet-Tolosan, France.,GeT PlaGE, INRA, US 1426, GenoToul, 31326, Castanet-Tolosan, France
| | - Diane Esquerré
- GENPhySE, INRA, ENVT, ENSAT, 31326, Castanet-Tolosan, France.,GeT PlaGE, INRA, US 1426, GenoToul, 31326, Castanet-Tolosan, France
| | - Christophe Klopp
- Bioinformatics facility, INRA, Genotoul, 31326, Castanet-Tolosan, France.,SIGENAE, INRA, 31326, Castanet-Tolosan, France
| | - Christian Diot
- PEGASE, INRA, Agrocampus Ouest, 16 Le Clos, 35590, Saint-Gilles, France.
| |
Collapse
|
60
|
Wang Q, Lu W, Yang J, Jiang L, Zhang Q, Kan X, Yang X. Comparative transcriptomics in three Passerida species provides insights into the evolution of avian mitochondrial complex I. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 28:27-36. [DOI: 10.1016/j.cbd.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 02/02/2023]
|
61
|
Lee CY, Hsieh PH, Chiang LM, Chattopadhyay A, Li KY, Lee YF, Lu TP, Lai LC, Lin EC, Lee H, Ding ST, Tsai MH, Chen CY, Chuang EY. Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant. Gigascience 2018; 7:4990948. [PMID: 29722814 PMCID: PMC5941149 DOI: 10.1093/gigascience/giy044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 04/13/2018] [Indexed: 01/10/2023] Open
Abstract
Background The Mikado pheasant (Syrmaticus mikado) is a nearly endangered species indigenous to high-altitude regions of Taiwan. This pheasant provides an opportunity to investigate evolutionary processes following geographic isolation. Currently, the genetic background and adaptive evolution of the Mikado pheasant remain unclear. Results We present the draft genome of the Mikado pheasant, which consists of 1.04 Gb of DNA and 15,972 annotated protein-coding genes. The Mikado pheasant displays expansion and positive selection of genes related to features that contribute to its adaptive evolution, such as energy metabolism, oxygen transport, hemoglobin binding, radiation response, immune response, and DNA repair. To investigate the molecular evolution of the major histocompatibility complex (MHC) across several avian species, 39 putative genes spanning 227 kb on a contiguous region were annotated and manually curated. The MHC loci of the pheasant revealed a high level of synteny, several rapidly evolving genes, and inverse regions compared to the same loci in the chicken. The complete mitochondrial genome was also sequenced, assembled, and compared against four long-tailed pheasants. The results from molecular clock analysis suggest that ancestors of the Mikado pheasant migrated from the north to Taiwan about 3.47 million years ago. Conclusions This study provides a valuable genomic resource for the Mikado pheasant, insights into its adaptation to high altitude, and the evolutionary history of the genus Syrmaticus, which could potentially be useful for future studies that investigate molecular evolution, genomics, ecology, and immunogenetics.
Collapse
Affiliation(s)
- Chien-Yueh Lee
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Ping-Han Hsieh
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Li-Mei Chiang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Amrita Chattopadhyay
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Kuan-Yi Li
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.,Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Fang Lee
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Liang-Chuan Lai
- Graduate Institute of Physiology, National Taiwan University, Taipei 10051, Taiwan
| | - En-Chung Lin
- Department of Animal Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsinyu Lee
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan.,Department of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan
| | - Shih-Torng Ding
- Department of Animal Science and Technology, National Taiwan University, Taipei 10617, Taiwan.,Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei 10055, Taiwan.,Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Institute of Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan University, Taipei, Taiwan
| | - Chien-Yu Chen
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.,Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Center for Systems Biology, National Taiwan University, Taipei 10672, Taiwan
| | - Eric Y Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan.,Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei 10055, Taiwan.,Graduate Institute of Chinese Medical Science, China Medical University, Taichung 40402, Taiwan
| |
Collapse
|
62
|
Tang J, Fang Q, Shao R, Shen J, He J, Niu D, Lu L. Digital gene-expression profiling analysis of the fatty liver of Landes geese fed different supplemental oils. Gene 2018; 673:32-45. [DOI: 10.1016/j.gene.2018.05.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/08/2018] [Accepted: 05/31/2018] [Indexed: 01/18/2023]
|
63
|
Birth and death of Mx genes and the presence/absence of genes regulating Mx transcription are correlated with the diversity of anti-pathogenicity in vertebrate species. Mol Genet Genomics 2018; 294:121-133. [DOI: 10.1007/s00438-018-1490-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/08/2018] [Indexed: 12/20/2022]
|
64
|
An intercross population study reveals genes associated with body size and plumage color in ducks. Nat Commun 2018; 9:2648. [PMID: 30018292 PMCID: PMC6050300 DOI: 10.1038/s41467-018-04868-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 05/31/2018] [Indexed: 12/15/2022] Open
Abstract
Comparative population genomics offers an opportunity to discover the signatures of artificial selection during animal domestication, however, their function cannot be directly revealed. We discover the selection signatures using genome-wide comparisons among 40 mallards, 36 indigenous-breed ducks, and 30 Pekin ducks. Then, the phenotypes are fine-mapped based on resequencing of 1026 ducks from an F2 segregating population generated by wild × domestic crosses. Interestingly, the two key economic traits of Pekin duck are associated with two selective sweeps with fixed mutations. A novel intronic insertion most possibly leads to a splicing change in MITF accounted for white duck down feathers. And a putative long-distance regulatory mutation causes continuous expression of the IGF2BP1 gene after birth which increases body size by 15% and feed efficiency by 6%. This study provides new insights into genotype-phenotype associations in animal research and constitutes a promising resource on economically important genes in fowl.
Collapse
|
65
|
Tang J, Fang Q, Lu M, Shao R, Shen J, Lu L, Niu D. The Effect of Hydrated Sodium Calcium Aluminosilicate on Fatty Liver and the Composition of the Intestinal Microbiota in Overfed Landes Geese. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2018. [DOI: 10.1590/1806-9061-2017-0499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- J Tang
- Zhejiang University, China; Zhejiang Academy of Agricultural Sciences, China
| | - Q Fang
- Zhejiang Academy of Agricultural Sciences, China
| | - M Lu
- Kaier Environmental Technology Co., Ltd. of Hangzhou, China
| | - R Shao
- Rongyao goose industry Co., Ltd of Changxing, China
| | - J Shen
- Zhejiang Academy of Agricultural Sciences, China
| | - L Lu
- Zhejiang Academy of Agricultural Sciences, China
| | - D Niu
- Zhejiang University, China
| |
Collapse
|
66
|
First de novo whole genome sequencing and assembly of the pink-footed goose. Genomics 2018; 110:75-79. [DOI: 10.1016/j.ygeno.2017.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/24/2017] [Accepted: 08/26/2017] [Indexed: 11/17/2022]
|
67
|
Tang J, Lu M, Fang Q, Lu F, Shao R, Shen J, Lu D, He J, Lu L, Niu D. Effects of hydrated sodium calcium aluminosilicate on growth performance, fatty liver, intestine morphology, and serum parameters of overfed geese. ANIMAL PRODUCTION SCIENCE 2018. [DOI: 10.1071/an16823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In geese, overfeeding induces hepatic steatosis and makes the liver functions enhanced. Aluminosilicate absorbs toxins created by moulds in animal feeds and enhances nutrient absorption. In the present study, the effects of hydrated sodium calcium aluminosilicate (Improved HSCAS, Jumpstar) on the growth performance, fatty liver, serum parameters, and intestinal morphology of overfed Landes geese were evaluated. The study included two Control groups, a non-overfed Control (Control I) and an overfed Control (Control II), as well as a treatment group. The results showed that compared with the Control I group, liver weight, relative liver weight, abdominal fat weight, intestinal fat weight, villus height, total cholesterol, very low density lipoproteins, lipoprotein lipase, aspartate aminotransferase, IgM, and IgG in the HSCAS treatment group all significantly increased (P < 0.05) at Days 10 and 20. The villus height/crypt depth, triglycerides, cholinesterase, alanine aminotransferase, and serum IgA levels were higher than those in the Control I (P < 0.05) after 20 days of overfeeding. Compared with the Control II group, the relative abdominal fat weight, relative intestinal fat weight, and crypt depth in the HSCAS treatment group were significantly increased (P < 0.05) after 10 days of overfeeding, whereas villus height/crypt depth decreased (P < 0.05). Relative liver weight and IgA were higher in HACAS group after 20 days’ overfeeding (P < 0.05). HSCAS treatment also led to higher cholinesterase, very low density lipoproteins and decreased lipase, alanine aminotransferase (P > 0.05), and decreased aspartate aminotransferase levels than those in the Control II group (P < 0.05). In conclusion, HSCAS treatment had a beneficial effect on fatty liver production, intestinal development, and serum parameters in overfed Landes geese, which could enhance the health status of these geese.
Collapse
|
68
|
Chen F, Zhang H, Li J, Tian Y, Xu J, Chen L, Wei J, Zhao N, Yang X, Zhang W, Lu L. Identification of differentially expressed miRNAs in the fatty liver of Landes goose (Anser anser). Sci Rep 2017; 7:16296. [PMID: 29176640 PMCID: PMC5701175 DOI: 10.1038/s41598-017-16632-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/15/2017] [Indexed: 12/14/2022] Open
Abstract
Unlike mammals, in palmipedes de novo lipogenesis from diet takes place mostly in the liver. The French Landes Goose is famous for its high capacity and susceptibility to fatty liver production. While miRNAs play a critical role in the posttranscriptional regulation of gene expression, miRNAs that are involved in the regulation of goose hepatic steatosis have yet to be elucidated. Using high-throughput sequencing, we analyzed miRNAs expression profile of Landes goose liver after overfeeding for 21 days. Aan-miR-122-5p was the most frequently sequenced known miRNA, but it was unchanged after overfeeding. Compared with normal liver, we identified that 16 conserved miRNAs were up-regulated while the other 9 conserved miRNAs were down-regulated in fatty livers. Many of their predicted target genes played key roles in metabolic pathways leading to the development of hepatic steatosis in the goose by KEGG pathways analysis. ACSL1 and ELOVL6 were critical genes in hepatic lipid metabolism and had opposite expression patterns with aan-miR-203a and aan-miR-125b-5p, respectively. And we validated that aan-miR-203a and aan-miR-125b-5p might involve in the regulation of hepatic lipid metabolism by targeting ACSL1 and ELOVL6, respectively. These results add to our current understanding of the regulation network in goose lipid metabolism.
Collapse
Affiliation(s)
- Fang Chen
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, 430064, PR China.,Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China
| | - Hao Zhang
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, 430064, PR China.,Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China
| | - Jinjun Li
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China
| | - Yong Tian
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China
| | - Jing Xu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China
| | - Li Chen
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China
| | - Jintao Wei
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, 430064, PR China
| | - Na Zhao
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, 430064, PR China
| | - Xuehai Yang
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, 430064, PR China
| | - Wei Zhang
- Institute of Animal Husbandry and Veterinary Science, Hubei Academy of Agricultural Sciences/Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Wuhan, 430064, PR China
| | - Lizhi Lu
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China.
| |
Collapse
|
69
|
Takada N, Omae M, Sagawa F, Chi NC, Endo S, Kozawa S, Sato TN. Re-evaluating the functional landscape of the cardiovascular system during development. Biol Open 2017; 6:1756-1770. [PMID: 28982700 PMCID: PMC5703621 DOI: 10.1242/bio.030254] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The cardiovascular system facilitates body-wide distribution of oxygen, a vital process for the development and survival of virtually all vertebrates. However, the zebrafish, a vertebrate model organism, appears to form organs and survive mid-larval periods without a functional cardiovascular system. Despite such dispensability, it is the first organ to develop. Such enigma prompted us to hypothesize other cardiovascular functions that are important for developmental and/or physiological processes. Hence, systematic cellular ablations and functional perturbations were performed on the zebrafish cardiovascular system to gain comprehensive and body-wide understanding of such functions and to elucidate the underlying mechanisms. This approach identifies a set of organ-specific genes, each implicated for important functions. The study also unveils distinct cardiovascular mechanisms, each differentially regulating their expressions in organ-specific and oxygen-independent manners. Such mechanisms are mediated by organ-vessel interactions, circulation-dependent signals, and circulation-independent beating-heart-derived signals. A comprehensive and body-wide functional landscape of the cardiovascular system reported herein may provide clues as to why it is the first organ to develop. Furthermore, these data could serve as a resource for the study of organ development and function. Summary: The body-wide landscape of the cardiovascular functions during development is reported. Such landscape may provide clues as to why the cardiovascular system is the first organ to develop.
Collapse
Affiliation(s)
- Norio Takada
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan.,ERATO Sato Live Bio-Forecasting Project, Japan Science and Technology Agency (JST), Kyoto 619-0288, Japan
| | - Madoka Omae
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan.,Kyoto University, Graduate School of Biostudies, Kyoto 606-8303, Japan
| | - Fumihiko Sagawa
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan.,ERATO Sato Live Bio-Forecasting Project, Japan Science and Technology Agency (JST), Kyoto 619-0288, Japan
| | - Neil C Chi
- Division of Cardiovascular Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0613J, USA
| | - Satsuki Endo
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan.,ERATO Sato Live Bio-Forecasting Project, Japan Science and Technology Agency (JST), Kyoto 619-0288, Japan
| | - Satoshi Kozawa
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan.,ERATO Sato Live Bio-Forecasting Project, Japan Science and Technology Agency (JST), Kyoto 619-0288, Japan
| | - Thomas N Sato
- The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International (ATR), Kyoto 619-0288, Japan .,ERATO Sato Live Bio-Forecasting Project, Japan Science and Technology Agency (JST), Kyoto 619-0288, Japan.,Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA.,Centenary Institute, Sydney 2042, Australia
| |
Collapse
|
70
|
Qin S, Han H, Zhang K, Ding X, Bai S, Wang J, Zeng Q. Dietary fibre alleviates hepatic fat deposition via inhibiting lipogenic gene expression in meat ducks. J Anim Physiol Anim Nutr (Berl) 2017; 102:e736-e745. [DOI: 10.1111/jpn.12828] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/01/2017] [Indexed: 02/03/2023]
Affiliation(s)
- S. Qin
- Institute of Animal Nutrition; Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education; Sichuan Agricultural University; Chengdu China
| | - H. Han
- Institute of Animal Nutrition; Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education; Sichuan Agricultural University; Chengdu China
| | - K. Zhang
- Institute of Animal Nutrition; Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education; Sichuan Agricultural University; Chengdu China
| | - X. Ding
- Institute of Animal Nutrition; Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education; Sichuan Agricultural University; Chengdu China
| | - S. Bai
- Institute of Animal Nutrition; Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education; Sichuan Agricultural University; Chengdu China
| | - J. Wang
- Institute of Animal Nutrition; Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education; Sichuan Agricultural University; Chengdu China
| | - Q. Zeng
- Institute of Animal Nutrition; Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education; Sichuan Agricultural University; Chengdu China
| |
Collapse
|
71
|
Zhong H, Luo Y, Sun J, Wang C, Wang QG, Gao GL, Zhang KS, Li Q, Wang HW, Li J, Chen MJ, Wang YM, Zhao XZ. Goose FMO3 gene cloning, tissue expression profiling, polymorphism detection and association analysis with trimethylamine level in the egg yolk. Gene 2017; 632:25-35. [PMID: 28844670 DOI: 10.1016/j.gene.2017.08.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/31/2017] [Accepted: 08/23/2017] [Indexed: 11/24/2022]
Abstract
Flavin-containing monooxygenase 3 (FMO3) plays a critical role in catalyzing the conversion of trimethylamine (TMA) to trimethylamine-N-oxide (TMAO) in vivo. Despite the well-documented association between FMO3 mutations and a 'fishy' off-flavor eggs in chicken and quail, little information is available regarding the molecular characteristic of goose (Anser cygnoides) FMO3 and its relationship with the yolk TMA content. To fill these gaps, we cloned the full-length cDNA sequence of goose FMO3, which comprised 1851bp encoding 531 amino acids. FMO3 mRNA was dramatically expressed in liver than in other tissues in the geese. Eight single nucleotide polymorphisms (SNPs) were detected in the entire coding region. The CC genotype at the T669C site, GG at the A723G site, and AA at the G734A site of FMO3 were highly significantly associated with elevated TMA content in goose egg yolk (P<0.001). Carriers of the A allele of G734A or C allele of T885C had yolk TMA content that had a high probability of being elevated after feeding with additional choline chloride (P=0.0429, OR=4.1300, 95%CI=1.0390-16.4270, and P=0.0251, OR=4.6060, 95%CI=1.1620-18.2620, respectively). This work lays a foundation for studying the function of FMO3 and yolk TMA content in goose. However, studies using larger sample sizes and more goose breeds are required to determine whether the fishy off-flavor trait exists in goose.
Collapse
Affiliation(s)
- Hang Zhong
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China
| | - Yi Luo
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China
| | - Jing Sun
- Chongqing Academy of Animal Sciences, Chongqing, PR China
| | - Chao Wang
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China
| | - Qi-Gui Wang
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China
| | - Guang-Liang Gao
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China
| | - Ke-Shan Zhang
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China
| | - Qin Li
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China
| | - Hai-Wei Wang
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China
| | - Jing Li
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China
| | - Ming-Jun Chen
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China
| | - Yang-Ming Wang
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China
| | - Xian-Zhi Zhao
- Chongqing Academy of Animal Sciences, Chongqing, PR China; Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing, PR China.
| |
Collapse
|
72
|
Luan X, Cao Z, Xing Z, Liu M, Gao M, Meng B, Fan R. Comparative proteomic analysis of pituitary glands from Huoyan geese between pre-laying and laying periods using an iTRAQ-based approach. PLoS One 2017; 12:e0185253. [PMID: 28945779 PMCID: PMC5612699 DOI: 10.1371/journal.pone.0185253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 09/08/2017] [Indexed: 12/31/2022] Open
Abstract
In this study, we performed a comprehensive evaluation of the proteomic profile of the pituitary gland of the Huoyan goose during the laying period compared to the pre-laying period using an iTRAQ-based approach. Protein samples were prepared from pituitary gland tissues of nine pre-laying period and nine laying period geese. Then the protein samples from three randomly selected geese within each period were pooled in equal amounts to generate one biological sample pool. We identified 684 differentially expressed proteins, including 418 up-regulated and 266 down-regulated proteins. GO annotation and KEGG pathway analyses of these proteins were conducted. Some of these proteins were found to be associated with hormone and neurotransmitter secretion and transport, neuropeptide signalling and GnRH signalling pathways, among others. Subsequently, the modification of the abundance of three proteins (prolactin, chromogranin-A and ITPR3) was verified using western blotting. Our results will provide a new source for mining genes and gene products related to the egg-laying performance of Huoyan geese, and may provide important information for the conservation and utilization of local goose breeds.
Collapse
Affiliation(s)
- Xinhong Luan
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
- * E-mail:
| | - Zhongzan Cao
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Zhe Xing
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Mei Liu
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Ming Gao
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Bo Meng
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| | - Ruiming Fan
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, P.R. China
| |
Collapse
|
73
|
Pre- and post-prandial expression of genes involved in lipid metabolism at the end of the overfeeding period of mule ducks. Mol Cell Biochem 2017; 438:111-121. [DOI: 10.1007/s11010-017-3118-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/15/2017] [Indexed: 01/23/2023]
|
74
|
Ren J, Du X, Zeng T, Chen L, Shen J, Lu L, Hu J. Divergently expressed gene identification and interaction prediction of long noncoding RNA and mRNA involved in duck reproduction. Anim Reprod Sci 2017; 185:8-17. [PMID: 28886878 DOI: 10.1016/j.anireprosci.2017.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 01/21/2023]
Abstract
Long noncoding RNAs (lncRNAs) and divergently expressed genes exist widely in different tissues of mammals and birds, in which they are involved in various biological processes. However, there is limited information on their role in the regulation of normal biological processes during differentiation, development, and reproduction in birds. In this study, whole transcriptome strand-specific RNA sequencing of the ovary from young ducks (60days), first-laying ducks (160days), and old ducks, i.e., ducks that stopped laying eggs (490days) was performed. The lncRNAs and mRNAs from these ducks were systematically analyzed and identified by duck genome sequencing in the three study groups. The transcriptome from the duck ovary comprised 15,011 protein-coding genes and 2905 lncRNAs; all the lncRNAs were identified as novel long noncoding transcripts. The comparison of transcriptome data from different study groups identified 2240 divergent transcription genes and 135 divergently expressed lncRNAs, which differed among the groups; most of them were significantly downregulated with age. Among the divergent genes, 38 genes were related to the reproductive process and 6 genes were upregulated. Further prediction analysis revealed that 52 lncRNAs were closely correlated with divergent reproductive mRNAs. More importantly, 6 remarkable lncRNAs were correlated significantly with the conversion of the ovary in different phases. Our results aid in the understanding of the divergent transcriptome of duck ovary in different phases and the underlying mechanisms that drive the specificity of protein-coding genes and lncRNAs in duck ovary.
Collapse
Affiliation(s)
- Jindong Ren
- College of Animal Science and Technology, Northwest A & F University, No. 21 Xinong Road, Yangling, Shaanxi 712100, PR China; Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Xue Du
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Tao Zeng
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Li Chen
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Junda Shen
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Lizhi Lu
- Zhejiang Academy of Agricultural Sciences, No. 198 Shiqiao Road, Hangzhou, Zhejiang 310021, PR China.
| | - Jianhong Hu
- College of Animal Science and Technology, Northwest A & F University, No. 21 Xinong Road, Yangling, Shaanxi 712100, PR China.
| |
Collapse
|
75
|
Annabelle T, Karine R, Marie-Dominique B, Stéphane D, Karine G. Kinetics of expression of genes involved in glucose metabolism after the last meal in overfed mule ducks. Mol Cell Biochem 2017; 430:127-137. [DOI: 10.1007/s11010-017-2960-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/28/2017] [Indexed: 01/14/2023]
|
76
|
Transcriptome analysis of follicles reveals the importance of autophagy and hormones in regulating broodiness of Zhedong white goose. Sci Rep 2016; 6:36877. [PMID: 27833138 PMCID: PMC5105085 DOI: 10.1038/srep36877] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 10/21/2016] [Indexed: 12/15/2022] Open
Abstract
Broodiness, a maternal behavior and instinct for natural breeding in poultry, inhibits egg production and affects the poultry industry. Phenotypic and physiological factors influencing broodiness in poultry have been extensively studied, but the molecular regulation mechanism of broodiness remains unclear. Effective research strategies focusing on broodiness are hindered by limited understanding of goose developmental biology. Here we established the transcriptomes of goose follicles at egg-laying and broody stages by Illumina HiSeq platform and compared the sequenced transcriptomes of three types of follicles (small white, large white and small yellow). It was found that there were 92 up-regulated and 84 down-regulated transcription factors and 101 up-regulated and 51 down-regulated hormone-related genes. Many of these genes code for proteins involved in hormone response, follicular development, autophagy, and oxidation. Moreover, the contents of progesterone and estradiol in follicles were altered, and the autophagy levels of follicles were enhanced during the broody stage. These results suggest that hormone- and autophagy-signaling pathways are critical for controlling broodiness in the goose. We demonstrated that transcriptome analysis of egg-laying and broody Zhedong white goose follicles provided novel insights into broodiness in birds.
Collapse
|
77
|
Gao G, Zhao X, Li Q, He C, Zhao W, Liu S, Ding J, Ye W, Wang J, Chen Y, Wang H, Li J, Luo Y, Su J, Huang Y, Liu Z, Dai R, Shi Y, Meng H, Wang Q. Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose. Sci Rep 2016; 6:32961. [PMID: 27608918 PMCID: PMC5016989 DOI: 10.1038/srep32961] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 08/18/2016] [Indexed: 01/01/2023] Open
Abstract
The goose is an economically important waterfowl that exhibits unique characteristics and abilities, such as liver fat deposition and fibre digestion. Here, we report de novo whole-genome assemblies for the goose and swan goose and describe the evolutionary relationships among 7 bird species, including domestic and wild geese, which diverged approximately 3.4~6.3 million years ago (Mya). In contrast to chickens as a proximal species, the expanded and rapidly evolving genes found in the goose genome are mainly involved in metabolism, including energy, amino acid and carbohydrate metabolism. Further integrated analysis of the host genome and gut metagenome indicated that the most widely shared functional enrichment of genes occurs for functions such as glycolysis/gluconeogenesis, starch and sucrose metabolism, propanoate metabolism and the citrate cycle. We speculate that the unique physiological abilities of geese benefit from the adaptive evolution of the host genome and symbiotic interactions with gut microbes.
Collapse
Affiliation(s)
- Guangliang Gao
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Xianzhi Zhao
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Qin Li
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Chuan He
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China.,Shanghai Personal Biotechnology Limited Company, Shanghai 200231, P. R. China
| | - Wenjing Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China
| | - Shuyun Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China
| | - Jinmei Ding
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China
| | - Weixing Ye
- Shanghai Personal Biotechnology Limited Company, Shanghai 200231, P. R. China
| | - Jun Wang
- Shanghai Personal Biotechnology Limited Company, Shanghai 200231, P. R. China
| | - Ye Chen
- Shanghai Personal Biotechnology Limited Company, Shanghai 200231, P. R. China
| | - Haiwei Wang
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Jing Li
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Yi Luo
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| | - Jian Su
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China
| | - Yong Huang
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China
| | - Zuohua Liu
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China
| | - Ronghua Dai
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China
| | - Yixiang Shi
- Shanghai Personal Biotechnology Limited Company, Shanghai 200231, P. R. China
| | - He Meng
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, P. R. China
| | - Qigui Wang
- Chongqing Academy of Animal Science, Chongqing 402460, P. R. China.,Chongqing Engineering Research Center of Goose Genetic Improvement, Chongqing 402460, P. R. China
| |
Collapse
|
78
|
Liu L, Zhao X, Wang Q, Sun X, Xia L, Wang Q, Yang B, Zhang Y, Montgomery S, Meng H, Geng T, Gong D. Prosteatotic and Protective Components in a Unique Model of Fatty Liver: Gut Microbiota and Suppressed Complement System. Sci Rep 2016; 6:31763. [PMID: 27550859 PMCID: PMC4994046 DOI: 10.1038/srep31763] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/27/2016] [Indexed: 01/07/2023] Open
Abstract
Goose can develop severe hepatic steatosis without overt injury, thus it may serve as a unique model for uncovering how steatosis-related injury is prevented. To identify the markedly prosteatotic and protective mechanisms, we performed an integrated analysis of liver transcriptomes and gut microbial metagenomes using samples collected from overfed and normally-fed geese at different time points. The results indicated that the fatty liver transcriptome, initially featuring a ‘metabolism’ pathway, was later joined by ‘cell growth and death’ and ‘immune diseases’ pathways. Gut microbiota played a synergistic role in the liver response as microbial and hepatic genes affected by overfeeding shared multiple pathways. Remarkably, the complement system, an inflammatory component, was comprehensively suppressed in fatty liver, which was partially due to increased blood lactic acid from enriched Lactobacillus. Data from in vitro studies suggested that lactic acid suppressed TNFα via the HNF1α/C5 pathway. In conclusion, gut microbes and their hosts respond to excess energy influx as an organic whole, severe steatosis and related tolerance of goose liver may be partially attributable to gut microbiotic products and suppressed complement system, and lactic acid from gut microbiota participates in the suppression of hepatic TNFα/inflammation through the HNF1α/C5 pathway.
Collapse
Affiliation(s)
- Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xing Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qian Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoxian Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Lili Xia
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qianqian Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Biao Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yihui Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Sean Montgomery
- Department of Botany, University of British Columbia, 6270 University Boulevard, British Columbia, V6T 1Z4, Canada
| | - He Meng
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, China
| | - Tuoyu Geng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
79
|
Ottenburghs J, Megens HJ, Kraus RH, Madsen O, van Hooft P, van Wieren SE, Crooijmans RP, Ydenberg RC, Groenen MA, Prins HH. A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese. Mol Phylogenet Evol 2016; 101:303-313. [DOI: 10.1016/j.ympev.2016.05.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 04/27/2016] [Accepted: 05/20/2016] [Indexed: 11/26/2022]
|
80
|
Zeng M, Chen S, Wang M, Jia R, Zhu D, Liu M, Sun K, Yang Q, Wu Y, Chen X, Cheng A. Molecular identification and comparative transcriptional analysis of myxovirus resistance GTPase (Mx) gene in goose (Anser cygnoide) after H9N2 AIV infection. Comp Immunol Microbiol Infect Dis 2016; 47:32-40. [PMID: 27477505 DOI: 10.1016/j.cimid.2016.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/20/2016] [Accepted: 05/23/2016] [Indexed: 12/18/2022]
Abstract
Interferon (IFN)-induced myxovirus resistance (Mx) GTPases belong to the family of dynamin-like GTPases and control a diverse range of viruses. In this study, the identified goose Mx (goMx) mRNA is 2009bp long, shares partially conserved exons with other homologues, and shares highly conserved domains in its primary structure. The amino acid position 629 (629aa) of the goMx protein was identified as serine (Ser), in contrast to the Ser located at 631aa in chicken Mx, which is considered to be responsible for the lack of chicken Mx antiviral activity. In addition, the goMx 142aa residue in the dynamin family signature differs from that of other functional Mx proteins. Transcriptional analysis revealed that goMx was mainly expressed in the digestive, respiratory and immune systems in an age-specific manner. GoMx transcript levels in goose peripheral blood mononuclear cells (PBMCs) were found to be significantly up-regulated by various agonists and avian viruses. Furthermore, a time course study of the effects of H9N2 avian influenza virus (AIV) on goMx expression in infected goslings suggested that H9N2 AIV affected goMx expression. However, significant changes in goMx expression were observed in the trachea, lung and small intestine of infected birds. Altogether, these results indicate that goMx protein may have acquired its broad antiviral activity by changing only a few amino acids at select sites, even as it shares a conserved architectures with species.
Collapse
Affiliation(s)
- Miao Zeng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Kunfeng Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiaoyue Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| |
Collapse
|
81
|
Carvunis AR, Wang T, Skola D, Yu A, Chen J, Kreisberg JF, Ideker T. Evidence for a common evolutionary rate in metazoan transcriptional networks. eLife 2015; 4. [PMID: 26682651 PMCID: PMC4764585 DOI: 10.7554/elife.11615] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/17/2015] [Indexed: 12/13/2022] Open
Abstract
Genome sequences diverge more rapidly in mammals than in other animal lineages, such as birds or insects. However, the effect of this rapid divergence on transcriptional evolution remains unclear. Recent reports have indicated a faster divergence of transcription factor binding in mammals than in insects, but others found the reverse for mRNA expression. Here, we show that these conflicting interpretations resulted from differing methodologies. We performed an integrated analysis of transcriptional network evolution by examining mRNA expression, transcription factor binding and cis-regulatory motifs across >25 animal species, including mammals, birds and insects. Strikingly, we found that transcriptional networks evolve at a common rate across the three animal lineages. Furthermore, differences in rates of genome divergence were greatly reduced when restricting comparisons to chromatin-accessible sequences. The evolution of transcription is thus decoupled from the global rate of genome sequence evolution, suggesting that a small fraction of the genome regulates transcription. DOI:http://dx.doi.org/10.7554/eLife.11615.001 The genetic information that makes each individual unique is encoded in DNA molecules. Cells read this molecular instruction manual by a process called transcription, in which proteins called transcription factors bind to DNA in specific places and regulate which sections of the DNA will be expressed. These 'transcripts' are active molecules that determine the cell’s – and ultimately the individual’s – characteristics. However, it is not well understood how alterations in the DNA of different individuals or species can lead to changes in where the transcription factors bind, and in which transcripts are expressed. Carvunis, Wang, Skola et al. set out to determine if there is a relationship between how often DNA changes and how often transcription changes during the evolution of animals. The experiments examined the abundance of transcripts in the cells of a variety of animal species with close or distant evolutionary relationships. For example, the house mouse was compared to a close relative called the Algerian mouse, to another species of rodent (rat) and to humans. The experiments show that the changes in transcript abundances are happening at similar rates in mammals, birds and insects, even though DNA changes at very different rates in these groups of animals. This similarity was also observed for other aspects of transcription, such as in changes to where transcription factors bind to DNA. The next challenges are to find out what makes transcription evolve at such similar rates in these groups of animals, and whether these findings extend to other species and to other processes in cells. DOI:http://dx.doi.org/10.7554/eLife.11615.002
Collapse
Affiliation(s)
| | - Tina Wang
- Department of Medicine, University of California, San Diego, La Jolla, United States
| | - Dylan Skola
- Department of Medicine, University of California, San Diego, La Jolla, United States
| | - Alice Yu
- Department of Medicine, University of California, San Diego, La Jolla, United States
| | - Jonathan Chen
- Department of Medicine, University of California, San Diego, La Jolla, United States
| | - Jason F Kreisberg
- Department of Medicine, University of California, San Diego, La Jolla, United States
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, United States
| |
Collapse
|