|
|
|
Generation and Analysis of Expressed Sequence Tags (ESTs) from Muscle Full-Length cDNA Library of Wujin Pig |
ZHAO Su-mei, LIU Yong-gang, PAN Hong-bing, ZHANG Xi, GE Chang-rong, JIA Jun-jing , GAO Shi-zheng |
Yunnan Key Laboratory of Animal Nutrition and Feed, Yunnan Agricultural University, Kunming 650201, P.R.China |
|
|
摘要 Porcine skeletal muscle genes play a major role in determining muscle growth and meat quality. Construction of a full-length cDNA library is an effective way to understand the expression of functional genes in muscle tissues. In addition, novel genes for further research could be identified in the library. In this study, we constructed a full-length cDNA library from porcine muscle tissue. The estimated average size of the cDNA inserts was 1 076 bp, and the cDNA fullness ratio was 86.2%. A total of 1 058 unique sequences with 342 contigs (32.3%) and 716 singleton (67.7%) expressed sequence tags (EST) were obtained by clustering and assembling. Meanwhile, 826 (78.1%) ESTs were categorized as known genes, and 232 (21.9%) ESTs were categorized as unknown genes. 65 novel porcine genes that exhibit no identity in the TIGR gene index of Sus scrofa and 124 full-length sequences with unknown functions were deposited in the dbEST division of GenBank (accession numbers: EU650784-EU650788, GE843306, GH228978-GH229100). The abundantly expressed genes in porcine muscle tissue were related to muscle fiber development, energy metabolism and protein synthesis. Gene ontology analysis showed that sequences expressed in porcine muscle tissue contained a high percentage of binding activity, catalytic activity, structural molecule activity and motor activity, which involved mainly in metabolic, cellular and developmental process, distributed mainly in intracellular region. The sequence data generated in this study would provide valuable information for identifying porcine genes expressed in muscle tissue and help to advance the study on the structure and function of genes in pigs.
Abstract Porcine skeletal muscle genes play a major role in determining muscle growth and meat quality. Construction of a full-length cDNA library is an effective way to understand the expression of functional genes in muscle tissues. In addition, novel genes for further research could be identified in the library. In this study, we constructed a full-length cDNA library from porcine muscle tissue. The estimated average size of the cDNA inserts was 1 076 bp, and the cDNA fullness ratio was 86.2%. A total of 1 058 unique sequences with 342 contigs (32.3%) and 716 singleton (67.7%) expressed sequence tags (EST) were obtained by clustering and assembling. Meanwhile, 826 (78.1%) ESTs were categorized as known genes, and 232 (21.9%) ESTs were categorized as unknown genes. 65 novel porcine genes that exhibit no identity in the TIGR gene index of Sus scrofa and 124 full-length sequences with unknown functions were deposited in the dbEST division of GenBank (accession numbers: EU650784-EU650788, GE843306, GH228978-GH229100). The abundantly expressed genes in porcine muscle tissue were related to muscle fiber development, energy metabolism and protein synthesis. Gene ontology analysis showed that sequences expressed in porcine muscle tissue contained a high percentage of binding activity, catalytic activity, structural molecule activity and motor activity, which involved mainly in metabolic, cellular and developmental process, distributed mainly in intracellular region. The sequence data generated in this study would provide valuable information for identifying porcine genes expressed in muscle tissue and help to advance the study on the structure and function of genes in pigs.
|
Received: 11 October 2012
Accepted:
|
Fund: This work was supported by the National Basic Research Program of China (2007CB116201). |
Corresponding Authors:
ZHAO Su-mei, Tel: +86-871-65227796, Fax: +86-871-65227284, E-mail: zhaosm2009@126.com
E-mail: zhaosm2009@126.com
|
About author: ZHAO Su-mei, Tel: +86-871-65227796, Fax: +86-871-65227284, E-mail: zhaosm2009@126.com |
Cite this article:
ZHAO Su-mei, LIU Yong-gang, PAN Hong-bing, ZHANG Xi, GE Chang-rong, JIA Jun-jing , GAO Shi-zheng.
2014.
Generation and Analysis of Expressed Sequence Tags (ESTs) from Muscle Full-Length cDNA Library of Wujin Pig. Journal of Integrative Agriculture, 13(2): 378-386.
|
Bertani G R, Johnson R K, Robic A, Pomp D. 2003. Mapping of porcine ESTs obtained from the anterior pituitary. Animal Genetics, 34, 132-134 Caetano A R, Johnson R K, Pomp D. 2003. Generation and sequence characterization of a normalized cDNA library from swine ovarian follicles. Mammal Genome, 14, 65- 70. Chen C H, Lin E C, Cheng W T K, Sun H S, Mersmann H J, Ding S T. 2006. Abundantly expressed genes in pig adipose tissue: an expressed sequence tag approach. Animal Science, 84, 2673-2683 Davoli R, Fontanesi L, Zambonelli P, Bigi D, Gellin J, Yerle M, Milc J, Braglia S, Cenci V, Cagnazzo M, et al. 2002. Isolation of porcine expressed sequence tags for the construction of a first genomic transcript map of the skeletal muscle in pig. Animal Genetics, 33, 3-18 Davoli R, Zambonelli P, Bigi D, Fontanesi L, Russo V. 1999. Analysis of expressed sequence tags of porcine skeletal muscle. Genetics, 233, 181-188 Ewing B, Hillier L, Wendl M C, Green P. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Research, 81, 175-185 Fahrenkrug S C, Smith T P, Freking B A, Cho J, White J, Vallet J, Wise T, Rohrer G, Pertea G, Sultana R, et al. 2002. Porcine gene discovery by normalized DNA-library sequencing and EST cluster assembly. Mammal Genome, 13, 475-478 Fujisaki S, Sugiyama A, Eguchi T, Watanabe Y, Hiraiwa H, Honma D, Saito T, Yasue H. 2004. Analysis of a full-length cDNA library constructed from swine olfactory bulb for elucidation of expressed genes and their transcription initiation sites. Journal of Veterinary Medicine Science, 66, 15-23 Huang X, Madan A. 1999. CAP3: a DNA sequence assembly program. Genome Research, 9, 868-877 Huff-Lonergan E, Baas T J, Malek M, Dekkers J C, Prusa K, Rothschild M F. 2002. Correlations among selected pork quality traits. Journal of Animal Science, 80, 617-627 Kato S, Sekine S, Oh S W, Kim N S, Umezawa Y, Abe N, Yokoyama-Kobayashi M, Aoki T. 1994. Construction of a human full-length cDNA bank. Gene, 150, 243-250 Kim T H, Kim N S, Lim D, Lee K T, Oh J H, Park H S, Jang G W, Kim H Y, Jeon M, Choi B H, et al. 2006. Generation and analysis of large-scale expressed sequence tags (ESTs) from a full-length enriched cDNA library of porcine backfat tissue. BMC Genomics, 36, 1-9 Maruyama K, Sugano S. 1994. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene, 138, 171-174 Mikawa A, Suzuki H, Suzuki K, Toki D, Uenishi H, Awata T, Hamasima N. 2004. Characterization of 298 ESTs from porcine back fat tissue and their assignment to the SSRH radiation hybrid map. Mammal Genome, 15, 315-322 Nobis W, Ren X, Suchyta S P, Suchyta T R, Zanella A J, Coussens P M. 2003. Development of a porcine brain cDNA library, EST database, and microarray resource. Physiology Genomics, 16, 153-159 Oh J H, Kim Y S, Kim N S. 2003. An improved method for constructing a full-length enriched cDNA library using small amounts of total RNA as a starting material. Experimental and Molecular Medicine, 35, 586-590 Ponsuksili S, Wimmers K, Schellander K. 2001. Application of differential display RT-PCR to identify porcine liver ESTs. Gene, 280, 75-85 Rink A, Santschi E M, Beattie C W. 2002. Normalized cDNA libraries from a porcine model of orthopedic implant- associated infection. Mammal Genome, 13, 198-205 Smith T P, Fahrenkrug S C, Rohrer G A, Simmen F A, Rexroad C E, Keele J W. 2001. Mapping of expressed sequence tags from a porcine early embryonic cDNA library. Animal Genetics, 32, 66-72 Stapleton M, Carlson J, Brokstein P, Yu C, Champe M, George R, Guarin H, Kronmiller B, Pacleb J, Park S, et al. 2002. A Drosophila full-length cDNA resource. Genome Biology, 3, RESEARCH0080. Suzuki Y, Sugano S. 2001. Construction of a full-length enriched cDNA libraries. The oligo-capping method. Methods of Molecular Biology, 175, 143-153 Tuggle C K, Green J A, Fitzsimmons C, Woods R, Prather R S, Malchenko S, Soares B M, Kucaba T, Crouch K, Smith C, et al. 2003. EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human. Mammal Genome, 14, 565-579 Tuggle C K, Schmitz C B. 1994. Cloning and characterization of pig muscle cDNAs by an expressed sequence tag approach. Animal Biotechnology, 5, 1-13 Uenishi H, Eguchi T, Suzuki K, Sawazaki T, Toki D, Shinkai H, Okumura N, Hamasima N, Awata T. 2004. PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries. Nucleic Acids Research, 32, 484-488 Uenishi H, Eguchi-Ogawa T, Shinkai H, Okumura N, Suzuki K. 2007. PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences. Nucleic Acids Research, 35, 650-653 van Wijk H J, Arts D J, Matthews J O, Webster M, Ducro B J, Knol E F. 2005. Genetic parameters for carcass composition and pork quality estimated in a commercial production chain. Journal of Animal Science, 83, 324- 333. Wang J, Zhao S M, Song X L, Pan H B, Li W Z, Zhang Y Y, Gao S Z, Chen D W. 2012. Low protein diet up-regulate intramuscular lipogenic gene expression and down- regulate lipolytic gene expression in growth-finishing pigs. Livestock Science, 128, 119-128 Wang X L, Wu K L, Li N, Li C L, Qiu X M, Wang A H, Wu C X. 2006. Analysis of expressed sequence tags from skeletal muscle-specific cDNA library of Chinese native Xiang pig. Journal of Genetics and Genomics, 33, 984- 991. Whitworth K, Springer G K, Forrester L J, Spollen W G, Ries J, Lamberson W R, Bivens N, Murphy C N, Mathialagan N, Green J A, et al. 2004. Developmental expression of 2 489 gene clusters during pig embryogenesis: an expressed sequence tag project. Biology of Reproduction, 71, 1230-1243 Wintero A K, Fredholm M, Davies W 1996. Evaluation and characterization of a porcine small intestine cDNA library: analysis of 839 clones. Mammal Genome, 7, 509-517. Yao J, Coussens P M, Saama P, Suchyta S, Ernst C W. 2002. Generation of expressed sequence tags from a normalized porcine skeletal muscle cDNA library. Animal Biotechnology, 13, 211-222 Zhang Z, Schwartz S, Wangner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. Journal of Computer Biology, 1-2, 203-214 Zhao S M, Ren L J, Guo L, Cheng M L, Zhang X, Ge C R, Gao S Z. 2010a. Muscle lipid metabolism gene expression in pigs with different H-FABP genotypes. Livestock Science, 128, 101-107 Zhao S M, Ren L J, Zhang X, Gao S Z. 2009. Differential expression of lipid metabolism related genes in porcine muscle tissue leading to different intramuscular fat deposition. Lipids, 44, 1029-1037 Zhao S M, Wang J, Song X L, Zhang X, Ge C R, Gao S Z. 2010b. Impact of dietary protein on lipid metabolism related gene expression in porcine adipose tissue. Nutrition & Metabolism, 7, 6-19. |
No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|