非模式生物转录组研究

doi:10.3724/SP.J.1005.2013.00955

[an error occurred while processing this directive]

HEREDITAS ›› 2013, Vol. 35 ›› Issue (8): 955-970.doi: 10.3724/SP.J.1005.2013.00955

Previous Articles Next Articles

Studies on the transcriptomes of non-model organisms

LIU Hong-Liang, ZHENG Li-Ming, LIU Qing-Qing, QUAN Fu-Sheng, ZHANG Yong

Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A F University, Yangling 712100, China

Received:2013-01-27 Revised:2013-03-15 Online:2013-08-20 Published:2013-08-25

Abstract

Abstract:

The transcriptome represents the whole complement of RNA transcripts in cells or tissues and reflects the expressed genes at various life stages, tissue types, physiological states, and environmental conditions. Transcriptome analysis provides a comprehensive understanding of gene expression and its regulation. Non-model organism has many interesting traits of which model organisms lack, and the study of its transcriptome has great significance in solving the questions of genetic evolution, genetic breeding, ecology and so on. Because of absence of reference genome information, and traditional transcriptome research methods which are complicated to operate, long experimental period and costly, slow progress has been made in the research of non-model organism transcriptome. Fortunately, RNA sequencing (RNA-seq), the next-generation sequencing technology, has completely changed the way of transcriptome study, becoming an advanced technology on the investigation of non-model organism transcriptome. In this paper, we give a summary of the non-model organism transcriptome research using RNA-seq in recent years and briefly describe its general flow and principles from aspects of sample preparation, high throughput DNA sequencing, and bioinformatics analysis. Finally, questions that are still open and awaiting further research are also discussed.

Key words: transcriptome, non-model organism, RNA-seq

LIU Hong-Liang, ZHENG Li-Ming, LIU Qing-Qing, QUAN Fu-Sheng, ZHANG Yong. Studies on the transcriptomes of non-model organisms[J]. HEREDITAS, 2013, 35(8): 955-970.

References

[1] Li X, Chen GH, Zhang WY, Zhang XS. Genome-wide transcriptional analysis of maize endosperm in response to ae wx double mutations. J Genet Genom, 2010, 37(11): 749-762.

[2] 李湘龙, 柏斌, 吴俊, 邓启云, 周波. 第二代测序技术用于水稻和稻瘟菌互作早期转录组的分析. 遗传, 2012, 34(1): 102-112.

[3] Emrich SJ, Barbazuk WB, Li L, Schnable PS. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res, 2007, 17(1): 69-73.

[4] Ohtsu K, Smith MB, Emrich SJ, Borsuk LA, Zhou RL, Chen TL, Zhang XL, Timmermans MC, Beck J, Buckner B, Janick-Buckner D, Nettleton D, Scanlon MJ, Schnable PS. Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). Plant J, 2007, 52(3): 391-404.

[5] Jones-Rhoades MW, Borevitz JO, Preuss D. Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins. PloS Genet, 2007, 3(10): 1848-1861.

[6] Weber APM, Weber KL, Carr K, Wilkerson C, Ohlrogge JB. Sampling the arabidopsis transcriptome with massively parallel pyrosequencing. Plant Physiol, 2007, 144(1): 32-42.

[7] Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol, 2008, 17(7): 1636-1647.

[8] Cheung F, Win J, Lang JM, Hamilton J, Vuong H, Leach JE, Kamoun S, Levesque CA, Tisserat N, Buell CR. Analysis of the Pythium ultimum transcriptome using Sanger and pyrosequencing approaches. BMC Genomics, 2008, 9(1): 542.

[9] Novaes E, Drost DR, Farmerie WG, Pappas GJ, Grattapaglia D, Sederoff RR, Kirst M. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics, 2008, 9(1): 312.

[10] Bräutigam A, Shrestha RP, Whitten D, Wilkerson CG, Carr KM, Froehlich JE, Weber APM. Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: Comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes. J Biotechnol, 2008, 136(1-2): 44-53.

[11] Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics, 2009, 10(1): 219.

[12] Kristiansson E, Asker N, Förlin L, Larsson DGJ. Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing. BMC Genomics, 2009, 10(1): 345.

[13] Vega-Arreguín J, Ibarra-Laclette E, Jiménez-Moraila B, Martínez O, Vielle-Calzada J, Herrera-Estrella L, Herrera- Estrella A. Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing. BMC Genomics, 2009, 10(1): 299.

[14] Hale MC, McCormick CR, Jackson JR, DeWoody JA. Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics, 2009, 10(1): 203.

[15] Pauchet Y, Wilkinson P, van Munster M, Augustin S, Pauron D, ffrench-Constant RH. Pyrosequencing of the midgut transcriptome of the poplar leaf beetle Chrysomela tremulae reveals new gene families in Coleoptera. Insect Biochem Mol Biol, 2009, 39(5-6): 403-413.

[16] Wang W, Wang YJ, Zhang Q, Qi Y, Guo DJ. Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing. BMC Genomics, 2009, 10(1): 465.

[17] Alagna F, D’Agostino N, Torchia L, Servili M, Rao R, Pietrella M, Giuliano G, Chiusano ML, Baldoni L, Perrotta G. Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics, 2009, 10(1): 399.

[18] Barakat A, DiLoreto DS, Zhang Y, Smith C, Baier K, Powell WA, Wheeler N, Sederoff R, Carlson JE. Comparison of the transcri

Metrics

Comments

www.chinagene.cn
备案号：京ICP备09063187号

Studies on the transcriptomes of non-model organisms

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	Yan Guo, Lele Yang, Huayu Qi. Transcriptome analysis of mouse male germline stem cells reveals characteristics of mature spermatogonial stem cells [J]. Hereditas(Beijing), 2022, 44(7): 591-608.
[2]	Hongbo Luo, Pengbo Cao, Gangqiao Zhou. Prognostic and predictive value of a DNA methylation-driven transcriptional signature in hepatocellular carcinoma [J]. Hereditas(Beijing), 2020, 42(8): 775-787.
[3]	Kun Du, Chuyang Mao, Anyong Ren, Xuemei Wu, Qingling Li, Tingting Chen, Shiyi Chen, Songjia Lai. Analysis of gene expression profiles at different stages during preadipocyte differentiation in rabbits [J]. Hereditas(Beijing), 2020, 42(3): 309-320.
[4]	Ting Zheng, Mailin Gan, Linyuan Shen, Lili Niu, Zongyi Guo, Jinyong Wang, Shunhua Zhang, Li Zhu. circRNA on animal skeletal muscle development regulation [J]. Hereditas(Beijing), 2020, 42(12): 1178-1191.
[5]	Yue Zhang, Ying Feng, Fang Ma. Related genes and characteristic analysis of trophoblast cells during early embryo developmental cessation [J]. Hereditas(Beijing), 2020, 42(10): 1004-1016.
[6]	Qichao Yu,Bin Song,Xuanxuan Zou,Ling Wang,Dequan Liu,Bo Li,Kun Ma. Analysis of normal tissues adjacent to the tumour-specific expressed genes in breast cancer [J]. Hereditas(Beijing), 2019, 41(7): 625-633.
[7]	Tianpei Shi,Li Zhang. Application of whole transcriptomics in animal husbandry [J]. Hereditas(Beijing), 2019, 41(3): 193-205.
[8]	Jinchuan Wei,Tianyi Xu,Jing Wu,Xiaofeng Song. Molecular mechanisms of recursive splicing events in long introns of eukaryotes [J]. Hereditas(Beijing), 2019, 41(2): 89-97.
[9]	Gaohua Zhang, Shutao Yu, He Wang, Xuda Wang. Transcriptome profiling of high oleic peanut under low temperatureduring germination [J]. Hereditas(Beijing), 2019, 41(11): 1050-1059.
[10]	Yu Zhang,Suying Bai,Yue Ma. Comparative analysis on the transcriptomes of the prostates of muskrats at breeding stage and non-breeding stage [J]. Hereditas(Beijing), 2018, 40(6): 488-495.
[11]	Lan Ren,Rudan Xiao,Qian Zhang,Xiaomin Lou,Zhaojun Zhang,Xiangdong Fang. Synergistic regulation of the erythroid differentiation of K562 cells by KLF1 and KLF9 [J]. Hereditas(Beijing), 2018, 40(11): 998-1006.
[12]	Yajun Liu,Feng Zhang,Hongde Liu,Xiao Sun. The application of next-generation sequencing techniques in studying transcriptional regulation in embryonic stem cells [J]. Hereditas(Beijing), 2017, 39(8): 717-725.
[13]	Wanlong Huang,Xiuxiu Zhang,Ai Li,Xiangyang Miao. Identification of differentially expressed genes between subcutaneous and intramuscular adipose tissue of Large White pig using RNA-seq [J]. Hereditas(Beijing), 2017, 39(6): 501-511.
[14]	Kai Wei,Lei Ma. Concept development of housekeeping genes in the high-throughput sequencing era [J]. Hereditas(Beijing), 2017, 39(2): 127-134.
[15]	Guangqi Li, Congjiao Sun, Guiqin Wu, Fengying Shi, Aiqiao Liu, Hao Sun, Ning Yang. Transcriptome sequencing identifies potential regulatory genes involved in chicken eggshell brownness [J]. Hereditas(Beijing), 2017, 39(11): 1102-1111.