De novo assembly and characterization of Sophora japonica transcriptome using RNA-seq

BioMed Research International

Volumn 2014, Issue , 2014, Pages

  Zhu, Liucun ^a   Zhang, Ying ^b   Guo, Wenna ^a   Xu, Xin Jian ^a   Wang, Qiang ^c  

^a SHANGHAI UNIVERSITY   (China)

^b Yangzhou Breeding Biological Agriculture Technology Co Ltd   (China)

^c NANJING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

AMINO ACID SYNTHESIS; ARTICLE; CARBON METABOLISM; ENDOPLASMIC RETICULUM; FACTUAL DATABASE; GENE; GENE AND NUCLEIC ACID PARAMETERS; GENE EXPRESSION; GENE LENGTH; GENE MAPPING; GENE ONTOLOGY; NONHUMAN; ORTHOLOGY; PROTEIN DOMAIN; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PURINE METABOLISM; RIBOSOME; RNA SEQUENCE; RNA TRANSPORT; SIGNAL TRANSDUCTION; SOPHORA JAPONICA; SPLICEOSOME; UNIGENE; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; METABOLISM; METHODOLOGY; SEQUENCE ANALYSIS; SOPHORA;

DATABASES, GENETIC; GENE EXPRESSION PROFILING; SEQUENCE ANALYSIS, RNA; SOPHORA; TRANSCRIPTOME;

EID: 84893360798     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2014/750961     Document Type: Article

References (30)

1. Kim J. M., Yun-Choi H. S., Anti-platelet effects of flavonoids and flavonoid-glycosides from Sophora japonica. Archives of Pharmacal Research 2008 31 7 886 890 2-s2.0-49749115685 10.1007/s12272-001-1242-1
2. Ishida H., Umino T., Tsuji K., Kosuge T., Studies on the antihemostatic substances in herbs classified as hemostatics in traditional Chinese medicine. I. On the antihemostatic principles in Sophora japonica L. Chemical and Pharmaceutical Bulletin 1989 37 6 1616 1618 2-s2.0-0024312864 (Pubitemid 19176841)
3. Parchman T. L., Geist K. S., Grahnen J. A., Benkman C. W., Buerkle C. A., Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics 2010 11 1, article 180 2-s2.0-77951894310 10.1186/1471-2164-11-180
4. Dassanayake M., Haas J. S., Bohnert H. J., Cheeseman J. M., Shedding light on an extremophile lifestyle through transcriptomics. The New Phytologist 2009 183 3 764 775 2-s2.0-67650915750 10.1111/j.1469-8137.2009.02913.x
5. Alagna F., D'Agostino N., Torchia L., Servili M., Rao R., Pietrella M., Giuliano G., Chiusano M. L., Baldoni L., Perrotta G., Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics 2009 10, article 399 2-s2.0-70349662156 10.1186/1471-2164-10-399
6. Mutz K. O., Heilkenbrinker A., Lonne M., Walter J. G., Stahl F., Transcriptome analysis using next-generation sequencing. Current Opinion in Biotechnology 2013 24 1 22 30
7. Torres T. T., Metta M., Ottenwälder B., Schlötterer C., Gene expression profiling by massively parallel sequencing. Genome Research 2008 18 1 172 177 2-s2.0-38049091067 10.1101/gr.6984908
8. Clark M. S., Thorne M. A. S., Vieira F. A., Cardoso J. C. R., Power D. M., Peck L. S., Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing. BMC Genomics 2010 11 1, article 362 2-s2.0-77953125691 10.1186/1471-2164-11-362
9. Mortazavi A., Williams B. A., McCue K., Schaeffer L., Wold B., Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 2008 5 7 621 628 2-s2.0-46249106990 10.1038/nmeth.1226 (Pubitemid 351911867)
10. Shi C., Yang H., Wei C., Yu O., Zhang Z., Jiang C., Sun J., Li Y., Chen Q., Xia T., Wan X., Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics 2011 12, article 131 2-s2.0-79952045110 10.1186/1471-2164-12-131
11. Novaes E., Drost D. R., Farmerie W. G., Pappas G. J. Jr., Grattapaglia D., Sederoff R. R., Kirst M., High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 2008 9, article 312 2-s2.0-48249125753 10.1186/1471-2164-9-312
12. Gayral P., Melo-Ferreira J., Glemin S., Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap. PLoS Genetics 2013 9 4 e1003457
13. Wan L., Han J., Sang M., Li A., Wu H., Yin S., Zhang C., De novo transcriptomic analysis of an oleaginous microalga: pathway description and gene discovery for production of next-generation biofuels. PLoS ONE 2012 7 4 2-s2.0-84860005565 10.1371/journal.pone.0035142 e35142
14. Grabherr M. G., Haas B. J., Yassour M., Levin J. Z., Thompson D. A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., Di Palma F., Birren B. W., Nusbaum C., Lindblad-Toh K., Friedman N., Regev A., Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 2011 29 7 644 652 2-s2.0-79960264362 10.1038/nbt.1883
15. Li B., Dewey C. N., RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 2011 12, article 323 2-s2.0-79961123152 10.1186/1471-2105-12-323
16. Tatusov R. L., Natale D. A., Garkavtsev I. V., Tatusova T. A., Shankavaram U. T., Rao B. S., Kiryutin B., Galperin M. Y., Fedorova N. D., Koonin E. V., The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Research 2001 29 1 22 28 2-s2.0-0035162592 (Pubitemid 32054398)
17. Conesa A., Götz S., García-Gómez J. M., Terol J., Talón M., Robles M., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005 21 18 3674 3676 2-s2.0-24644503098 10.1093/bioinformatics/bti610 (Pubitemid 41264107)
18. Ye J., Fang L., Zheng H., Zhang Y., Chen J., Zhang Z., Wang J., Li S., Li R., Bolund L., Wang J., WEGO: a web tool for plotting GO annotations. Nucleic Acids Research 2006 34 W293 W297 2-s2.0-33747846582 10.1093/nar/gkl031 (Pubitemid 44529781)
19. Kanehisa M., Goto S., Kawashima S., Okuno Y., Hattori M., The KEGG resource for deciphering the genome. Nucleic Acids Research 2004 32 D277 D280 2-s2.0-0345863935 (Pubitemid 38081656)
20. Moriya Y., Itoh M., Okuda S., Yoshizawa A. C., Kanehisa M., KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research 2007 35 W182 W185 2-s2.0-34547588704 10.1093/nar/gkm321
21. Szklarczyk D., Franceschini A., Kuhn M., Simonovic M., Roth A., Minguez P., Doerks T., Stark M., Muller J., Bork P., Jensen L. J., von Mering C., The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research 2011 39 1 D561 D568 2-s2.0-78651324347 10.1093/nar/gkq973
22. Ferreira R. M., Rybarczyk-Filho J. L., Dalmolin R. J., Castro M. A., Moreira J. C., Brunnet L. G., de Almeida R. M., Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks. PloS ONE 2013 8 2 e56579
23. Xu X., Zhou M., Rank-dependent deactivation in network evolution. Physical Review E 2009 80 6 2-s2.0-73649127977 10.1103/PhysRevE.80.066105 066105
24. Guo H., Xian J. A., Wang A. L., Ye C. X., Miao Y. T., Trascriptome analysis of the Pacific white shrimp Litopenaeus vannamei exposed to nitrite by RNA-seq. Fish and Shellfish Immunology 2013 35 6 2008 2016
25. Gross S. M., Martin J. A., Simpson J., Abraham-Juarez M. J., Wang Z., Visel A., De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Genomics 2013 14, article 563
26. Liu J., Yin T., Ye N., Chen Y., Yin T., Liu M., Hassani D., Transcriptome analysis of the differentially expressed genes in the male and female shrub willows (Salix suchowensis). PloS ONE 2013 8 4 e60181
27. Fan H., Xiao Y., Yang Y., Xia W., Mason A. S., Xia Z., Qiao F., Zhao S., Tang H., RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches. PloS ONE 2013 8 3 e59997
28. Ong W. D., Voo L. Y., Kumar V. S., De novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing. PloS ONE 2012 7 10 e46937
29. Jeong H., Mason S. P., Barabási A.-L., Oltvai Z. N., Lethality and centrality in protein networks. Nature 2001 411 6833 41 42 2-s2.0-0035799707 10.1038/35075138 (Pubitemid 32428180)
30. Ravasz E., Somera A. L., Mongru D. A., Oltvai Z. N., Barabási A.-L., Hierarchical organization of modularity in metabolic networks. Science 2002 297 5586 1551 1555 2-s2.0-0037199968 10.1126/science.1073374 (Pubitemid 34971002)