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Article; Agriculture and Environmental Biotechnology

Sequencing and comparative genomics analysis in Senecio scandens Buch.-Ham. Ex D. Don, based on full-length cDNA library

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Pages 805-812 | Received 06 Jan 2014, Accepted 10 Mar 2014, Published online: 28 Oct 2014

References

  • Thanh T, Chi V, Abdullah M, Omar H, Noroozi M, Ky H, Napis S. Construction of cDNA library and preliminary analysis of expressed sequence tags from green microalga Ankistrodesmus convolutus Corda. Mol Biol Rep. 2011;38:177–182. doi:10.1007/s11033-010-0092-4
  • Li X, Shangguan L, Song C, Wang C, Gao Z, Yu H, Fang J. Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers. BMC Genet. 2010;11:66. doi:10.1186/1471-2156-11-66
  • Passos MAN, de Oliveira Cruz V, Emediato FL, de Camargo Teixeira C, Souza MT, Matsumoto T, Renno Azevedo VC, Ferreira CF, Amorim EP, de Alencar Figueiredo LF, Martins NF, de Jesus Barbosa Cavalcante M, Baurens FC, da Silva OB Jr, Pappas GJ Jr, Pignolet L, Abadie C, Ciampi AY, Piffanelli P, Miller RN. Development of expressed sequence tag and expressed sequence tag-simple sequence repeat marker resources for Musa acuminata. AoB Plants. 2012;pls030. doi:10.1093/aobpla/pls030
  • Yamada-Akiyama H, Akiyama Y, Ebina M, Xu Q, Tsuruta S-i, Yazaki J, Kishimoto N, Kikuchi S, Takahara M, Takamizo T, Sugita S-i, Nakagawa H. Analysis of expressed sequence tags in apomictic guineagrass (Panicum maximum). J Plant Physiol. 2009;166:750–761. doi:10.1016/j.jplph.2008.10.001
  • Khaembah EN, Irving LJ, Thom ER, Faville MJ, Easton HS, Matthew C. Leaf rubisco turnover in a perennial ryegrass (Lolium perenne L.) mapping population: genetic variation, identification of associated QTL, and correlation with plant morphology and yield. J Exp Bot. 2013;64:1305–1316. doi:10.1093/jxb/ers384
  • Kunkeaw S, Yoocha T, Sraphet S, Boonchanawiwat A, Boonseng O, Lightfoot DA, Triwitayakorn K, Tangphatsornruang S. Construction of a genetic linkage map using simple sequence repeat markers from expressed sequence tags for cassava (Manihot esculenta Crantz). Mol Breed. 2011;27:67–75. doi:10.1007/s00122-010-1520-5
  • Numa H, Itoh T. Megante: a web-based system for integrated plant genome annotation. Plant Cell Physiol. 2014;55(1):e2. doi:10.1093/pcp/pct157
  • Rudd S. Expressed sequence tags: alternative or complement to whole genome sequence. Trends Plant Sci. 2003;8:321–329. doi:10.1016/S1360-1385(03)00131-6
  • Zhuang J, Xiong AS, Peng R-H, Gao F, Zhu B, Zhang J, Fu XY, Jin X-F, Chen J-M, Zhang Z, Qiao Y-S, Yao Q-H. Analysis of Brassica rapa ESTs: gene discovery and expression patterns of AP2/ERF family genes. Mol Biol Rep. 2010;37:2485–2492. doi:10.1007/s11033-009-9763-4
  • Shao ZT, Cong X, Yuan J-d, Yang G-w, Chen Y, Pan J, An L-g. Construction and characterization of a cDNA library from head kidney of Japanese sea bass (Lateolabrax japonicus). Mol Biol Rep. 2009;36:2031–2037. doi:10.1007/s11033-009-9536-0
  • Tabata S. Impact of genomics approaches on plant genetics and physiology. J Plant Res. 2002;115:271–275. doi:10.1007/s10265-002-0036-8
  • Abe H, Narusaka Y, Sasaki I, Hatakeyama K, Shin S, Narusaka M, Fukami-Kobayashi K, Matsumoto S, Kobayashi M. Development of full-length cDNAs from Chinese cabbage (Brassica rapa Subsp. pekinensis) and identification of marker genes for defence response. DNA Res. 2011;18:277–289. doi:10.1093/dnares/dsr018
  • Seki M, Narusaka M, Kamiya A, Ishida J, Satou M, Sakurai T, Nakajima M, Enju A, Akiyama K, Oono Y. Functional annotation of a full-length Arabidopsis cDNA collection. Science. 2002;296:141–145. doi:10.1126/science.1071006
  • Qian G, Ping J, Lu J, Zhang Z, Wang L, Xu D. Construction of full-length cDNA library and development of EST-derived simple sequence repeat (EST-SSR) markers in Senecio scandens. Biochem Genet. 2014;52:in press. doi:10.1007/s10528-014-9662-9
  • Shapiro E, Baneyx F. Stress-based identification and classification of antibacterial agents: second-generation Escherichia coli reporter strains and optimization of detection. Antimicrob Agents Chemother. 2002;46:2490–2497. doi:10.1128/AAC.46.8.2490-2497.2002
  • Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 2001;11:1095–1099. doi:10.1101/gr.180501
  • Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998;8:186–194. doi:10.1101/gr.8.3.175
  • Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 1998;8:967–974. doi:10.1101/gr.8.9.967
  • Huang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res. 1999;9:868–877. doi:10.1101/gr.9.9.868
  • Franco GR, Adams MD, Soares MB, Simpson AJG, Venter JC, Pena SDJ. Identification of new Schistosoma mansoni genes by the EST strategy using a directional cDNA library. Gene. 1995;152:141–147. doi:10.1016/0378-1119(94)00747-G
  • Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 2003;31:224–228. doi:10.1093/nar/gkg076
  • Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN. The COG database: an updated version includes eukaryotes. BMC Bioinform. 2003;4:41. doi:10.1186/1471-2105-4-41
  • Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller V, Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. doi:10.1093/nar/25.17.3389
  • Thompson JD, Higgin DG, Gibson TJ. Clustal W improving the sensitive of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weigh matrix choice. Nucleic Acids Res. 1994;22:4673–4680. doi:10.1093/nar/22.22.4673
  • Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A, Akiyama K, Kurotani A, Yoshida T, Mochida K, Kasuga M, Todaka D, Maruyama K, Nakashima K, Enju A, Mizukado S, Ahmed S, Yoshiwara K, Harda K, Tsubokura Y, Hayashi M, Sato S, Anai T, Ishimoto M, Funatsuki H, Teraishi M, Osaki M, Shinano T, Akashi R, Sakaki Y, Yamaguchi-Shinozaki K, Shinozaki K. Sequencing and analysis of approximately 40 000 soybean cDNA clones from a full-length-enriched cDNA library. DNA Res. 2008;15:333–346. doi:10.1093/dnares/dsn024
  • Adams MD, Kerlavage AR, Fleischmann RD, Fuldner RA, Bult CJ, Lee NH, Kirkness EF, Weinstock KG, Gocayne JD, White O. Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature. 1995;377(6547 suppl):3–17.
  • Nanjo T, Futamura N, Nishiguchi M, Igasaki T, Shinozaki K, Shinohara K. Characterization of full-length enriched expressed sequence tags of stress-treated poplar leaves. Plant Cell Physiol. 2004;45:1738–1748. doi:10.1093/pcp/pci009
  • Kong Q, Xiang C, Yu Z, Zhang C, Liu F, Peng C, Peng X. Mining and charactering microsatellites in Cucumis melo expressed sequence tags from sequence database. Mol Ecol Notes. 2007;7:281–283. doi:10.1111/j.1471-8286.2006.01580.x
  • Thiel T, Michalek W, Varshney RK, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet. 2003;106:411–422. doi:10.1007/s00122-002-1031-0
  • Fan L, Zhang M-Y, Liu Q-Z, Li L-T, Song Y, Wang L-F, Wang L-F, Zhang S-L, Wu J. Transferability of newly developed pear SSR markers to other Rosaceae species. Plant Mol Biol Rep. 2013;31:1271–1282. doi:10.1007/s11105-013-0586-z
  • Kakizaki T, Kato T, Fukino N, Ishida M, Hatakeyama K, Matsumoto S. Identification of quantitative trait loci controlling late bolting in Chinese cabbage (Brassica rapa L.) parental line Nou 6 gou. Breed Sci. 2011;61:151–159. doi:10.1270/jsbbs.61.151
  • Stephenson P, Baker D, Girin T. A rich TILLING resource for studying gene function in Brassica rapa. BMC Plant Biol. 2010;10:62. doi:10.1186/1471-2229-10-62
  • Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya M, Shibata K, Sasaki N. Izawa M. High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics. 1996;37:327–336. doi:10.1006/geno.1996.0567
  • Gupta PK, Varshney RK. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica. 2000;113:163–85. doi:10.1023/A:1003910819967
  • Jia J, Fu J, Zheng J, Zhou X, Huai J, Wang J, Wang M, Zhang Y, Chen X, Zhang J. Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings. Plant J. 2006;48:710–727. doi:10.1111/j.1365-313X.2006.02905.x
  • Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science. 2003;301:376–379. doi:10.1126/science.1081288