1,653
Views
8
CrossRef citations to date
0
Altmetric
Articles

Transcriptome sequencing and characterization for Kappaphycus alvarezii

, , , , &
Pages 400-407 | Received 02 Jul 2014, Accepted 23 Mar 2015, Published online: 02 Sep 2015

REFERENCES

  • Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25: 3389–3402.
  • Andersson, M., Schubert, H., Pedersen, M. & Snoeijs, P. (2006). Different patterns of carotenoid composition and photosynthesis acclimation in two tropical red algae. Marine Biology, 149: 653–665.
  • Ask, E.I. & Azanza, R.V. (2002). Advances in cultivation technology of commercial eucheumatoid species: a review with suggestions for future research. Aquaculture, 206: 257–277.
  • Bhattacharya, D., Price, D.C., Chan, C.X., Qiu, H., Rose, N., Ball, S., Weber, A.P.M., Arias, M.C., Henrissat, B., Coutinho, P.M., Krishnan, A., Zauner, S., Morath, S., Hilliou, F., Egizi, A., Perrineau, M.M. & Yoon, H.S. (2013). Genome of the red alga Porphyridium purpureum. Nature Communications, 4: 1941.
  • Bixler, H.J. & Porse, H. (2010). A decade of change in the seaweed hydrocolloids industry. Journal of Applied Phycology, 23: 321–335.
  • Brown, T.A. & Shrift, A. (1981). Exclusion of selenium from proteins of selenium-tolerant astragalus species. Plant Physiology, 67: 1051–1053.
  • Cameron, M., Williams, H.E. & Cannane, A. (2004). Improved gapped alignment in BLAST. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1: 116–129.
  • Chan, C.X., Blouin, N.A., Zhuang, Y.Y., Zauner, S., Prochnik, S.E., Lindquist, E., Lin, S.J., Benning, C., Lohr, M., Yarish, C., Gantt, E., Grossman, A.R., Lu, S., Muller, K., Stiller, J.W., Brawley, S.H. & Bhattacharya, D. (2012). Porphyra (Bangiophyceae) transcriptomes provide insights into red algal development and metabolism. Journal of Phycology, 48: 1328–1342.
  • Collen, J., Porcel, B., Carre, W., Ball, S.G., Chaparro, C., Tonon, T., Barbeyron, T., Michel, G., Noel, B., Valentin, K., Elias, M., Artiguenave, F., Arun, A., Aury, J.M., Barbosa-Neto, J.F., Bothwell, J.H., Bouget, F.Y., Brillet, L., Cabello-Hurtado, F., Capella-Gutierrez, S., Charrier, B., Cladiere, L., Cock, J.M., Coelho, S.M., Colleoni, C., Czjzek, M., Da Silva, C., Delage, L., Denoeud, F., Deschamps, P., Dittami, S.M., Gabaldon, T., Gachon, C.M.M., Groisillier, A., Herve, C., Jabbari, K., Katinka, M., Kloareg, B., Kowalczyk, N., Labadie, K., Leblanc, C., Lopez, P.J., McLachlan, D.H., Meslet-Cladiere, L., Moustafa, A., Nehr, Z., Collen, P.N., Panaud, O., Partensky, F., Poulain, J., Rensing, S.A., Rousvoal, S., Samson, G., Symeonidi, A., Weissenbach, J., Zambounis, A., Wincker, P., & Boyen, C. (2013). Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the archaeplastida. Proceedings of the National Academy of Sciences USA, 110: 5247–5252.
  • Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M. & Robles, M. (2005). Blast2Go: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21: 3674–3676.
  • Dawes, C.J. & Koch, E.W. (1991). Branch, micropropagule and tissue-culture of the red algae Eucheuma denticulatum and Kappaphycus alvarezii farmed in the Philippines. Journal of Applied Phycology, 3: 247–257.
  • de Paula, E.J., Pereira, R.T.L. & Ohno, M. (1999). Strain selection in Kappaphycus alvarezii var. alvarezii (Solieriaceae, Rhodophyta) using tetraspore progeny. Journal of Applied Phycology, 11: 111–121.
  • Du, H., Bao, Z., Hou, R., Wang, S., Su, H., Yan, J., Tian, M., Li, Y., Wei, W., Lu, W., Hu, X., Wang, S. & Hu, J. (2012). Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867). PloS ONE, 7: e33311.
  • Ellis, D.R. & Salt, D.E. (2003). Plants, selenium and human health. Current Opinion in Plant Biology, 6: 273–279.
  • Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q.D., Chen, Z.H., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B.W., Nusbaum, C., Lindblad-Toh, K., Friedman, N. & Regev, A. (2011). Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29: 644–652.
  • Hao, D.C., Ma, P., Mu, J., Chen, S.L., Xiao, P.G., Peng, Y., Huo, L., Xu, L.J. & Sun, C. (2012). De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum. Science China – Life Sciences, 55: 452–466.
  • Ho, C.-L., Teoh, S., Teo, S.-S., Rahim, R. & Phang, S.-M. (2009). Profiling the transcriptome of Gracilaria changii (Rhodophyta) in response to light deprivation. Marine Biotechnology, 11: 513–519.
  • Hou, R., Bao, Z.M., Wang, S., Su, H.L., Li, Y., Du, H.X., Hu, J.J. & Hu, X.L. (2011). Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX. PloS ONE, 6: e21560.
  • Hua, W., Zheng, P., He, Y., Cui, L., Kong, W. & Wang, Z. (2014). An insight into the genes involved in secoiridoid biosynthesis in Gentiana macrophylla by RNA-Seq. Molecular Biology Reports, 41: 4817–4825.
  • Hurtado, A.Q., Agbayani, R.F., Sanares, R. & de Castro-Mallare, M.T.R. (2001). The seasonality and economic feasibility of cultivating Kappaphycus alvarezii in Panagatan Cays, Caluya, Antique, Philippines. Aquaculture, 199: 295–310.
  • Iseli, C., Jongeneel, C.V. & Bucher, P. (1999). ESTscan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proceedings of the International Conference on Intelligent Systems – Molecular Biology, 199: 138–148.
  • Kim, H.Y., Fomenko, D.E., Yoon, Y.E. & Gladyshev, V.N. (2006). Catalytic advantages provided by selenocysteine in methionine-s-sulfoxide reductases. Biochemistry, 45: 13697–13704.
  • Kowalczyk, N., Carre, W., Brillet, L., Corre, E., Porcel, B., Da Silva, C., Boyen, C. & Collen, J. (2011). Transcriptomic analysis of life stages of the red alga Chondrus crispus. European Journal of Phycology, 46: 96–97.
  • Li, D.J., Deng, Z., Qin, B., Liu, X.H. & Men, Z.H. (2012). De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics, 13: 192.
  • Liu, C.L., Huang, X.H. & Liu, J.G. (2009). The primary application of ISSR analysis on strains identification of Kappaphycus alvarezii. Marine Sciences, 33: 50–53.
  • Liu, C.L., Wang, X.L., Huang, X.H. & Liu, J.G. (2011). Identification of hypo-osmotically induced genes in Kappaphycus alvarezii (Solieriaceae, Rhodophyta) through expressed sequence tag analysis. Botanica Marina, 54: 557–562.
  • Liu, T.M., Zhu, S.Y., Tang, Q.M., Chen, P., Yu, Y.T. & Tang, S.W. (2013). De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud). BMC Genomics, 14: 125.
  • Lobanov, A., Fomenko, D., Zhang, Y., Sengupta, A., Hatfield, D. & Gladyshev, V. (2007). Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life. Genome Biology, 8: 1–16.
  • Lu, M.W., Ngou, F.H., Chao, Y.M., Lai, Y.S., Chen, N.Y., Lee, F.Y. & Chiou, P.P. (2012). Transcriptome characterization and gene expression of Epinephelus spp. in endoplasmic reticulum stress-related pathway during betanodavirus infection in vitro. BMC Genomics, 13: 651.
  • Matsuzaki, M., Misumi, O., Shin-I, T., Maruyama, S., Takahara, M., Miyagishima, S.Y., Mori, T., Nishida, K., Yagisawa, F., Yoshida, Y., Nishimura, Y., Nakao, S., Kobayashi, T., Momoyama, Y., Higashiyama, T., Minoda, A., Sano, M., Nomoto, H., Oishi, K., Hayashi, H., Ohta, F., Nishizaka, S., Haga, S., Miura, S., Morishita, T., Kabeya, Y., Terasawa, K., Suzuki, Y., Ishii, Y., Asakawa, S., Takano, H., Ohta, N., Kuroiwa, H., Tanaka, K., Shimizu, N., Sugano, S., Sato, N., Nozaki, H., Ogasawara, N., Kohara, Y. & Kuroiwa, T. (2004). Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature, 428: 653–657.
  • McClung, C.R. (2006). Plant circadian rhythms. Plant Cell, 18: 792–803.
  • Mendoza, W.G., Montano, N.E., Ganzon-Fortes, E.T. & Villanueva, R.D. (2002). Chemical and gelling profile of ice-ice infected carrageenan from Kappaphycus striatum (Schmitz) Doty “sacol” strain (Solieriaceae, Gigartinales, Rhodophyta). Journal of Applied Phycology, 14: 409–418.
  • Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5: 621–628.
  • Nakamura, Y., Sasaki, N., Kobayashi, M., Ojima, N., Yasuike, M., Shigenobu, Y., Satomi, M., Fukuma, Y., Shiwaku, K., Tsujimoto, A., Kobayashi, T., Nakayama, I., Ito, F., Nakajima, K., Sano, M., Wada, T., Kuhara, S., Inouye, K., Gojobori, T. & Ikeo, K. (2013). The first symbiont-free genome sequence of marine red alga, susabi-nori (Pyropia yezoensis). PloS ONE, 8: e57122.
  • Novoselov, S.V., Rao, M., Onoshko, N.V., Zhi, H., Kryukov, G.V., Xiang, Y., Weeks, D.P., Hatfield, D.L. & Gladyshev, V.N. (2002). Selenoproteins and selenocysteine insertion system in the model plant cell system, Chlamydomonas reinhardtii. EMBO Journal, 21: 3681–3693.
  • Pang, T., Liu, J.G., Liu, Q., Zhang, L.T. & Lin, W. (2012). Impacts of glyphosate on photosynthetic behaviors in Kappaphycus alvarezii and Neosiphonia savatieri detected by JIP-test. Journal of Applied Phycology, 24: 467–473.
  • Pertea, G., Huang, X.Q., Liang, F., Antonescu, V., Sultana, R., Karamycheva, S., Lee, Y., White, J., Cheung, F., Parvizi, B., Tsai, J. & Quackenbush, J. (2003). TIGR gene indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics, 19: 651–652.
  • Rodrigueza, M.R.C. & Montaño, M.N.E. (2007). Bioremediation potential of three carrageenophytes cultivated in tanks with seawater from fish farms. Journal of Applied Phycology, 19: 755–762.
  • Schonknecht, G., Chen, W.H., Ternes, C.M., Barbier, G.G., Shrestha, R.P., Stanke, M., Brautigam, A., Baker, B.J., Banfield, J.F., Garavito, R.M., Carr, K., Wilkerson, C., Rensing, S.A., Gagneul, D., Dickenson, N.E., Oesterhelt, C., Lercher, M.J. & Weber, A.P.M. (2013). Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science, 339: 1207–1210.
  • Schubert, H., Gerbersdorf, S., Titlyanov, E., Titlyanova, T., Granbom, M., Pape, C., & Luning, K. (2004). Circadian rhythm of photosynthesis in Kappaphycus alvarezii (Rhodophyta): independence of the cell cycle and possible photosynthetic clock targets. European Journal of Phycology, 39: 423–430.
  • Sors, T.G., Martin, C.P. & Salt, D.E. (2009). Characterization of selenocysteine methyltransferases from astragalus species with contrasting selenium accumulation capacity. Plant Journal, 59: 110–122.
  • Sui, C., Zhang, J., Wei, J.H., Chen, S.L., Li, Y., Xu, J.S., Jin, Y., Xie, C.X., Gao, Z.H., Chen, H.J., Yang, C.M., Zhang, Z. & Xu, Y.H. (2011). Transcriptome analysis of Bupleurum chinense focusing on genes involved in the biosynthesis of saikosaponins. BMC Genomics, 12: 539.
  • Wang, Z.Y., Fang, B.P., Chen, J.Y., Zhang, X.J., Luo, Z.X., Huang, L.F., Chen, X.L. & Li, Y.J. (2010). De novo assembly and characterization of root transcriptome using illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas). BMC Genomics, 11: 726.
  • Xiao, J., Jin, X., Jia, X., Wang, H., Cao, A., Zhao, W., Pei, H., Xue, Z., He, L., Chen, Q. & Wang, X. (2013). Transcriptome-based discovery of pathways and genes related to resistance against Fusarium head blight in wheat landrace Wangshuibai. BMC Genomics, 14: 197.
  • Xie, C.T., Li, B., Xu, Y., Ji, D.H. & Chen, C.S. (2013). Characterization of the global transcriptome for Pyropia haitanensis (Bangiales, Rhodophyta) and development of cSSR markers. BMC Genomics, 14: 107.
  • Yang, H., Mao, Y.X., Kong, F.N., Yang, G.P., Ma, F. & Wang, L. (2011). Profiling of the transcriptome of Porphyra yezoensis with solexa sequencing technology. Chinese Science Bulletin, 56: 2119–2130.
  • Ye, J., Fang, L., Zheng, H., Zhang, Y., Chen, J., Zhang, Z., Wang, J., Li, S., Li, R., Bolund, L. & Wang, J. (2006). WEGO: a web tool for plotting go annotations. Nucleic Acids Research, 34: W293–W297.
  • Zhang, J.A., Liang, S., Duan, J.L., Wang, J., Chen, S.L., Cheng, Z.S., Zhang, Q., Liang, X.Q., & Li, Y.R. (2012a). De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.).BMC Genomics, 13: 90.
  • Zhang, X.W., Ye, N.H., Liang, C.W., Mou, S.L., Fan, X., Xu, J.F., Xu, D. & Zhuang, Z.M. (2012b). De novo sequencing and analysis of the Ulva linza transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems. BMC Genomics, 13: 565.
  • Zwolak, I. & Zaporowska, H. (2012). Selenium interactions and toxicity: a review. Selenium interactions and toxicity. Cell Biology and Toxicology, 28: 31–46.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.