AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae

BMC Genomics

Wen-Chi Chang⁴  Ching-Nen Nathan Chen²  Tsung-Lin Liu⁴  Bo-Kai Justin Hsu¹  Chia-Hung Chien³  Yi-Fan Chiang-Hsieh³  Han-Qin Zheng⁴ 

[1]Yourgene Bioscience Company Ltd, New Taipei City 23863, Taiwan

[2]Institute of Marine Biology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan

[3]Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 70101, Taiwan

[4]Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 70101, Taiwan

关键词: Gene expression;    Systems biology;    Next-generation sequencing;    Pathway;    Algae;   

Others  :  1217763
DOI  :  10.1186/1471-2164-15-196

 received in 2013-12-04, accepted in 2014-02-26,  发布年份 2014

【 摘 要 】

Background

Algae are important non-vascular plants that have many research applications, including high species diversity, biofuel sources, and adsorption of heavy metals and, following processing, are used as ingredients in health supplements. The increasing availability of next-generation sequencing (NGS) data for algae genomes and transcriptomes has made the development of an integrated resource for retrieving gene expression data and metabolic pathway essential for functional analysis and systems biology. In a currently available resource, gene expression profiles and biological pathways are displayed separately, making it impossible to easily search current databases to identify the cellular response mechanisms. Therefore, in this work the novel AlgaePath database was developed to retrieve transcript abundance profiles efficiently under various conditions in numerous metabolic pathways.

Description

AlgaePath is a web-based database that integrates gene information, biological pathways, and NGS datasets for the green algae Chlamydomonas reinhardtii and Neodesmus sp. UTEX 2219–4. Users can search this database to identify transcript abundance profiles and pathway information using five query pages (Gene Search, Pathway Search, Differentially Expressed Genes (DEGs) Search, Gene Group Analysis, and Co-expression Analysis). The transcript abundance data of 45 and four samples from C. reinhardtii and Neodesmus sp. UTEX 2219–4, respectively, can be obtained directly on pathway maps. Genes that are differentially expressed between two conditions can be identified using Folds Search. The Gene Group Analysis page includes a pathway enrichment analysis, and can be used to easily compare the transcript abundance profiles of functionally related genes on a map. Finally, the Co-expression Analysis page can be used to search for co-expressed transcripts of a target gene. The results of the searches will provide a valuable reference for designing further experiments and for elucidating critical mechanisms from high-throughput data.

Conclusions

AlgaePath is an effective interface that can be used to clarify the transcript response mechanisms in different metabolic pathways under various conditions. Importantly, AlgaePath can be mined to identify critical mechanisms based on high-throughput sequencing. To our knowledge, AlgaePath is the most comprehensive resource for integrating numerous databases and analysis tools in algae. The system can be accessed freely online at http://algaepath.itps.ncku.edu.tw webcite.

【 授权许可】

   
2014 Zheng et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]McKendry P: Energy production from biomass (part 1): overview of biomass. Bioresour Technol 2002, 83(1):37-46.
• [2]McKendry P: Energy production from biomass (part 2): conversion technologies. Bioresour Technol 2002, 83(1):47-54.
• [3]Martin MA: First generation biofuels compete. N Biotechnol 2010, 27(5):596-608.
• [4]Fan J, Yan C, Andre C, Shanklin J, Schwender J, Xu C: Oil accumulation is controlled by carbon precursor supply for fatty acid synthesis in Chlamydomonas reinhardtii. Plant Cell Physiol 2012, 53(8):1380-1390.
• [5]Singh J, Gu S: Commercialization potential of microalgae for biofuels production. Renew Sust Energ Rev 2010, 14(9):2596-2610.
• [6]Lommer M, Specht M, Roy AS, Kraemer L, Andreson R, Gutowska MA, Wolf J, Bergner SV, Schilhabel MB, Klostermeier UC, Beiko RG, Rosenstiel P, Hippler M, Laroche J: Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation. Genome Biol 2012, 13(7):R66. BioMed Central Full Text
• [7]Çetinkaya Dönmez G, Aksu Z, Öztürk A, Kutsal T: A comparative study on heavy metal biosorption characteristics of some algae. Process Biochem 1999, 34(9):885-892.
• [8]Roy D, Greenlaw PN, Shane BS: Adsorption of heavy metals by green algae and ground rice hulls. J Environ Sci Health Part A 1993, 28(1):37-50.
• [9]Gupta V, Shrivastava A, Jain N: Biosorption of Chromium (VI) from Aqueous solutions by green algae spirogyra species. Water Res 2001, 35(17):4079-4085.
• [10]Katz ME, Wright JD, Miller KG, Cramer BS, Fennel K, Falkowski PG: Biological overprint of the geological carbon cycle. Mar Geol 2005, 217(3):323-338.
• [11]Longhurst AR: Role of the marine biosphere in the global carbon cycle. Limnol Oceanogr 1991, 36(8):1507-1526.
• [12]Wang ST, Pan YY, Liu CC, Chuang LT, Chen CNN: Characterization of a green microalga UTEX 2219–4: effects of photosynthesis and osmotic stress on oil body formation. Bot Stud 2011, 52(3):305-312.
• [13]Boyle NR, Page MD, Liu B, Blaby IK, Casero D, Kropat J, Cokus SJ, Hong-Hermesdorf A, Shaw J, Karpowicz SJ, Gallaher SD, Johnson S, Benning C, Pellegrini M, Grossman A, Merchant SS: Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J Biol Chem 2012, 287(19):15811-15825.
• [14]Fang W, Si Y, Douglass S, Casero D, Merchant SS, Pellegrini M, Ladunga I, Liu P, Spalding MH: Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. Plant Cell 2012, 24(5):1876-1893.
• [15]Fischer BB, Ledford HK, Wakao S, Huang SG, Casero D, Pellegrini M, Merchant SS, Koller A, Eggen RI, Niyogi KK: Singlet oxygen resistant 1 links reactive electrophile signaling to singlet oxygen acclimation in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A 2012, 109(20):E1302-E1311.
• [16]Gonzalez-Ballester D, Casero D, Cokus S, Pellegrini M, Merchant SS, Grossman AR: RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. Plant Cell 2010, 22(6):2058-2084.
• [17]Miller R, Wu G, Deshpande RR, Vieler A, Gartner K, Li X, Moellering ER, Zauner S, Cornish AJ, Liu B, Bullard B, Sears BB, Kuo MH, Hegg EL, Shachar-Hill Y, Shiu SH, Benning C: Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism. Plant Physiol 2010, 154(4):1737-1752.
• [18]Urzica EI, Adler LN, Page MD, Linster CL, Arbing MA, Casero D, Pellegrini M, Merchant SS, Clarke SG: Impact of oxidative stress on ascorbate biosynthesis in Chlamydomonas via regulation of the VTC2 gene encoding a GDP-L-galactose phosphorylase. J Biol Chem 2012, 287(17):14234-14245.
• [19]Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P: Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv. Bioinform 2008, 2008:420747.
• [20]Patel RV, Nahal HK, Breit R, Provart NJ: BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species. Plant J cCell Mole Biol 2012, 71(6):1038-1050.
• [21]Latendresse M, Paley S, Karp PD: Browsing metabolic and regulatory networks with BioCyc. Methods Mol Biol 2012, 804:197-216.
• [22]Lopez D, Casero D, Cokus SJ, Merchant SS, Pellegrini M: Algal functional annotation tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. BMC Bioinform 2011, 12:282. BioMed Central Full Text
• [23]Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS: Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 2012, 40(Database issue):D1178-D1186.
• [24]Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD: The Pfam protein families database. Nucleic Acids Res 2012, 40(Database issue):D290-D301.
• [25]Mi H, Muruganujan A, Thomas PD: PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res 2013, 41(Database issue):D377-D386.
• [26]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(1):41. BioMed Central Full Text
• [27]Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(4):357-359.
• [28]Kent WJ: BLAT---the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664.
• [29]Hu Q, Sommerfeld M, Jarvis E, Ghirardi M, Posewitz M, Seibert M, Darzins A: Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances. Plant J Cell Mole Biol 2008, 54(4):621-639.
• [30]Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30.
• [31]Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG: Exploring the human genome with functional maps. Genome Res 2009, 19(6):1093-1106.
• [32]Rosenberg JN, Oyler GA, Wilkinson L, Betenbaugh MJ: A green light for engineered algae: redirecting metabolism to fuel a biotechnology revolution. Curr Opin Biol 2008, 19(5):430-436.
• [33]Rismani-Yazdi H, Haznedaroglu BZ, Bibby K, Peccia J: Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels. BMC Genomics 2011, 12:148. BioMed Central Full Text
• [34]Wang ZT, Ullrich N, Joo S, Waffenschmidt S, Goodenough U: Algal lipid bodies: stress induction, purification, and biochemical characterization in wild-type and starchless Chlamydomonas reinhardtii. Eukaryot Cell 2009, 8(12):1856-1868.
• [35]Zhang Z, Shrager J, Jain M, Chang CW, Vallon O, Grossman AR: Insights into the survival of Chlamydomonas reinhardtii during sulfur starvation based on microarray analysis of gene expression. Eukaryot Cell 2004, 3(5):1331-1348.
• [36]Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, et al.: The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 2007, 318(5848):245-250.