Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina

Handle URI:
http://hdl.handle.net/10754/561511
Title:
Rapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritina
Authors:
Wang, Hao; Zhang, Huoming ( 0000-0001-5416-0358 ) ; Wong, Yuehim; Voolstra, Christian R. ( 0000-0003-4555-3795 ) ; Ravasi, Timothy ( 0000-0002-9950-465X ) ; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Qian, Peiyuan
Abstract:
Non-model organisms represent the majority of life forms in our planet. However, the lack of genetic information hinders us to understand the unique biological phenomena in non-model organisms at the molecular level. In this study, we applied a tandem transcriptome and proteome profiling on a non-model marine fouling organism, Bugula neritina. Using a 454 pyrosequencing platform with the updated titanium reagents, we generated a total of 48M bp transcriptome data consisting of 131 450 high-quality reads. Of these, 122 650 reads (93%) were assembled to produce 6392 contigs with an average length of 538 bases and the remaining 8800 reads were singletons. Of the total 15 192 unigenes, 13 863 ORFs were predicated, of which 6917 were functionally annotated based on gene ontology and eukaryotic orthologous groups. Subsequent proteome analysis identified and quantified 882 proteins from B. neritina. These results would provide fundamental and important information for the subsequent studies of molecular mechanism in larval biology, development, antifouling research. Furthermore, we demonstrated, for the first time, the combined use of two high-throughput technologies as a powerful approach for accelerating the studies of non-model but otherwise important species. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA.
KAUST Department:
KAUST Global Collaborative Research Program; Biosciences Core Lab; Biological and Environmental Sciences and Engineering (BESE) Division; Marine Science Program; Red Sea Research Center (RSRC); Bioscience Program; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Applied Mathematics and Computational Science Program; Reef Genomics Lab; Integrative Systems Biology Lab
Publisher:
Wiley-VCH Verlag
Journal:
Proteomics
Issue Date:
10-Jun-2010
DOI:
10.1002/pmic.201000056
PubMed ID:
20540116
Type:
Article
ISSN:
16159853
Sponsors:
The pyrosequencing raw data were submitted to the SRA of NCBI with the accession number SRA010777.2. The authors thank Dr. On On Lee and Dr. Shawn Arallno for comments and suggestions of this manuscript. This work was supported by an Award No. SA-00040/UKC0016 of the King Abdullah University of Science & Technology (KAUST), the RGC grants of HKSAR (662408, N HKUST602/09, AoE/P-04/04-02-II) to P.-Y Qian.
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Bioscience Program; Marine Science Program; Biosciences Core Lab; Applied Mathematics and Computational Science Program; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorWang, Haoen
dc.contributor.authorZhang, Huomingen
dc.contributor.authorWong, Yuehimen
dc.contributor.authorVoolstra, Christian R.en
dc.contributor.authorRavasi, Timothyen
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorQian, Peiyuanen
dc.date.accessioned2015-08-02T09:13:08Zen
dc.date.available2015-08-02T09:13:08Zen
dc.date.issued2010-06-10en
dc.identifier.issn16159853en
dc.identifier.pmid20540116en
dc.identifier.doi10.1002/pmic.201000056en
dc.identifier.urihttp://hdl.handle.net/10754/561511en
dc.description.abstractNon-model organisms represent the majority of life forms in our planet. However, the lack of genetic information hinders us to understand the unique biological phenomena in non-model organisms at the molecular level. In this study, we applied a tandem transcriptome and proteome profiling on a non-model marine fouling organism, Bugula neritina. Using a 454 pyrosequencing platform with the updated titanium reagents, we generated a total of 48M bp transcriptome data consisting of 131 450 high-quality reads. Of these, 122 650 reads (93%) were assembled to produce 6392 contigs with an average length of 538 bases and the remaining 8800 reads were singletons. Of the total 15 192 unigenes, 13 863 ORFs were predicated, of which 6917 were functionally annotated based on gene ontology and eukaryotic orthologous groups. Subsequent proteome analysis identified and quantified 882 proteins from B. neritina. These results would provide fundamental and important information for the subsequent studies of molecular mechanism in larval biology, development, antifouling research. Furthermore, we demonstrated, for the first time, the combined use of two high-throughput technologies as a powerful approach for accelerating the studies of non-model but otherwise important species. © 2010 Wiley-VCH Verlag GmbH & Co. KGaA.en
dc.description.sponsorshipThe pyrosequencing raw data were submitted to the SRA of NCBI with the accession number SRA010777.2. The authors thank Dr. On On Lee and Dr. Shawn Arallno for comments and suggestions of this manuscript. This work was supported by an Award No. SA-00040/UKC0016 of the King Abdullah University of Science & Technology (KAUST), the RGC grants of HKSAR (662408, N HKUST602/09, AoE/P-04/04-02-II) to P.-Y Qian.en
dc.publisherWiley-VCH Verlagen
dc.subjectAnimal proteomicsen
dc.subjectBugula neritinaen
dc.subjectLarval metamorphosisen
dc.subjectPyrosequencingen
dc.subjectTranscriptomeen
dc.titleRapid transcriptome and proteome profiling of a non-model marine invertebrate, Bugula neritinaen
dc.typeArticleen
dc.contributor.departmentKAUST Global Collaborative Research Programen
dc.contributor.departmentBiosciences Core Laben
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentMarine Science Programen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.contributor.departmentBioscience Programen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentApplied Mathematics and Computational Science Programen
dc.contributor.departmentReef Genomics Laben
dc.contributor.departmentIntegrative Systems Biology Laben
dc.identifier.journalProteomicsen
kaust.authorZhang, Huomingen
kaust.authorVoolstra, Christian R.en
kaust.authorRavasi, Timothyen
kaust.authorBajic, Vladimir B.en

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