Sequencing and De Novo Analysis of a Coral Larval Transcriptome Using 454 GSFlx

Simple item page
dc.contributor.utaustinauthorMeyer, Elien_US
dc.contributor.utaustinauthorAglyamova, Galina V.en_US
dc.contributor.utaustinauthorWang, Shien_US
dc.contributor.utaustinauthorMatz, Mikhail V.en_US
dc.creatorMeyer, Elien_US
dc.creatorAglyamova, Galina V.en_US
dc.creatorWang, Shien_US
dc.creatorBuchanan-Carter, Jadeen_US
dc.creatorAbrego, Daviden_US
dc.creatorColbourne, John K.en_US
dc.creatorWillis, Bette L.en_US
dc.creatorMatz, Mikhail V.en_US
dc.date.accessioned2016-10-28T19:49:50Z
dc.date.available2016-10-28T19:49:50Z
dc.date.issued2009-05en_US
dc.description.abstractNew methods are needed for genomic-scale analysis of emerging model organisms that exemplify important biological questions but lack fully sequenced genomes. For example, there is an urgent need to understand the potential for corals to adapt to climate change, but few molecular resources are available for studying these processes in reef-building corals. To facilitate genomics studies in corals and other non-model systems, we describe methods for transcriptome sequencing using 454, as well as strategies for assembling a useful catalog of genes from the output. We have applied these methods to sequence the transcriptome of planulae larvae from the coral Acropora millepora. Results: More than 600,000 reads produced in a single 454 sequencing run were assembled into similar to 40,000 contigs with five-fold average sequencing coverage. Based on sequence similarity with known proteins, these analyses identified similar to 11,000 different genes expressed in a range of conditions including thermal stress and settlement induction. Assembled sequences were annotated with gene names, conserved domains, and Gene Ontology terms. Targeted searches using these annotations identified the majority of genes associated with essential metabolic pathways and conserved signaling pathways, as well as novel candidate genes for stress-related processes. Comparisons with the genome of the anemone Nematostella vectensis revealed similar to 8,500 pairs of orthologs and similar to 100 candidate coral-specific genes. More than 30,000 SNPs were detected in the coral sequences, and a subset of these validated by re-sequencing. Conclusion: The methods described here for deep sequencing of the transcriptome should be widely applicable to generate catalogs of genes and genetic markers in emerging model organisms. Our data provide the most comprehensive sequence resource currently available for reef-building corals, and include an extensive collection of potential genetic markers for association and population connectivity studies. The characterization of the larval transcriptome for this widely-studied coral will enable research into the biological processes underlying stress responses in corals and evolutionary adaptation to global climate change.en_US
dc.description.departmentIntegrative Biologyen_US
dc.description.sponsorshipLilly Endowment, Inc.en_US
dc.description.sponsorshipThe University Information Technology Services (UITS)en_US
dc.description.sponsorshipThe Center for Genomics and Bioinformatics Computing Groupen_US
dc.identifierdoi:10.15781/T29P2W86R
dc.identifier.citationMeyer, Eli, Galina V. Aglyamova, Shi Wang, Jade Buchanan-Carter, David Abrego, John K. Colbourne, Bette L. Willis, and Mikhail V. Matz. "Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx." BMC genomics, Vol. 10, No. 1 (May, 2009): 1.en_US
dc.identifier.doi10.1186/1471-2164-10-219en_US
dc.identifier.issn1471-2164en_US
dc.identifier.urihttp://hdl.handle.net/2152/43166
dc.language.isoEnglishen_US
dc.relation.ispartofen_US
dc.relation.ispartofserialBMC Genomicsen_US
dc.rightsAdministrative deposit of works to Texas ScholarWorks: This works author(s) is or was a University faculty member, student or staff member; this article is already available through open access or the publisher allows a PDF version of the article to be freely posted online. The library makes the deposit as a matter of fair use (for scholarly, educational, and research purposes), and to preserve the work and further secure public access to the works of the University.en_US
dc.rights.restrictionOpenen_US
dc.subjectreef-building coralsen_US
dc.subjectgreat-barrier-reefen_US
dc.subjectgene-expressionen_US
dc.subjectclimate-changeen_US
dc.subjectmontastraea-faveolataen_US
dc.subjectlife sciencesen_US
dc.subjectsnp discoveryen_US
dc.subjectgenomeen_US
dc.subjectacroporaen_US
dc.subjectconservationen_US
dc.subjectbiotechnology & applied microbiologyen_US
dc.subjectgenetics & heredityen_US
dc.titleSequencing and De Novo Analysis of a Coral Larval Transcriptome Using 454 GSFlxen_US
dc.typeArticleen_US

Access full-text files

Original bundle

Now showing 1 - 1 of 1
Thumbnail Image
Name:
2009_05_Meyer.pdf
Size:
443.75 KB
Format:
Adobe Portable Document Format
Download

License bundle

Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.65 KB
Format:
Plain Text
Description:
Download

Collections

UT Faculty/Researcher Works