A. palmata Transcriptome Public

From Polato et al. 2011, PLos ONE: "A cDNA library from a sample enriched for symbiont free larval tissue was sequenced on the 454 GS-FLX platform. Over 960,000 reads were obtained and assembled into 42,630 contigs. Annotation data was acquired for 57% of the assembled sequences. Analysis of the assembled sequences indicated that 83–100% of all A. palmata transcripts were tagged, and provided a rough estimate of the total number genes expressed in our samples (∼18,000–20,000). The coral annotation data contained many of the same molecular components as in the Bilateria, particularly in pathways associated with oxidative stress and DNA damage repair, and provided evidence that homologs of p53, a key player in DNA repair pathways, has experienced selection along the branch separating Cnidaria and Bilateria. Transcriptome wide screens of paralog groups and transition/transversion ratios highlighted genes including: green fluorescent proteins, carbonic anhydrase, and oxidative stress proteins; and functional groups involved in protein and nucleic acid metabolism, and the formation of structural molecules. These results provide a starting point for study of adaptive evolution in corals."

README

TITLE: A. palmata Transcriptome

CREATORS:
Sheila A Kitchen
Iliana Brigitta Baums

CONTRIBUTORS:
Nicholas T. Polato
J. Cristobal Vera

PROJECT DATES: December 28, 2011

PROJECT DESCRIPTION:
From Polato et al. 2011, PLos ONE: "A cDNA library from a sample enriched for symbiont
free larval tissue was sequenced on the 454 GS-FLX platform. Over 960,000 reads were
obtained and assembled into 42,630 contigs. Annotation data was acquired for 57% of the
assembled sequences. Analysis of the assembled sequences indicated that 83���100% of all
A. palmata transcripts were tagged, and provided a rough estimate of the total number
genes expressed in our samples (���18,000���20,000). The coral annotation data contained
many of the same molecular components as in the Bilateria, particularly in pathways
associated with oxidative stress and DNA damage repair, and provided evidence that
homologs of p53, a key player in DNA repair pathways, has experienced selection along
the branch separating Cnidaria and Bilateria. Transcriptome wide screens of paralog groups
and transition/transversion ratios highlighted genes including: green fluorescent proteins,
carbonic anhydrase, and oxidative stress proteins; and functional groups involved in protein a
nd nucleic acid metabolism, and the formation of structural molecules. These results provide
a starting point for study of adaptive evolution in corals."

DATA DESCRIPTION:
The file is in the FASTa format. A widely used text format for genetic, genomic and protein sequence data.
For more information see https://fasta.bioch.virginia.edu/fastawww2/fastalist2.shtml

GENETIC SOURCE:
Acropora palmata (Elkhorn Coral)

USAGE:
Most genetics software will open the file type. It is text based as well, so easily manipulated with
any programming language.

FILE MANIFEST or DATA STRUCTURE
ApaltranscriptomePolato.fa

RELATED PUBLICATIONS:
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028634

CITATION:

Polato, Nicholas, Vera, Christobal, Baums, Iliana B. 2011. A. palmata Transcriptome. doi:10.18113/S1ZW52

LICENSING:

Creative Commons Attribution 4.0 International

Items in this Work

User Activity Date
User Sheila A Kitchen has attached /concern/file_sets/qrf55z863f to A. palmata Transcriptome 9 months ago
User Robert K Olendorf has updated A. palmata Transcriptome 9 months ago
User Sheila A Kitchen has attached Apal_transcriptome_Polato.fa to A. palmata Transcriptome 9 months ago
File could not be sent to SHARE Notify 9 months ago
User Sheila A Kitchen has deposited A. palmata Transcriptome 9 months ago