Marine Genomics

A dataset used for establishing whether diatom genes are closer to red algae or green ones. Based on genomes of P. tricornutum, Th. pseudonana, S. acus subsp. radians, F. solaris, F. cylindrus and P.-n. multiseries, as well as all available diatom transcriptomes from MMETSP. The dataset includes ML and UPGMA trees, Likelihood mapping raw data, alignments used for the above and the results of DIAMOND search of diatom predicted proteins against NCBI nr.

Transcriptome of Acropora gemmifera. Sample collected in Southern Taiwan at 3 - 4 m depth.

This is a fasta alignment of the amino acid sequences analysed in this paper. Most sequences are identified by GenBank accession number. Accessions from the DDBJ or EMBL are specified by "accession from". The Nerita, Georissa and Pleuropoma sequences are identified by the contig number in the partial assemblies referred to in the manuscript. The GenBank accession numbers for these are MF380517 - MF380527 and MF510930 - MF510933. The GenBank Crassostrea gigas sequences are identified by CGI and the locus-tag. Human aquaporins are identified by the aquaporin type followed by the GenBank accession number. Sequences beginning with PC are deduced from the transcriptome data for Pomacea canaliculata published by Sun et al. 2012. (De novo assembly of the transcriptome of an invasive snail and its multiple ecological applications. Mol. Ecol. Resources 12, 1133–1144.)

A fasta file of all consensus muscle contig sequences.

Gene expression profile from gill and muscle tissue samples. Juvenile abalones were exposed to a temperature ramp (+3 °C day−1) under hypoxia (50% air saturation) and hypercapnia (~1000 μatm pCO2), both individually and in combination. Experiments are denoted as control (warming under normoxic normocapnia), hypoxia (warming under hypoxic normocapnia), hypercapnia (warming under normoxic hypercapnia, and combined (warming under hypoxic hypercapnia). The table is arranged to be used with the R package MCMC.qPCR (Matz et al., 2013).

Metabolomic analysis has shown the chemical richness of the sponge-associated actinomycetes Streptomyces sp. SBT349, Nonomureae sp. SBT364, and Nocardiopsis sp. SBT366. The genomes of these actinomycetes were sequenced and the genomic potential for secondary metabolism was evaluated. Their draft genomes have sizes of 8.0, 10, and 5.8Mb having 687, 367, and 179 contigs with a GC content of 71.6, 70.7, and 72.7%, respectively. Moreover, antiSMASH 3.0 predicted 108, 149, and 75 secondary metabolite gene clusters, respectively which highlight the metabolic capacity of the three actinomycete species to produce diverse classes of natural products.