Illumina TruSeq adapters and poly-A tails were trimmed from raw reads using the Fastx_toolkit clipper function. Fastq_quality_filter was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 80% of bases within a\u00a0read\u00a0meeting this quality score requirement. Any remaining raw sequences less than 50 base pairs in length were also removed. Merged files were assembled\u00a0de novo\u00a0using Trinity (Grabherr et al. 2011). The resulting assembly was filtered to remove contigs less than 200 bp in length. Trinity-assembled contigs which exhibited sequence overlap were grouped into isogroups which were then used for sequence homology searches (BLASTx E-value \u2264 10-4) against the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (Kanehisa 2006).<\/p>\n
Gene biogeographical distributions -\u00a020 genes of interest were selected in the study to investigate the molecular basis of iron and light limitation in polar diatoms. Reference sequences for each of these genes were obtained from the\u00a0F.\u00a0cylindrus\u00a0and\u00a0P.\u00a0tricornutum\u00a0JGI genome portals and\u00a0T.\u00a0pseudonana\u00a0and\u00a0T.\u00a0oceanica\u00a0NCBI and GenBank repositories. Reference sequences were identified in the transcriptomes by translated nucleotide homology searches (tBLASTn) with an e-value cutoff of <10-5. A reciprocal tBLASTn homology search was performed for each transcriptome against the KEGG GENES database, using the single-directional\u00a0best-hit\u00a0method in the KAAS online tool to ensure consistent gene annotations (Moriya et al. 2007).<\/p>\n
Subsequently, reference sequences were identified in the MMETSP protein database by BLASTp (e-value <10-5) homology searches among the diatom transcriptomes. The transcriptomes and their associated latitude and longitude were obtained from iMicrobe Data Commons (Project Code CAM_P_0001000) and the National Center for Marine Algae and Microbiota (NCMA). Custom Matlab scripts allowed global biogeographical distribution of key genes of interest to be mapped.<\/p><\/div>","@type":"rdf:HTML"}],"http:\/\/ocean-data.org\/schema\/hasBriefDescription":[{"@value":"BLASTp homology data from genes obtained in samples collected on LMG1411.","@language":"en-US"}],"http:\/\/purl.org\/dc\/terms\/description":[{"@value":"
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