This article is part of the supplement: Eleventh International Conference on Bioinformatics (InCoB2012): Computational Biology

Open Access Proceedings

Metagenomic profiles of free-living archaea, bacteria and small eukaryotes in coastal areas of Sichang island, Thailand

Naraporn Somboonna1*, Anunchai Assawamakin2, Alisa Wilantho2, Sithichoke Tangphatsornruang2 and Sissades Tongsima2

Author Affiliations

1 Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand

2 Genome Institute, National Center for Genetic Engineering and Biotechnology, Klong 1, Klong Luang, Pathum thani 12120, Thailand

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BMC Genomics 2012, 13(Suppl 7):S29  doi:10.1186/1471-2164-13-S7-S29

Published: 13 December 2012

Additional files

Additional File 1:

Marine characteristics of Tha Wang coast, Tham Phang coast, and 67 GOS sites. Geographical and chemical properties include site description, latitude and longitude, depth level, temperature, salinity in practical salinity unit (psu; formerly called parts per thousand), pH and conductivity. Information of all GOS, in numerical order based on the GOS station names, was downloaded from https://portal.camera.calit2.net/gridsphere/gridsphere webcite.

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Additional File 2:

Agarose-electrophoretic gel showing 3 Tha Wang and 3 Tham Phang metagenomic DNAs. Left lane is a 10 kb DNA marker where the top band is at 12 kb, and right lane is 80 ng of a 40 kb fosmid control.

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Additional File 3:

Schematic diagrams of free-living prokaryotic (A-C) and eukaryotic (D-F) species at Tha Wang and Tham Phang coasts. For 16S rDNA reads, each identified read, representing by a red (Tha Wang) or blue (Tham Phang) dot, is annotated to genus and species level by BLASTN with E-value ≤ 1E-08 against NCBI non-redundant databases. For 18S rDNA reads, each identified read, representing by a red (Tha Wang) or blue (Tham Phang) dot, is annotated to genus and species level by BLASTN with E-value ≤ 1E-08 against NCBI non-redundant, EMBL and SILVA databases. Pale red and blue color dot represents inclusion of significant hits with 1E-08 < E-value ≤ 1E-02. In C and F, grey dot represents species found in both Tha Wang and Tham Phang. Each dot was placed on a circular diagram in respect to its species annotation. Species were arranged following their relative genetic distances among one another. Dot size refers to a percent relative abundance as more than one read could be annotated the same species. Different typefont color represents species belonging to different phylum. See Methods for details.

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Additional File 4:

Similarity coefficient values representing relatedness among pairs of prokaryotic community structures of Tha Wang, Tham Phang and 67 GOS. Different pairs of the 16S rDNA metagenomic profiles belonging to coastal Tha Wang, coastal Tham Phang, and 67 GOS were compared via Thetayc and Thetan similarity coefficients. Thetayc and Thetan were computed using mothur with default parameters and at distance of 0.03 [18]. The results were ranged in the order starting from the most closely related to the farthest related pairs of communities. Identical community structures have Thetayc and Thetan equal to zero.

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