Additional file 1: of Development of a genus-specific next generation sequencing approach for sensitive and quantitative determination of the Legionella microbiome in freshwater systems

The additional file provides supplementary material contained in Figures S1 to S9 and Tables S1 to S6. Figure S1. Comparison of cumulative 16S rRNA gene V3-V4 sequences abundance with sequence identity to L. pneumophila ATCC 33152T using KAPA HiFi and HotStarTaq DNA polymerases. Figure S2. Error rate profiling with KAPA HiFi and HotStarTaq DNA polymerases. Figure S3. Hypervariable regions within the 16S rRNA gene in the genus Legionella. Figure S4. Phylogenetic resolution of the 16S rRNA gene V3-V4 region for the genus Legionella, amplified by primer pair Lgsp17F/Lgsp28R. Figure S5. Sequence identity of Legionella 16S rRNA gene V3-V4 sequences to the sequences of L. pneumophila ATCC 33152T. Figure S6. Rarefaction curves of Legionella OTUs diversity for 7 water samples using the genus-specific NGS approach. Figure S7. Within-sample and inter-sample distinctiveness of Legionella microbiome structure. Figure S8. Rarefaction curves of bacterial OTUs diversity for 7 water samples using the pan-bacterial NGS approach. Figure S9. Sensitive quantitative determination of L. pneumophila by the genus-specific and pan-bacterial NGS approach. Table S1a. Nucleotide sequences of Legionella genus-specific NGS primers, targeting 16S rRNA gene, used in the first amplification step (target-specific) of the library preparation for Illumina MiSeq Sequencing. Table S1b. Nucleotide sequences of primers, targeting 16S rRNA gene, used in the second amplification step (multiplexing) of the library preparation for Illumina MiSeq Sequencing. Table S2. Alpha-diversity of Legionella community between replicates (n = 3) within each of the 7 water samples analysed. Table S3. Bray-Curtis similarity (BC) and Spearman rank correlation (rs) of Legionella community between replicates (n = 3) within each of the 7 water samples analysed. Table S4. Taxonomic assignment of 16S rRNA gene sequences affiliated to genus Legionella. Table S5. Relative abundance (%) of Legionella phylotypes in the 7 freshwater samples analysed. Table S6. Quantification of Legionella spp. and L. pneumophila by NGS. (DOCX 998 kb

Green Software Lab

<p>In this poster we describe the current techniques under study in the Green Software Lab, Portugal.</p

Additional file 3: of Production of β-ionone by combined expression of carotenogenic and plant CCD1 genes in Saccharomyces cerevisiae

Maps of plasmids construct in this study

Example of an electropherogram obtained for the HGDP-CEPH 0452 sample with the 46 AIM-INDEL multiplex (markers are identified by MID number).

<p>Example of an electropherogram obtained for the HGDP-CEPH 0452 sample with the 46 AIM-INDEL multiplex (markers are identified by MID number).</p

Ancestral membership proportions for testing population samples from different continental origins using the HGDP-CEPH diversity panel genetic data as training sets.

<p>Angola (Africa); Portugal (Europe); Taiwan (East Asia); Brazilian Amazonas tribes (Native America); Belém is an example of a highly admixed Brazilian city in northeastern Amazonas.</p

Ancestral membership proportions for HGDP-CEPH diversity panel samples from five continental origins using a set of 46 AIM-INDELs (based on STRUCTURE results from 3 independent runs treated in CLUMPP and plotted with <i>distruct</i>; individuals were first sorted by geographic origin of population, and within those by ascending population code and HGDP individual number).

<p>AFR: Africa; EUR: Europe; EAS: East Asia; NAM: Native America; OCE: Oceania.</p

Ancestral membership proportions for HGDP-CEPH diversity panel samples and testing populations from four continental origins.

<p>(AFR: Africa; EUR: Europe; EAS: East Asia; NAM: Native America).</p

AIM-INDELs used in the multiplex.

<p>*Nomenclature according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029684#pone.0029684-Weber1" target="_blank">[7]</a> and Marshfield Diallelic Insertion/Deletion Polymorphisms database;</p><p>**Mapping data according to dbSNP (build 132).</p

Evaluating the X Chromosome-Specific Diversity of Colombian Populations Using Insertion/Deletion Polymorphisms

<div><p>The European and African contribution to the pre-existing Native American background has influenced the complex genetic pool of Colombia. Because colonisation was not homogeneous in this country, current populations are, therefore, expected to have different proportions of Native American, European and African ancestral contributions. The aim of this work was to examine 11 urban admixed populations and a Native American group, called Pastos, for 32 X chromosome indel markers to expand the current knowledge concerning the genetic background of Colombia. The results revealed a highly diverse genetic background comprising all admixed populations, harbouring important X chromosome contributions from all continental source populations. In addition, Colombia is genetically sub-structured, with different proportions of European and African influxes depending on the regions. The samples from the North Pacific and Caribbean coasts have a high African ancestry, showing the highest levels of diversity. The sample from the South Andean region showed the lowest diversity and significantly higher proportion of Native American ancestry than the other samples from the North Pacific and Caribbean coasts, Central-West and Central-East Andean regions, and the Orinoquian region. The results of admixture analysis using X-chromosomal markers suggest that the high proportion of African ancestry in the North Pacific coast was primarily male driven. These men have joined to females with higher Native American and European ancestry (likely resulting from a classic colonial asymmetric mating type: European male x Amerindian female). This high proportion of male-mediated African contributions is atypical of colonial settings, suggesting that the admixture occurred during a period when African people were no longer enslaved. In the remaining regions, the African contribution was primarily female-mediated, whereas the European counterpart was primarily male driven and the Native American ancestry contribution was not gender biased.</p></div

Outlining the Ancestry Landscape of Colombian Admixed Populations - Fig 1

<p>Map of the continental territory of Columbia showing the five main regions and geographical locations of sampling sites (a). The Andean sub-regions considered in the present work and their sample sizes are also indicated (b).</p