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Not AvailableWhole genome sequencing (WGS) using next generation sequencing technologies paves the way to sequence the mitochondrial genomes with greater ease and lesser time. Here, we used the WGS data of Clarias batrachus, generated from Roche 454 and Ion Torrent sequencing platforms, to assemble the complete mitogenome using both de novo and reference based approaches. Both the methods yielded almost similar results and the best assembled mitogenome was of 16,510 bp size (GenBank Acc. No. KM259918). The mitogenome annotation resulted in 13 coding genes, 22 tRNA genes, 2 rRNA genes and one control region, and the gene order was found to be identical with other catfishes. Variation analyses between assembled and the reference (GenBank Acc. No. NC_023923) mitogenome revealed 51 variations. The phylogenetic analysis of coding DNA sequences and tRNA supports the monophyly of catfishes. Two SSRs were identified in C. batrachus mitogenome, out of which one was unique to this species. Based on the relative rate of gene evolution, protein coding mitochondrial genes were found to evolve at a much faster pace than the D-loop, which in turn are followed by the rRNAs; the tRNAs showed wide variability in the rate of sequence evolution, and on average evolve the slowest. Among the coding genes, ND2 evolves most rapidly. The variations present in the coding regions of the mitogenome and their comparative analyses with other catfish species may be useful in species conservation and management programs.Not Availabl

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Not AvailableWhole genome sequencing (WGS) using next generation sequencing technologies paves the way to sequencethe mitochondrial genomes with greater ease and lesser time. Here, we used the WGS data ofClarias batrachus,generated from Roche 454 and Ion Torrent sequencing platforms, to assemble the complete mitogenome usingbothde novoand reference based approaches. Both the methods yielded almost similar results and the bestassembled mitogenome was of 16,510 bp size (GenBank Acc. No. KM259918). The mitogenome annotationresulted in 13 coding genes, 22 tRNA genes, 2 rRNA genes and one control region, and the gene order wasfound to be identical with other catfishes. Variation analyses between assembled and the reference (GenBankAcc. No. NC_023923) mitogenome revealed 51 variations. The phylogenetic analysis of coding DNA sequencesand tRNA supports the monophyly of catfishes. Two SSRs were identified inC. batrachusmitogenome, out ofwhich one was unique to this species. Based on the relative rate of gene evolution, protein coding mitochondrialgenes were found to evolve at a much faster pace than theD-loop, which in turn are followed by the rRNAs; thetRNAs showed wide variability in the rate of sequence evolution, and on average evolve the slowest. Among thecoding genes,ND2evolves most rapidly. The variations present in the coding regions of the mitogenome andtheir comparative analyses with other catfish species may be useful in species conservation and management programsDepartment of Biotechnology, Ministry of Science and Technology,Gov. of India, New Delhi, India vide Sanction Grant No. BT/PR3688/AAQ/3/571/201

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

Malassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina, (Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens. Malassezia are typically isolated from warm-blooded animals, are dominant members of the human skin mycobiome and are associated with common skin disorders. To characterize the genetic basis of the unique phenotypes of Malassezia spp., we sequenced the genomes of all 14 accepted species and used comparative genomics against a broad panel of fungal genomes to comprehensively identify distinct features that define the Malassezia gene repertoire: gene gain and loss; selection signatures; and lineage-specific gene family expansions. Our analysis revealed key gene gain events (64) with a single gene conserved across all Malassezia but absent in all other sequenced Basidiomycota. These likely horizontally transferred genes provide intriguing gain-of-function events and prime candidates to explain the emergence of Malassezia. A larger set of genes (741) were lost, with enrichment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation to skin's carbohydrate-deficient environment. Gene family analysis revealed extensive turnover and underlined the importance of secretory lipases, phospholipases, aspartyl proteases, and other peptidases. Combining genomic analysis with a re-evaluation of culture characteristics, we establish the likely lipid-dependence of all Malassezia. Our phylogenetic analysis sheds new light on the relationship between Malassezia and other members of Ustilaginomycotina, as well as phylogenetic lineages within the genus. Overall, our study provides a unique genomic resource for understanding Malassezia niche-specificity and potential virulence, as well as their abundance and distribution in the environment and on human skin

Assembly and annotation statistics for <i>Malassezia</i> genomes in this study.

<p>*CBS: CBS-KNAW Fungal Biodiversity Centre, <a href="http://www.cbs.knaw.nl/" target="_blank">http://www.cbs.knaw.nl/</a>;</p><p>TB: Teun Boekhout;</p><p>ATCC: The Global Bioresource Center, <a href="http://www.atcc.org" target="_blank">www.atcc.org</a>.</p><p>Note the statistics for the previously reported <i>M</i>. <i>globosa</i> [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005614#pgen.1005614.ref002" target="_blank">2</a>] and <i>M</i>. <i>sympodialis</i> [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005614#pgen.1005614.ref014" target="_blank">14</a>] assemblies are provided for reference.</p

Lipid specificity and extensive turnover in the lipase gene family.

<p>A) Representative lipid assimilation assay images. Letters correspond to lipid wells (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005614#pgen.1005614.s028" target="_blank">S5 Table</a>). White letters indicate no growth, while green letters indicate growth on visual scale. B) Gene gains and losses in phosphoesterase family PF04185, where “+” indicates the number of gene gain events while “-” indicates the number of gene loss events. Shaded numbers indicate the estimated gene copy number in the most recent common ancestor and gene copy numbers in the observed species.</p

Characterizing the diversity of <i>Malassezia</i> in skin samples.

<p>A) The relative abundance of various <i>Malassezia</i> species (y-axis) in skin samples from different body sites (labels on the x-axis) and individuals (separated by white columns) is depicted. Samples where >99% of reads came from <i>M</i>. <i>globosa</i> and <i>M restricta</i> are not shown here. The numbers of samples and the numbers of individuals in which each species was found is indicated in the legend on the right. B) Z-score transformed normalized read counts for the top 10 copy number variable genes in <i>M</i>. <i>restricta</i> 7877 (measured in terms of coefficient of variation of normalized counts) across six skin samples.</p

Correctness and completeness of <i>Malassezia</i> assembly and annotation.

<p>A) Assembly completeness in terms of partial and complete core eukaryotic genes that can be detected in each genome. As shown here, the assemblies from this study are comparable to published references for <i>M</i>. <i>globosa</i> and <i>M</i>. <i>sympodialis</i> and are very similar to the gold-standard <i>S</i>. <i>cerevisiae</i> genome. B) Whole-genome alignment of the assembly of <i>M</i>. <i>globosa</i> 7966 in this study as compared to the published reference, highlighting the robust assembly and the lack of clear misassemblies. C) Comparison of an annotation of <i>M</i>. <i>globosa</i> 7966 in this study with the reference annotation, using alignments to <i>S</i>. <i>cerevisiae</i> as a gold-standard. Y-axis indicates the BLAST bitscore difference between the top matches from the new and old annotations to the same <i>S</i>. <i>cerevisiae</i> protein. X-axis indicates the number of <i>S</i>. <i>cerevisiae</i> proteins. Red circles indicate <i>S</i>. <i>cerevisiae</i> proteins with a better match to the new annotation. Blue circles indicate <i>S</i>. <i>cerevisiae</i> proteins with a better match to the reference annotation.</p

Comparison of annotation quality for the iterative annotation pipeline in this study with a reference annotation.

<p>Results shown are for the <i>M</i>. <i>globosa</i> genome.</p