第774回 千葉医学会例会・第二内科例会 6.

ML tree made using homologous genes based on intronic ORF of trnMe tRNA in Florideophyceae. (PDF 131 kb

PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of -0

<p><b>Copyright information:</b></p><p>Taken from "PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of "</p><p>http://www.biomedcentral.com/1471-2148/8/6</p><p>BMC Evolutionary Biology 2008;8():6-6.</p><p>Published online 15 Jan 2008</p><p>PMCID:PMC2254586.</p><p></p> are performed: I. The paths from to , , and are (→ → → ), (→ y → → ), and (→ → ) respectively. II. The longest shared segment among the three paths is (→ ). III. The LCA of , , and is . IV. The subtree rooted by contains only , , and . V. , , and are monophyletic in the clade rooted by

PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of -1

<p><b>Copyright information:</b></p><p>Taken from "PhyloSort: a user-friendly phylogenetic sorting tool and its application to estimating the cyanobacterial contribution to the nuclear genome of "</p><p>http://www.biomedcentral.com/1471-2148/8/6</p><p>BMC Evolutionary Biology 2008;8():6-6.</p><p>Published online 15 Jan 2008</p><p>PMCID:PMC2254586.</p><p></p> are performed: I. The paths from to , , and are (→ → → ), (→ y → → ), and (→ → ) respectively. II. The longest shared segment among the three paths is (→ ). III. The LCA of , , and is . IV. The subtree rooted by contains only , , and . V. , , and are monophyletic in the clade rooted by

Turtle

<p>We present a novel method that balances time, space and accuracy requirements to efficiently extract frequent k-mers even for high coverage libraries and large genomes such as human. Our method is designed to minimize cache-misses in a cache-efficient manner by using a Pattern-blocked Bloom filter to remove infrequent k-mers from consideration in combination with a novel sort-and-compact scheme, instead of a Hash, for the actual counting. While this increases theoretical complexity, the savings in cache misses reduce the empirical running times. A variant can resort to a counting Bloom filter for even larger savings in memory at the expense of false negatives in addition to the false positives common to all Bloom filter based approaches. A comparison to the state-of-the-art shows reduced memory requirements and running times.</p

Phylogenomic Revisit for Green Contribution to Diatoms

<p><strong>Talk</strong> - Phylogenomic Revisit for Green Contribution to Diatoms</p> <p><strong>Meeting</strong> - The molecular life of diatoms, 25 – 28 June 2013 | Paris, France</p> <p><strong>Abstract</strong></p> <p>According to Cavalier-Smith’s 1999 “chromalveolate hypothesis”, diatoms and other chlorophyll <em>c</em>-containing algae evolved through a secondary endosymbiosis event, in which a protist, probably a heterotroph, engulfed a red alga, which gave rise to the red plastid in the ancestor of this supergroup. Thus, a significant red algal contribution to the nuclear genome of the chromalveolates was expected as a result of endosymbiotic gene transfer. However, A few years ago, we reported the identification of more than 1000 genes of green algal origin in the nuclear genome of the two diatoms <em>Thalassiosira pseudonana</em> and <em>Phaeodactylum tricornutum</em> using a phylogenomic approach. That was an intriguing and unexpected result with the contribution of the green lineage exceeding that of the red lineage by about 500 nuclear genes. We interpreted these data as a potential cryptic green endosymbiont that had once inhabited the chromalveolate host, donated genetic material, and then was lost. Our proposal has been criticized with a consensus argument suggesting that undersampling of red algal genomes back in 2009 led to an overestimation of the green contribution. Now, in the light of additional novel transcriptomic and genomic red algal datasets, we have reanalyzed the phylogeny of nuclear genes in diatoms and other chromalveolates to compare and contrast the red and green algal genetic footprints in these genomes. Here, we are going to show the results of a large-scale phylogenomic and manual analysis, providing insights into the “greening” of diatom and chromalveolate genomes.</p> <p></p

Shown are the Men proteins that control the enzymatic steps necessary for the conversion of chorismate to the final product MQ in bacteria and PhQ in cyanobacteria and in photosynthetic eukaryotes

Bayesian majority rule consensus tree of a concatenated alignment of MenF and MenD proteins. The nodal numbers represent bootstrap support values inferred using PHYML (left of slash mark) and neighbor joining (1000 replicates, right of slash mark). Only bootstrap values >50% are shown. For the sake of clarity only support values at nodes of highest interest have been included in the figure. The thick branches have a BPP > 0.95. The branch lengths in this tree are proportional to the number of substitutions per site (see scale in figure). genes encoded as clusters in chromosomes of prokaryotes and in the plastid genome of Cyanidiales (black boxes), as well as the architecture of the gene (yellow boxes) in nuclear genomes of photosynthetic eukaryotes, are indicated for each taxon. The break in the 5' terminus of in higher plants indicates a gene-splitting event during evolution [18]. In addition, in plants F is an individual gene distinct from . The gene cluster in the plastid of was only partially sequenced. White boxes with numbers inside indicate the number of genes with functions unrelated to the menaquinone biosynthesis that separate the genes. Double slashes indicate a large chromosomal separation between genes. According to their structure, gene clusters can be divided in two groups (Group 1 and Group 2) that are correlated with the tree topology. This tree was arbitrarily rooted on the branch leading to the Actinobacteria.<p><b>Copyright information:</b></p><p>Taken from "Evidence of a chimeric genome in the cyanobacterial ancestor of plastids"</p><p>http://www.biomedcentral.com/1471-2148/8/117</p><p>BMC Evolutionary Biology 2008;8():117-117.</p><p>Published online 23 Apr 2008</p><p>PMCID:PMC2412073.</p><p></p

The Chromalveolate Hypothesis

<p>Two putative “supergroups” of anciently derived photosynthetic eukaryotes exist in <a href="http://en.wikipedia.org/wiki/Tree_of_life_(science)" target="_blank">the tree of life</a>, the <a href="http://en.wikipedia.org/wiki/Archaeplastida" target="_blank">Archaeplastida</a> (i.e., Plantae; red, green [including plants], and glaucophyte algae) and the <a href="http://en.wikipedia.org/wiki/Chromalveolata" target="_blank">Chromalveolata</a> (cryptophytes, haptophytes, and stramenopiles, alveolates). It is widely accepted that the photosynthetic organelle (plastid) of Plantae traces its origin to <strong>primary <a href="http://en.wikipedia.org/wiki/Endosymbiosis" target="_blank">endosymbiosis</a></strong>, whereby a unicellular protist (the ‘host’) engulfed and retained a photosynthetic cyanobacterium (the endosymbiont). This momentous step in evolution likely occurred in the late <a href="http://en.wikipedia.org/wiki/Paleoproterozoic" target="_blank">Paleoproterozoic</a> about 1.5 billion years ago with the resulting proto-alga being the putative common ancestor of this eukaryotic supergroup. Under the most parsimonious scenario, a single Plantae ancestor underwent the exceptional process of primary endosymbiosis described above that was ultimately driven by ecological pressures acting on the host genome. Once established, the primary plastid has apparently never been lost by Plantae hosts. In contrast to Plantae, the chromalveolates gained their widespread plastid through <strong>secondary endosymbiosis</strong> (i.e., eukaryote-eukaryote), whereby under the most prominent hypothesis, a red alga was engulfed and reduced to a secondary plastid. This event occurred about 1.2 billion years ago and gave rise to the putative photosynthetic ancestor of this supergroup.</p

Turtle: Identifying frequent k-mers with cache-efficient algorithms

<p>We present a novel method that balances time, space and accuracy requirements to efficiently extract frequent k-mers even for high coverage libraries and large genomes such as human. Our method is designed to minimize cache-misses in a cache-efficient manner by using a Pattern-blocked Bloom filter to remove infrequent k-mers from consideration in combination with a novel sort-and-compact scheme, instead of a Hash, for the actual counting. While this increases theoretical complexity, the savings in cache misses reduce the empirical running times. A variant can resort to a counting Bloom filter for even larger savings in memory at the expense of false negatives in addition to the false positives common to all Bloom filter based approaches. A comparison to the state-of-the-art shows reduced memory requirements and running times.</p

Turtle Software.

<p>We present a novel method that balances time, space and accuracy requirements to efficiently extract frequent k-mers even for high coverage libraries and large genomes such as human. Our method is designed to minimize cache-misses in a cache-efficient manner by using a Pattern-blocked Bloom filter to remove infrequent $k$-mers from<br>consideration in combination with a novel sort-and-compact scheme, instead of a Hash, for the actual counting. While this increases theoretical complexity, the savings in cache misses reduce<br>the empirical running times. A variant can resort to a counting Bloom filter for even larger savings in memory at the expense of false negatives in addition to the false positives common to<br>all Bloom filter based approaches. A comparison to the state-of-the-art shows reduced memory requirements and running times.</p> <p> </p

Chlorobi and the cyanobacterial groups Oscillatoriales and Nostocales form sister clades, suggesting a HGT between these taxa

The position of diatoms (i.e., and ) MenH is indicated by the red arrow. These highly diverged long branched sequences were excluded from the final analysis. The numbers at the nodes are PHYML bootstrap values (500 replicates). Only bootstrap values >50% are shown. For the sake of clarity only support values at nodes of highest interest have been included in the figure. The thick branches have a BPP > 0.95. The branch lengths in this tree are proportional to the number of substitutions per site (see scale in figure).<p><b>Copyright information:</b></p><p>Taken from "Evidence of a chimeric genome in the cyanobacterial ancestor of plastids"</p><p>http://www.biomedcentral.com/1471-2148/8/117</p><p>BMC Evolutionary Biology 2008;8():117-117.</p><p>Published online 23 Apr 2008</p><p>PMCID:PMC2412073.</p><p></p