Complete Sequence and Analysis of the Mitochondrial Genome of Hemiselmis andersenii CCMP644 (Cryptophyceae)

<p>Abstract</p> <p>Background</p> <p>Cryptophytes are an enigmatic group of unicellular eukaryotes with plastids derived by secondary (i.e., eukaryote-eukaryote) endosymbiosis. Cryptophytes are unusual in that they possess four genomes–a host cell-derived nuclear and mitochondrial genome and an endosymbiont-derived plastid and 'nucleomorph' genome. The evolutionary origins of the host and endosymbiont components of cryptophyte algae are at present poorly understood. Thus far, a single complete mitochondrial genome sequence has been determined for the cryptophyte <it>Rhodomonas salina</it>. Here, the second complete mitochondrial genome of the cryptophyte alga <it>Hemiselmis andersenii </it>CCMP644 is presented.</p> <p>Results</p> <p>The <it>H. andersenii </it>mtDNA is 60,553 bp in size and encodes 30 structural RNAs and 36 protein-coding genes, all located on the same strand. A prominent feature of the genome is the presence of a ~20 Kbp long intergenic region comprised of numerous tandem and dispersed repeat units of between 22–336 bp. Adjacent to these repeats are 27 copies of palindromic sequences predicted to form stable DNA stem-loop structures. One such stem-loop is located near a GC-rich and GC-poor region and may have a regulatory function in replication or transcription. The <it>H. andersenii </it>mtDNA shares a number of features in common with the genome of the cryptophyte <it>Rhodomonas salina</it>, including general architecture, gene content, and the presence of a large repeat region. However, the <it>H. andersenii </it>mtDNA is devoid of inverted repeats and introns, which are present in <it>R. salina</it>. Comparative analyses of the suite of tRNAs encoded in the two genomes reveal that the <it>H. andersenii </it>mtDNA has lost or converted its original <it>trnK(uuu) </it>gene and possesses a <it>trnS</it>-derived '<it>trnK(uuu)</it>', which appears unable to produce a functional tRNA. Mitochondrial protein coding gene phylogenies strongly support a variety of previously established eukaryotic groups, but fail to resolve the relationships among higher-order eukaryotic lineages.</p> <p>Conclusion</p> <p>Comparison of the <it>H. andersenii </it>and <it>R. salina </it>mitochondrial genomes reveals a number of cryptophyte-specific genomic features, most notably the presence of a large repeat-rich intergenic region. However, unlike <it>R. salina</it>, the <it>H. andersenii </it>mtDNA does not possess introns and lacks a Lys-tRNA, which is presumably imported from the cytosol.</p

Retrotransposons and tandem repeat sequences in the nuclear genomes of cryptomonad algae

The cryptomonads are an enigmatic group of unicellular eukaryotic algae that possess two nuclear genomes, having acquired photosynthesis by the uptake and retention of a eukaryotic algal endosymbiont. The endosymbiont nuclear genome, or nucleomorph, of the cryptomonad Guillardia theta has been completely sequenced: at only 551 kilobases (kb) and with a gene density of approximately 1 gene/kb, it is a model of compaction. In contrast, very little is known about the structure and composition of the cryptomonad host nuclear genome. Here we present the results of two small-scale sequencing surveys of fosmid clone libraries from two distantly related cryptomonads, Rhodomonas salina CCMP1319 and Cryptomonas paramecium CCAP977/2A, corresponding to approximately 150 and approximately 235 kb of sequence, respectively. Very few of the random end sequences determined in this study show similarity to known genes in other eukaryotes, underscoring the considerable evolutionary distance between the cryptomonads and other eukaryotes whose nuclear genomes have been completely sequenced. Using a combination of fosmid clone end-sequencing, Southern hybridizations, and PCR, we demonstrate that Ty3-gypsy long-terminal repeat (LTR) retrotransposons and tandem repeat sequences are a prominent feature of the nuclear genomes of both organisms. The complete sequence of a 30.9-kb genomic fragment from R. salina was found to contain a full-length Ty3-gypsy element with near-identical LTRs and a chromodomain, a protein module suggested to mediate the site-specific integration of the retrotransposon. The discovery of chromodomain-containing retroelements in cryptomonads further expands the known distribution of the so-called chromoviruses across the tree of eukaryotes.Peer reviewed: YesNRC publication: Ye

Complete Sequence and Analysis of the Mitochondrial Genome of CCMP644 (Cryptophyceae)-5

Ment and a single large intergenic region. Protein-coding genes and ribosomal RNA genes are labeled outside the circle, whereas transfer RNAs and open reading frames of unknown functions are labeled on the inside. '' may be a pseudogene (see main text for discussion). Genes are color-coded according to functional categories: green for ribosomal protein genes, gray for genes involved in oxidative phosphorylation, pink for the protein translocase protein gene , salmon for ribosomal subunit genes, and black for open reading frames with unknown functions.<p><b>Copyright information:</b></p><p>Taken from "Complete Sequence and Analysis of the Mitochondrial Genome of CCMP644 (Cryptophyceae)"</p><p>http://www.biomedcentral.com/1471-2164/9/215</p><p>BMC Genomics 2008;9():215-215.</p><p>Published online 12 May 2008</p><p>PMCID:PMC2397417.</p><p></p

Complete Sequence and Analysis of the Mitochondrial Genome of CCMP644 (Cryptophyceae)-0

Ment and a single large intergenic region. Protein-coding genes and ribosomal RNA genes are labeled outside the circle, whereas transfer RNAs and open reading frames of unknown functions are labeled on the inside. '' may be a pseudogene (see main text for discussion). Genes are color-coded according to functional categories: green for ribosomal protein genes, gray for genes involved in oxidative phosphorylation, pink for the protein translocase protein gene , salmon for ribosomal subunit genes, and black for open reading frames with unknown functions.<p><b>Copyright information:</b></p><p>Taken from "Complete Sequence and Analysis of the Mitochondrial Genome of CCMP644 (Cryptophyceae)"</p><p>http://www.biomedcentral.com/1471-2164/9/215</p><p>BMC Genomics 2008;9():215-215.</p><p>Published online 12 May 2008</p><p>PMCID:PMC2397417.</p><p></p

Complete Sequence and Analysis of the Mitochondrial Genome of CCMP644 (Cryptophyceae)-6

dispersed among tandem repeats. Slight variations of each repeat unit are color-coded and/or marked with strips or a star symbol. Predicted nucleotide deletions within a repeat unit are highlighted with arrowheads: the size of the deletion is also provided. The positions of three kinds of DNA stem-loop forming sequences, Type I-a, I-b, and II, are labeled with "hairpin" symbols.<p><b>Copyright information:</b></p><p>Taken from "Complete Sequence and Analysis of the Mitochondrial Genome of CCMP644 (Cryptophyceae)"</p><p>http://www.biomedcentral.com/1471-2164/9/215</p><p>BMC Genomics 2008;9():215-215.</p><p>Published online 12 May 2008</p><p>PMCID:PMC2397417.</p><p></p

Management and outcomes in critically ill nonagenarian versus octogenarian patients

Background: Intensive care unit (ICU) patients age 90 years or older represent a growing subgroup and place a huge financial burden on health care resources despite the benefit being unclear. This leads to ethical problems. The present investigation assessed the differences in outcome between nonagenarian and octogenarian ICU patients. Methods: We included 7900 acutely admitted older critically ill patients from two large, multinational studies. The primary outcome was 30-day-mortality, and the secondary outcome was ICU-mortality. Baseline characteristics consisted of frailty assessed by the Clinical Frailty Scale (CFS), ICU-management, and outcomes were compared between octogenarian (80-89.9 years) and nonagenarian (>= 90 years) patients. We used multilevel logistic regression to evaluate differences between octogenarians and nonagenarians. Results: The nonagenarians were 10% of the entire cohort. They experienced a higher percentage of frailty (58% vs 42%; p < 0.001), but lower SOFA scores at admission (6 +/- 5 vs. 7 +/- 6; p < 0.001). ICU-management strategies were different. Octogenarians required higher rates of organ support and nonagenarians received higher rates of life-sustaining treatment limitations (40% vs. 33%; p < 0.001). ICU mortality was comparable (27% vs. 27%; p = 0.973) but a higher 30-day-mortality (45% vs. 40%; p = 0.029) was seen in the nonagenarians. After multivariable adjustment nonagenarians had no significantly increased risk for 30-day-mortality (aOR 1.25 (95% CI 0.90-1.74; p = 0.19)). Conclusion: After adjustment for confounders, nonagenarians demonstrated no higher 30-day mortality than octogenarian patients. In this study, being age 90 years or more is no particular risk factor for an adverse outcome. This should be considered- together with illness severity and pre-existing functional capacity - to effectively guide triage decisions