Primary photosynthetic eukaryotes contain gene copies of both plastidic and chlamydial origin

Numbers above the branch show bootstrap values for maximum likelihood and distance analyses, respectively. Asterisks indicate values lower than 50%. 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (). Enoyl-ACP reductase (. Note that in panel (a) sequences from red algae and glaucophytes are of plastidic origin, whereas those from green plants, apicomplexans, haptophytes, and chlorarachniophytes are of chlamydial origin. Also note that that in panel (b) sequences from green plants, diatoms, chlorarachniophytes, and apicomplexans form a strongly supported group, whereas cyanobacterial and red alga homologs form another group. Colors represent different phylogenetic affiliations.<p><b>Copyright information:</b></p><p>Taken from "Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?"</p><p>http://genomebiology.com/2007/8/6/R99</p><p>Genome Biology 2007;8(6):R99-R99.</p><p>Published online 4 Jun 2007</p><p>PMCID:PMC2394758.</p><p></p

Phylogenetic analyses of chlamydiae-like genes in primary photosynthetic eukaryotes

Numbers above the branch show bootstrap values for maximum likelihood and distance analyses, respectively. Asterisks indicate values lower than 50%. 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (). 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (). β-Ketoacyl-ACP synthase (). Aspartate transaminase. Note that red algal and green plant sequences form a well supported monophyletic group with environmental homologs. mt, mitochondrial precursor. Colors represent different phylogenetic affiliations.<p><b>Copyright information:</b></p><p>Taken from "Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?"</p><p>http://genomebiology.com/2007/8/6/R99</p><p>Genome Biology 2007;8(6):R99-R99.</p><p>Published online 4 Jun 2007</p><p>PMCID:PMC2394758.</p><p></p

Transcriptome Sequencing and <i>De Novo</i> Analysis of Cytoplasmic Male Sterility and Maintenance in JA-CMS Cotton

<div><p>Cytoplasmic male sterility (CMS) is the failure to produce functional pollen, which is inherited maternally. And it is known that anther development is modulated through complicated interactions between nuclear and mitochondrial genes in sporophytic and gametophytic tissues. However, an unbiased transcriptome sequencing analysis of CMS in cotton is currently lacking in the literature. This study compared differentially expressed (DE) genes of floral buds at the sporogenous cells stage (SS) and microsporocyte stage (MS) (the two most important stages for pollen abortion in JA-CMS) between JA-CMS and its fertile maintainer line JB cotton plants, using the Illumina HiSeq 2000 sequencing platform. A total of 709 (1.8%) DE genes including 293 up-regulated and 416 down-regulated genes were identified in JA-CMS line comparing with its maintainer line at the SS stage, and 644 (1.6%) DE genes with 263 up-regulated and 381 down-regulated genes were detected at the MS stage. By comparing the two stages in the same material, there were 8 up-regulated and 9 down-regulated DE genes in JA-CMS line and 29 up-regulated and 9 down-regulated DE genes in JB maintainer line at the MS stage. Quantitative RT-PCR was used to validate 7 randomly selected DE genes. Bioinformatics analysis revealed that genes involved in reduction-oxidation reactions and alpha-linolenic acid metabolism were down-regulated, while genes pertaining to photosynthesis and flavonoid biosynthesis were up-regulated in JA-CMS floral buds compared with their JB counterparts at the SS and/or MS stages. All these four biological processes play important roles in reactive oxygen species (ROS) homeostasis, which may be an important factor contributing to the sterile trait of JA-CMS. Further experiments are warranted to elucidate molecular mechanisms of these genes that lead to CMS.</p></div

Venn diagram of DE gene counts at the SS and MS stages for JA-CMS and JB floral buds.

<p>B2 = SS stage of JA-CMS, K2 = SS stage of JB, K3 = MS stage of JB, B3 = MS stage of JA-CMS (from right to left).</p

GO analysis results of DE genes at the SS and MS stages between JA-CMS and JB.

<p>Notes: 1) BP = Biological process, CC = Cellular component, MF = Molecular function; Q value = FDR corrected p value. 2) Only GO categories with FDR q value ≤ 0.05 are presented here. 3) GO categories are arranged based on q values from smallest to largest at the SS stage.</p><p>GO analysis results of DE genes at the SS and MS stages between JA-CMS and JB.</p

Up-regulated photosynthesis and flavonoid biosynthesis related genes in JA-CMS at the SS and/or MS stages.

<p>Note: Fold = log₂(fold change). Significant DE genes were determined based on |log₂(fold change)|>1 and FDR q value<0.005.</p><p>Up-regulated photosynthesis and flavonoid biosynthesis related genes in JA-CMS at the SS and/or MS stages.</p

Legislative Documents

Also, variously referred to as: House bills; House documents; House legislative documents; legislative documents; General Court documents

Data_Sheet_1_Horizontal Gene Transfer From Bacteria and Plants to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis.PDF

<p>Arbuscular mycorrhizal fungi (AMF) belong to Glomeromycotina, and are mutualistic symbionts of many land plants. Associated bacteria accompany AMF during their lifecycle to establish a robust tripartite association consisting of fungi, plants and bacteria. Physical association among this trinity provides possibilities for the exchange of genetic materials. However, very few horizontal gene transfer (HGT) from bacteria or plants to AMF has been reported yet. In this study, we complement existing algorithms by developing a new pipeline, Blast2hgt, to efficiently screen for putative horizontally derived genes from a whole genome. Genome analyses of the glomeromycete Rhizophagus irregularis identified 19 fungal genes that had been transferred between fungi and bacteria/plants, of which seven were obtained from bacteria. Another 18 R. irregularis genes were found to be recently acquired from either plants or bacteria. In the R. irregularis genome, gene duplication has contributed to the expansion of three foreign genes. Importantly, more than half of the R. irregularis foreign genes were expressed in various transcriptomic experiments, suggesting that these genes are functional in R. irregularis. Functional annotation and available evidence showed that these acquired genes may participate in diverse but fundamental biological processes such as regulation of gene expression, mitosis and signal transduction. Our study suggests that horizontal gene influx through endosymbiosis is a source of new functions for R. irregularis, and HGT might have played a role in the evolution and symbiotic adaptation of this arbuscular mycorrhizal fungus.</p

Taxonomic distributions at the phylum (a) and class level (b) for sub-trees of the rpS5 sequences sampled by AST, SS, and RS, respectively.

<p>The y-axis gives the number of phyla/classes covered by the sampled sequences, and the x-axis represents the number of sampled sequences <i>m</i>. The original non-redundant set covers 19 phyla and 33 classes (see Section 3.2.1 for details).</p

AST algorithm.

<p>(a) Workflow of the AST algorithm. (b) An example of the sampling procedure of AST. Each circle represents one taxon: C-all <i>Cellular Organism</i>; A-<i>Archaea</i>; B-<i>Bacteria</i>; A1 is an archaeal taxon labeled as A1, similar for A2, A3, B1, and B2. The number listed on the left shoulder of the circle (outside the rectangle) is the number of sequences from the taxon labeled in the circle, and the number listed on the right shoulder of each circle is the number of sampled sequences by AST from the taxon in the circle. In this example there are a total of 11 homologous sequences in all cellular organisms, among which 8 belong to archaea, 3 from bacteria and none from eukaryotes.</p