Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants

<p>Abstract</p> <p>Background</p> <p>Gene ortholog identification is now a major objective for mining the increasing amount of sequence data generated by complete or partial genome sequencing projects. Comparative and functional genomics urgently need a method for ortholog detection to reduce gene function inference and to aid in the identification of conserved or divergent genetic pathways between several species. As gene functions change during evolution, reconstructing the evolutionary history of genes should be a more accurate way to differentiate orthologs from paralogs. Phylogenomics takes into account phylogenetic information from high-throughput genome annotation and is the most straightforward way to infer orthologs. However, procedures for automatic detection of orthologs are still scarce and suffer from several limitations.</p> <p>Results</p> <p>We developed a procedure for ortholog prediction between <it>Oryza sativa </it>and <it>Arabidopsis thaliana</it>. Firstly, we established an efficient method to cluster <it>A. thaliana </it>and <it>O. sativa </it>full proteomes into gene families. Then, we developed an optimized phylogenomics pipeline for ortholog inference. We validated the full procedure using test sets of orthologs and paralogs to demonstrate that our method outperforms pairwise methods for ortholog predictions.</p> <p>Conclusion</p> <p>Our procedure achieved a high level of accuracy in predicting ortholog and paralog relationships. Phylogenomic predictions for all validated gene families in both species were easily achieved and we can conclude that our methodology outperforms similarly based methods.</p

Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods

Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (Musa acuminata)

GreenPhylDB: a database for plant comparative genomics

GreenPhylDB (http://greenphyl.cirad.fr) is a comprehensive platform designed to facilitate comparative functional genomics in Oryza sativa and Arabidopsis thaliana genomes. The main functions of GreenPhylDB are to assign O. sativa and A. thaliana sequences to gene families using a semi-automatic clustering procedure and to create ‘orthologous’ groups using a phylogenomic approach. To date, GreenPhylDB comprises the most complete list of plant gene families, which have been manually curated (6421 families). GreenPhylDB also contains all of the phylogenomic relationships computed for 4375 families. A total of 492 TAIR, 1903 InterPro and 981 KEGG families and subfamilies were manually curated using the clusters created with the TribeMCL software. GreenPhylDB integrates information from several other databases including UniProt, KEGG, InterPro, TAIR and TIGR. Several entry points can be used to display phylogenomic relationships for A. thaliana or O. sativa sequences, using TAIR, TIGR gene ID, family name, InterPro, gene alias, UniProt or protein/nucleic sequence. Finally, a powerful phylogenomics tool, GreenPhyl Ortholog Search Tool (GOST), was incorporated into GreenPhylDB to predict orthologous relationships between O. sativa/A. thaliana protein(s) and sequences from other plant species

GreenPhylDB v2.0: comparative and functional genomics in plants

GreenPhylDB is a database designed for comparative and functional genomics based on complete genomes. Version 2 now contains sixteen full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene families. For each gene cluster or gene family, easy access to gene composition, protein domains, publications, external links and orthologous gene predictions is provided. Web interfaces have been further developed to improve the navigation through information related to gene families. New analysis tools are also available, such as a gene family ontology browser that facilitates exploration. GreenPhylDB is a component of the South Green Bioinformatics Platform (http://southgreen.cirad.fr/) and is accessible at http://greenphyl.cirad.fr. It enables comparative genomics in a broad taxonomy context to enhance the understanding of evolutionary processes and thus tends to speed up gene discovery

Liver retransplantation as a therapeutic method in graft dysfunctions in the immediate postoperative period

Departament Chirurgie Generală, I.C. Fundeni, București, România, Al XIII-lea Congres al Asociației Chirurgilor „Nicolae Anestiadi” și al III-lea Congres al Societății de Endoscopie, Chirurgie miniminvazivă și Ultrasonografie ”V.M.Guțu” din Republica MoldovaCu toate că în ultimii ani au apărut progrese importante în domeniul hepatic, problema prevenirii apariției disfuncției și eșecului post-transplant nu a prezentat progrese semnificative. Intrucât disfuncția hepatică primară influențează dramatic evoluția grefei și a pacientului transplantat hepatic, prevenirea acestui fenomen devine obligatoriu. Creșterea penuriei de organe și a numărului persoanelor aflate pe lista de așteptare a dus la folosirea unor grefe ce depășesc criteriile normale de selecție pentru recoltare precum și transplantarea unor donatori considerați marginali. Aceste circumstanțe au adus în prim plan importanța diagnosticării și tratamentului disfuncției hepatice primare. Conceptul de disfuncție hepatică primară nu este clar definit. Există un spectru de evenimente ce definesc disfuncția hepatică postoperatorie precoce: non funcția primară (PNF), nonfuncția întârziată, funcția slabă/săracă inițială (initial poor function – IPF), non funcția inițială, insuficiența hepatică primară și disfuncția primară. Distincția între aceste entități ia în considerare gradul disfuncției hepatice, necesitatea retransplantării urgente, precum și apariția și durata acestor evenimente după transplantul hepatic.Although important progress has been made over the last few years, the problem of preventing dysfunction and post-transplant liver failure has not shown significant progress. Since primary liver dysfunction dramatically influences the progress of the graft and the liver transplant patient, prevention of this phenomenon becomes obligatory. The increase in organ shortage and the number of people on the waiting list led to the use of grafts that exceeded the normal selection criteria for harvesting as well as the transplantation of marginal donors. These circumstances have highlighted the importance of diagnosis and treatment of primary hepatic dysfunction. The concept of primary liver dysfunction is not clearly defined. There is a spectrum of events that defines early postoperative liver dysfunction: primary non-function (PNF), delayed dysfunction, initial poor function (IPF), primary hepatic failure, and primary dysfunction. The distinction between these entities takes into account the degree of hepatic dysfunction, the need for urgent retransplantation, and the occurrence and duration of these events after liver transplantation

Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)

Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees

South Green Galaxy: a suite of tools for plant genomics

Playwright: N/A Director: N/A Academic Year: 2000-2001https://scholarworks.sjsu.edu/production_images/2682/thumbnail.jp