Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTEs were assembled into 81,429 contigs. of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTEs sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTEs coincided with DNA regions predicted as encoding exons by GENSCAN

Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa

Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X.fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grape-growing region of California. Comparative analyses with a previously sequenced X.fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X.fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X.fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies

Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis.

Submitted by Ana Maria Fiscina Sampaio ([email protected]) on 2016-02-04T17:03:16Z No. of bitstreams: 1 Nascimento ATLO Comparative genomics of two....pdf: 540725 bytes, checksum: 25afb9fa02dcbdfe748ffdb0fedba3c5 (MD5)Approved for entry into archive by Ana Maria Fiscina Sampaio ([email protected]) on 2016-02-12T13:21:56Z (GMT) No. of bitstreams: 1 Nascimento ATLO Comparative genomics of two....pdf: 540725 bytes, checksum: 25afb9fa02dcbdfe748ffdb0fedba3c5 (MD5)Made available in DSpace on 2016-02-12T13:21:56Z (GMT). No. of bitstreams: 1 Nascimento ATLO Comparative genomics of two....pdf: 540725 bytes, checksum: 25afb9fa02dcbdfe748ffdb0fedba3c5 (MD5) Previous issue date: 2004Instituto Butantan, Centro de Biotecnologia. São Paulo, SP, BrasilFundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / Universidade Federal da Bahia. Hospital Universitário Professor Edgard Santos, Serviço de Imunologia. Salvador, BA, BrasilWeill Medical College of Cornell University. Division of International Medicine and Infectious Disease. New York, NYInstituto Butantan, Centro de Biotecnologia. São Paulo, SP, BrasilUniversidade de São Paulo. Escola Superior de Agricultura Luiz de QueirozInstituto Butantan, Centro de Biotecnologia. São Paulo, SP, BrasilUniversity of California. Los Angeles School of Medicine. New York, New York / Veterans Affairs Greater Los Angeles Healthcare System. Division of Infectious Diseases. Los Angeles, CaliforniaVeterans Affairs Greater Los Angeles Healthcare System. Division of Infectious Diseases. Los Angeles, CaliforniaKIT (Koninklijk Instituut voor de Tropen / Royal Tropical Institute), KIT Biomedical Research. Amsterdam, The NetherlandsInstituto de Ciências Biomédicas. Universidade de São Paulo, SP, BrasilInstituto de Biociências. Universidade de São Paulo, SP, BrasilInstituto de Ciências Biomédicas. Universidade de São Paulo, SP, BrasilInstituto Butantan, Centro de Biotecnologia. São Paulo, SP, BrasilInstituto Butantan, Centro de Biotecnologia. São Paulo, SP, BrasilInstituto Butantan, Centro de Biotecnologia. São Paulo, SP, BrasilInstituto Oswaldo Cruz. Departamento de Bioquímica e Biologia Molecular. Rio de Janeiro, RJ, Brasil 11Universidade Federal de Pelotas. Centro de Biotecnologia. Pelotas, RGS, BrasilVeterans Affairs Greater Los Angeles Healthcare System. Division of Infectious Diseases. Los Angeles, California BrasilInstituto de Ciências Biomédicas. Universidade de São Paulo, SP, BrasilUniversidade de São Paulo. Faculdade de Ciências Agrárias eUniversidade de São Paulo. Faculdade de Ciências Agrárias eInstituto Butantan, Centro de Biotecnologia. São Paulo, SP, BrasilUniversidade Federal de São Carlos, Centro de Ciências Agrárias.Universidade Estadual de Feira de Santana (UEFS). Laboratório de Pesquisa em Microbiologia (LAPEM). Departamento de Ciências Biológicas. Feira de Santana, Bahia, BrasilFaculdade de Ciencias Farmaceuticas de Ribeirão Preto. Ribeirão Preto, SP, BrasilUniversidade de São Paulo. Faculdade de Filosofia, Ciências e Letras. Ribeirão Preto São Paulo, SP, BrasilUniversidade de São Paulo. Faculdade de Filosofia, Ciências e Letras. Ribeirão Preto São Paulo, SP, Brasil 17Instituto Biológico. Universidade de São Paulo, SP, BrasilUniversidade Federal do Rio Grande do Norte. Centro de Biociências. Natal, RGN, BrasilInstituto Butantan, Centro de Biotecnologia. São Paulo, SP, BrasilInstituto de Ciências Biomédicas. Universidade de São Paulo, SP, BrasilFaculdade de Ciências Agronômicas. São Paulo, SP, BrasilUniversidade de São Paulo. Faculdade de Ciências Agrárias eUniversidade de São Paulo. Faculdade de Ciências Agrárias eInstituto de Biociências. São Paulo, SP, BrasilUniversidade Estadual Paulista, Botucatu, Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, Mogi das Cruzes, SP, BrasilUniversidade Estadual Paulista, Botucatu, Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, Mogi das Cruzes, SP, BrasilDepartamento de Genética e Evolução. Mogi das Cruzes, SP, BrasilInstituto de Computação. São Paulo, SP, BrasilUniversidade Federal da Bahia. Hospital Universitário Professor Edgard Santos, Serviço de Imunologia. Salvador, BA, BrasilUniversidade Federal do Rio Grande do Norte. Centro de Biociências. Natal, RGN, BrasilCentro de Energia Nuclear na Agricultura. São Paulo, SP, BrasilLudwig Institute for Cancer Research. New York, NYUniversidade de São Paulo. Faculdade de Ciências Agrárias e Veterinárias. São Paulo, SP, Brasil. Universidade Estadual Paulista, Jaboticabal. Piracicaba, SP, BrasilUniversidade de São Paulo. Escola Superior de Agricultura Luiz de Queiroz. São Paulo, SP, BrasilInstituto de Computação. São Paulo, SP, BrasilInstituto de Biociências. Universidade de São Paulo, SP, BrasilLeptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in accidental hosts, including humans. Complete genome sequencing of Leptospira interrogans serovar Copenhageni and comparative analysis with the available Leptospira interrogans serovar Lai genome reveal that despite overall genetic similarity there are significant structural differences, including a large chromosomal inversion and extensive variation in the number and distribution of insertion sequence elements. Genome sequence analysis elucidates many of the novel aspects of leptospiral physiology relating to energy metabolism, oxygen tolerance, two-component signal transduction systems, and mechanisms of pathogenesis. A broad array of transcriptional regulation proteins and two new families of afimbrial adhesins which contribute to host tissue colonization in the early steps of infection were identified. Differences in genes involved in the biosynthesis of lipopolysaccharide O side chains between the Copenhageni and Lai serovars were identified, offering an important starting point for the elucidation of the organism's complex polysaccharide surface antigens. Differences in adhesins and in lipopolysaccharide might be associated with the adaptation of serovars Copenhageni and Lai to different animal hosts. Hundreds of genes encoding surface-exposed lipoproteins and transmembrane outer membrane proteins were identified as candidates for development of vaccines for the prevention of leptospirosis

Genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits

The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome

Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription–PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning