RESUMEN
Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.
Asunto(s)
Mapeo Contig/métodos , Lino/genética , Genoma de Planta/genética , Anotación de Secuencia Molecular/métodos , Secuencia de Bases , Mapeo Cromosómico , Cromosomas Artificiales Bacterianos , ADN de Plantas/química , ADN de Plantas/genética , Etiquetas de Secuencia Expresada , Biblioteca de Genes , Secuenciación de Nucleótidos de Alto Rendimiento , Datos de Secuencia Molecular , Estructura Terciaria de Proteína , Análisis de Secuencia de ADNRESUMEN
Retroelements have proved useful for molecular marker studies and play an important role in genome evolution. Ty1-copia retrotransposons are ubiquitous and heterogeneous in plant genomes, and although many elements have been isolated and characterized, almost no information about them is available in the literature for Phaseolus vulgaris L. We report here the isolation and characterization of new RNase long terminal repeat (LTR) sections of the Ty1-copia group for this crop plant. RNAse sections showed conserved amino acids with the downstream sections corresponding to the polypurine-tract and 5' sections of 3' LTRs. The RNase sections were aligned using ClustalX to find potential relationships between sequences. A comparison with this analysis was made using the partition analysis of quasispecies package (PAQ), which is specific for quasispecies-like populations. The analysis revealed eight distinct groups. To uncover LTR variability and potential conserved promoter motifs, we also designed new primers from the presumed polypurine-tract regions. A similarity search found short stretches similar to upstream and downstream regions of some genes. Conserved motifs, corresponding to transcription factor binding sites, were discovered through MatInspector software and two sequences characterized. From a putative LTR fragment, we then designed a new primer, which, through sequence-specific amplification polymorphism (SSAP), showed numerous polymorphic bands between two distinct P. vulgaris accessions.
Asunto(s)
Variación Genética , Phaseolus/genética , Filogenia , Polimorfismo Genético , Retroelementos/genética , Ribonucleasas/genética , Secuencia de Bases , Secuencia Conservada/genética , Cartilla de ADN , Datos de Secuencia Molecular , Alineación de Secuencia , Análisis de Secuencia de ADN , Especificidad de la Especie , Secuencias Repetidas Terminales/genéticaRESUMEN
Se presentó un caso interesante y a la vez infrecuente de un lipoma del mesenterio como causa de oclusión mecánica del intestino delgado bajo
Asunto(s)
Adulto , Humanos , Femenino , Lipoma/complicaciones , Mesenterio , Obstrucción Intestinal/etiología , Neoplasias Peritoneales/complicacionesRESUMEN
Se presentó un caso interesante y a la vez infrecuente de un lipoma del mesenterio como causa de oclusión mecánica del intestino delgado bajo
