title: Characterizing the citrus cultivar Carrizo genome through 454 shotgun sequencing.
abstract: The citrus cultivar Carrizo is the single most important rootstock to the US citrus industry and has resistance or tolerance to a number of major citrus diseases, including citrus tristeza virus, foot rot, and Huanglongbing (HLB, citrus greening). A Carrizo genomic sequence database providing approximately 3.5×genome coverage (haploid genome size approximately 367 Mb) was populated through 454 GS FLX shotgun sequencing. Analysis of the repetitive DNA fraction indicated a total interspersed repeat fraction of 36.5%. Assembly and characterization of abundant citrus Ty3/gypsy elements revealed a novel type of element containing open reading frames encoding a viral RNA-silencing suppressor protein (RNA binding protein, rbp) and a plant cytokinin riboside 5′-monophosphate phosphoribohydrolase-related protein (LONELY GUY, log). Similar gypsy elements were identified in the Populus trichocarpa genome. Gene-coding region analysis indicated that 24.4% of the nonrepetitive reads contained genic regions. The depth of genome coverage was sufficient to allow accurate assembly of constituent genes, including a putative phloem-expressed gene. The development of the Carrizo database (http://citrus.pw.usda.gov/) will contribute to characterization of agronomically significant loci and provide a publicly available genomic resource to the citrus research community.
authors: USDA-ARS, Western Regional Research Center, Albany, CA 94710, USA. william.belknap@ars.usda.gov
authors: William R
authors: WR
authors: Belknap
authors: Yi
authors: Y
authors: Wang
authors: Naxin
authors: N
authors: Huo
authors: Jiajie
authors: J
authors: Wu
authors: David R
authors: DR
authors: Rockhold
authors: Yong Q
authors: YQ
authors: Gu
authors: Ed
authors: E
authors: Stover
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002957:Citrus / Q000235:genetics*; D018556:Crops, Agricultural / Q000235:genetics; D015342:DNA Probes / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D030541:Databases, Genetic; D018745:Genome, Plant; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D052585:Phloem / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid; D018626:Retroelements; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D015342:DNA Probes; D018744:DNA, Plant; D010940:Plant Proteins; D016601:RNA-Binding Proteins; D018626:Retroelements