Location: Crop Improvement and Genetics ResearchTitle: Characterizing the citrus variety Carrizo genome through 454 shotgun sequencing Author
Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/19/2011
Publication Date: 12/1/2011
Citation: Belknap, W.R., Wang, Y., Wu, J., Huo, N., Rockhold, D.R., Gu, Y.Q., Stover, E.W. 2011. Characterizing the citrus variety Carrizo genome through 454 shotgun sequencing. Genome. 54:1005-1015. doi:10.1139/G11-070. Interpretive Summary: Citrus production is of importance both in the U.S. and globally in terms of economic impact and significance to nutrition, The production of citrus worldwide is currently threatened by the presence and spread of the disease Huanglongbing (HLB), which is now in most of the major citrus growing countries in the world, including the U.S. To date, no HLB-resistant citrus types have been identified compelling industry interest in application of biotechnological approaches to solve this problem. The efficient application of this technology to citrus improvement in general, and HLB resistance in particular, requires detailed understanding of the citrus genome. In this manuscript we report the acquisition and analysis of initial sequence of the citrus genome. The rootstock variety Carrizo, which contains a number of genes of agronomic interest, was subjected to “survey sequence” analysis, which covers about 95% of the genome. This sequence was then analyzed to characterize repetitive DNA and genic regions, and to demonstrate utility in gene isolation, as well as identification of novel tools for citrus breeders. These data will provide a foundation for studying genetics/genomics of rootstock characteristics to facilitate efficient screening and selection of improved rootstock varieties using marker-assisted selection. A Carrizo genomic sequence database (USDA Public Citrus Genome Database, http://citrus.pw.usda.gov/) has been established to allow open access to this data to the citrus research community.
Technical Abstract: Citrus production is of global importance both in economic impact and significance to nutrition. The number of natural citrus species appears extremely limited. The genome size is small (haploid approximately 367 Mb), arranged on 18 chromosomes. The citrus variety Carrizo, generated by a ‘Washington’ navel orange x Poncirus trifoliata cross, is the single most important rootstock to the U.S. citrus industry. In addition, Carrizo has resistance or tolerance to a number of major citrus diseases, including as citrus tristeza virus, foot rot and huanglongbing (HLB, citrus greening). The development of the Carrizo genomics resources will contribute to characterization of agronomically significant loci, as well as will be invaluable to the research community involved with the improvement of this important tree fruit crop. A Carrizo genomic sequence database providing approximately 3.5× genome coverage was populated through 454 GS FLX shotgun sequencing. The database is composed of approximately 3.5 million reads with an average read length of 365 bp. Analysis of the repetitive DNA fraction revealed 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 (RNA binding protein, rbp) and a retrotransposed plant cytokinin riboside 5'-monophosphate phosphoribohydrolase-related (LONLEY GUY, log) proteins. Similar gypsy elements were identified in the Populus trichocarpa genome. Gene coding region analysis was carried out on the non-repetitive 454 reads by performing BLAST searches against the citrus EST sequences. This analysis indicated that 24.4% of the non-repetitive reads contained "genic" regions. The depth of genome coverage was sufficient to allow accurate assembly of constituent genes, including a putative phloem-expressed gene. In this work the analyses of 3.5 X genomic sequence data for the citrus variety Carrizo is reported. This database provides a genomic resource to the citrus research community with demonstrated utility in assembly of genes of interest and interspersed repeated domains.