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Characterizing the citrus cultivar Carrizo genome through 454 shotgun sequencing.
- Source :
-
Genome . Dec2011, Vol. 54 Issue 12, p1005-1015. 11p. - Publication Year :
- 2011
-
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 () will contribute to characterization of agronomically significant loci and provide a publicly available genomic resource to the citrus research community. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 08312796
- Volume :
- 54
- Issue :
- 12
- Database :
- Academic Search Index
- Journal :
- Genome
- Publication Type :
- Academic Journal
- Accession number :
- 78233501
- Full Text :
- https://doi.org/10.1139/g11-070