Identification of novel members in sweet orange carotenoid biosynthesis gene families

Novel expressed and genomic members in sweet orange (Citrus sinensis [L.] Osbeck) carotenoid biosynthesis gene families have been identified through mining of an expressed sequence tags (ESTs) database and hybridization with a bacterial artificial chromosome (BAC) library. These new expressed members included one phytoene synthase (PSY), one phytoene desaturase (PDS), ten zeta-carotene desaturases (ZDS), one lycopene beta-cyclase (LCYB), one lycopene epsilon-cyclase (LCYE), four carotenoid beta-ring hydroxylases (CHYB), and one capsanthin/capsorubin synthase (CCS). Most unigenes with multiple ESTs, including the ones containing the known genes and these new members, were heterozygous, in which putative single nucleotide polymorphisms distinguished two alleles. According to digital gene expression profiling, fruit was the primary tissue where at least one member of each gene family was specifically or highly expressed. Digital expression levels varied among the members and tissues. According to Southern hybridization of the identified BAC clones, genomic members of the families were either clustered in a single BAC contig or distributed in several different contigs. PSY has four members in one contig, PDS two in one, ZDS 12 in three, LCYB 11 in three, LCYE three in two, CHYB eight in one, and CCS 14 in four, respectively. The number of the genomic members in most families tended to be more than that of the expressed members, suggesting that some genomic members may not be expressed or structurally functional. These new carotenoid gene members, along with much first-hand genomic information, can be used further for functional genomics and genetic mapping.