Pseudoziziphus celata Transcriptome or Gene expression

Large-scale DNA sequence data may enable development of genetic resources in endangered species, thereby facilitating conservation efforts. Ziziphus celata, a federally-endangered, self-incompatible plant species occurring in Florida, USA, is one species for which genetic resources are necessary to facilitate new introductions and augmentations essential for recovery of the species. We used 454 pyrosequencing of a Z. celata normalized floral cDNA library to create a genomic resource for gene and marker discovery. A half-plate GS-FLX Titanium run yielded 655,337 reads averaging 250 bp. 474,025 reads were assembled de novo into 84,645 contigs averaging 408 bp, while 181,312 reads remained unassembled. 47% and 43% of contig consensus sequences had BLAST matches to known proteins in the Uniref50 and TAIR9 annotated protein databases, respectively; many contigs fully represented orthologous proteins in TAIR9. 22,707 unique genes were sequenced, indicating substantial coverage of the Z. celata transcriptome. We detected SNPs and SSRs and developed thousands of SSR primers for use in future genetic studies. As a first step towards understanding self incompatibility in Z. celata, we identified sequences belonging to the gene family encoding self incompatibility. This study demonstrates the efficacy of 454 transcriptome sequencing for rapid gene and marker discovery in an endangered plant.