Assembly, Gene Annotation and Marker Development Using 454 Floral Transcriptome Sequences in Ziziphus Celata (Rhamnaceae), a Highly Endangered, Florida Endemic Plant

• Published in: DNA research Vol. 19; no. 1; pp. 1 - 9
• Main Authors: Edwards, Christine E, Parchman, Thomas L, Weekley, Carl W
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.02.2012
• Subjects: Biological and medical sciences; cDNA libraries; complementary DNA; Computational Biology - methods; Endangered Species; Florida; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling; genes; Genes, Plant; Genes. Genome; Genetic Markers; Genetics of eukaryotes. Biological and molecular evolution; High-Throughput Nucleotide Sequencing; indigenous species; Microsatellite Repeats; Molecular and cellular biology; Molecular genetics; Molecular Sequence Annotation; proteins; sequence analysis; Sequence Analysis, DNA; single nucleotide polymorphism; titanium; Transcription. Transcription factor. Splicing. Rna processing; Transcriptome; Ziziphus; Ziziphus - genetics; Florida; United States; North America; America; microsatellites; S-locus; transcriptome; conservation genetics; Vegetals; Conservation; Transcriptome; Biological marker; Endemy; Annotation; Plant; Gene; Transcriptomics; Dicotyledones; Microsatellite DNA; Angiospermae; Ziziphus; Development; Genetics; Spermatophyta; Locus; Rhamnaceae
• ISSN: 1340-2838; 1756-1663
• DOI: 10.1093/dnares/dsr037

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. A total of 474 025 reads were assembled de novo into 84 645 contigs averaging 408 bp, while 181 312 reads remained unassembled. Forty-seven 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. A total of 22 707 unique genes were sequenced, indicating substantial coverage of the Z. celata transcriptome. We detected single-nucleotide polymorphisms and simple sequence repeats (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.