论文部分内容阅读
Background:Ipomoea trifida (H.B.K.) G.Don.is one closest wild relative of cultivated sweetpotato.It owns abiotic and biotic stress resistance and can be used to improve the sweetpotato.Especially, the diploid L trifida is a good reference module plant of the genome sequencing, transcriptome and Self-incompatibility for complicated highly heterozygous hexaploid sweetpotato.Thus, high throughput transcriptoms sequencing is needed to generate enormous transcript sequences from wild elite genes discovery and molecular marker development.Results: Using high-throughput illumina RNA-seq, the transcriptome of dipolid L trifida was analyzed at an unprecedented depth (6.69 gigabase pairs).Approximate 47.4 million reads were obtained, trimmed, and assembled into 65,731 unigenes, with an average length of 959.1bp and N50 1198 bp.The number of unigenes of was about 47 times higher than existing L trifida EST sequences deposited in Genbank (as of October 2013).Based on sequence similarity search with known protein database and following annotation, 52,783 unigenes (80.3%) were annotated by the NR databases, 39,803 unigenes were annotated by GO terms, and 15,937 unigenes were assigned to 290 KEGG pathways.Compared with transcriptome data from our hexaploid cultivar Xushu 18 by Blast, 54,510 (83%) out of the 65,731 unigenesin theI.trifida transcriptome were mapped to 48,571 (88%) out of the 55,181unigenesin theI.batatas transcriptome with the e-value 1.0 e-10.Furthermore, microsatellites (single sequence repeats) were detected as potential molecular markers in L trifida.100 hundred primer pairs for SSRs were designed for validation of the amplification and polymorphism.The result showed that 93 of 100 primer pairs were successfully amplified and 68 of them exhibited polymorphismsbetween diploid and hexaploid.Conclusion/Significance: This is the first report of a transcriptome database for diploid Ipomoea trifida, which enriches the genomic resources of sweetpotato wild relatives.Also, some novel special unigenes concerned with starch metabolic process, regulation of flower development and response to abotic and botic stress, was detected in transcriptome sequences of Ltrifida compared to that of hexaploid cultivar, And our novel development of SSR marker can be potentially used to diversity amplification among different ploidy level accessions in Ipomoea.