title: Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery.
abstract: Next generation sequencing technologies have proven to be a rapid and cost-effective means to assemble and characterize gene content and identify molecular markers in various organisms. Pepper (Capsicum annuum L., Solanaceae) is a major staple vegetable crop, which is economically important and has worldwide distribution. High-throughput transcriptome profiling of two pepper cultivars, Mandarin and Blackcluster, using 454 GS-FLX pyrosequencing yielded 279,221 and 316,357 sequenced reads with a total 120.44 and 142.54Mb of sequence data (average read length of 431 and 450 nucleotides). These reads resulted from 17,525 and 16,341 'isogroups' and were assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both the cultivars, respectively. Assembled sequences were annotated functionally based on homology to genes in multiple public databases. Detailed sequence variant analysis identified a total of 9701 and 12,741 potential SNPs which eventually resulted in 1025 and 1059 genotype specific SNPs, for both the varieties, respectively, after examining SNP frequency distribution for each mapped unigenes. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.
authors.affiliation: Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon 440-706, Republic of Korea. Electronic address: aykyun@korea.kr.
authors.forename: Yul-Kyun
authors.initials: YK
authors.lastname: Ahn
authors.forename: Swati
authors.initials: S
authors.lastname: Tripathi
authors.forename: Jeong-Ho
authors.initials: JH
authors.lastname: Kim
authors.forename: Young-Il
authors.initials: YI
authors.lastname: Cho
authors.forename: Hye-Eun
authors.initials: HE
authors.lastname: Lee
authors.forename: Do-Sun
authors.initials: DS
authors.lastname: Kim
authors.forename: Jong-Gyu
authors.initials: JG
authors.lastname: Woo
authors.forename: Myeong-Cheoul
authors.initials: MC
authors.lastname: Cho
mesh_terms: D002212:Capsicum / Q000145:classification* / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods; D020869:Gene Expression Profiling; D015723:Gene Library; D056726:Genetic Association Studies; D005819:Genetic Markers; D049810:Genetic Speciation; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide / Q000502:physiology; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D005819:Genetic Markers
keywords: A; BLAST; Basic Local Alignment Search Tool; C; Capsicum annuum; DNA complementary to RNA; EST; G; GO; GS-FLX; Gene Ontology; Genome Sequencer FLX system; Mb; N; NCBI; NGS; National Center for Biotechnology Information; PCR; QTL; RNA; SNP; SNPs; SSR; T; Transcriptome assembly; U; adenosine; any nucleoside; base pair(s); bp; cDNA; cytidine; d; dATP; dCTP; dGTP; dNTP; dTTP; deoxyadenosine triphosphate; deoxycytidine triphosphate; deoxyguanosine triphosphate; deoxyribo; deoxyribonucleoside triphosphate; deoxythymidine triphosphate; double strand(ed); ds; expressed sequence tag; guanosine; i; inorganic pyrophosphate; kb; kilobase(s) or 1000bp; mRNA; megabytes; messenger ribo nucleic acid; next generation sequencing; oligo; oligodeoxyribonucleotide; polymerase chain reaction; quantitative trait Locus; ribo nucleic acid; simple sequence repeat; single nucleotide polymorphism; single strand(ed); single-stranded template DNA; ss; sstDNA; thymidine; uridine