Mining of haplotype-based expressed sequence tag single nucleotide polymorphisms in citrus

Publication Overview
TitleMining of haplotype-based expressed sequence tag single nucleotide polymorphisms in citrus
AuthorsChen C and Gmitter FG.
TypeJournal Article
Journal NameBMC Genomics
Volume14
Year2013
Page(s)746
CitationChen C and Gmitter FG. Mining of haplotype-based expressed sequence tag single nucleotide polymorphisms in citrus. BMC Genomics. 2013. 14: 746.

Abstract

BACKGROUND: Single nucleotide polymorphisms (SNPs), the most abundant variations in a genome, have been widely used in various studies. Detection and characterization of citrus haplotype-based expressed sequence tag (EST) SNPs will greatly facilitate further utilization of these gene-based resources. RESULTS: In this paper, haplotype-based SNPs were mined out of publicly available citrus expressed sequence tags (ESTs) from different citrus cultivars (genotypes) individually and collectively for comparison. There were a total of 567,297 ESTs belonging to 27 cultivars in varying numbers and consequentially yielding different numbers of haplotype-based quality SNPs. Sweet orange (SO) had the most (213,830) ESTs, generating 11,182 quality SNPs in 3,327 out of 4,228 usable contigs. Summed from all the individually mining results, a total of 25,417 quality SNPs were discovered - 15,010 (59.1%) were transitions (AG and CT), 9,114 (35.9%) were transversions (AC, GT, CG, and AT), and 1,293 (5.0%) were insertion/deletions (indels). A vast majority of SNP-containing contigs consisted of only 2 haplotypes, as expected, but the percentages of 2 haplotype contigs varied widely in these citrus cultivars. BLAST of the 25,417 25-mer SNP oligos to the Clementine reference genome scaffolds revealed 2,947 SNPs had "no hits found", 19,943 had 1 unique hit / alignment, 1,571 had one hit and 2+ alignments per hit, and 956 had 2+ hits and 1+ alignment per hit. Of the total 24,293 scaffold hits, 23,955 (98.6%) were on the main scaffolds 1 to 9, and only 338 were on 87 minor scaffolds. Most alignments had 100% (25/25) or 96% (24/25) nucleotide identities, accounting for 93% of all the alignments. Considering almost all the nucleotide discrepancies in the 24/25 alignments were at the SNP sites, it served well as in silico validation of these SNPs, in addition to and consistent with the rate (81%) validated by sequencing and SNaPshot assay. CONCLUSIONS: High-quality EST-SNPs from different citrus genotypes were detected, and compared to estimate the heterozygosity of each genome. All the SNP oligo sequences were aligned with the Clementine citrus genome to determine their distribution and uniqueness and for in silico validation, in addition to SNaPshot and sequencing validation of selected SNPs.
Features
This publication contains information about 25,417 features:
Feature NameUniquenameType
Swingle_7954_contig1873_p600_GASwingle_7954_contig1873_p600_GAgenetic_marker
Swingle_7954_contig1873_p621_ATSwingle_7954_contig1873_p621_ATgenetic_marker
Swingle_7954_contig1873_p77_A-Swingle_7954_contig1873_p77_A-genetic_marker
Swingle_7954_contig1879_p635_AGSwingle_7954_contig1879_p635_AGgenetic_marker
Swingle_7954_contig1879_p779_TASwingle_7954_contig1879_p779_TAgenetic_marker
Swingle_7954_contig1884_p717_TCSwingle_7954_contig1884_p717_TCgenetic_marker
Swingle_7954_contig1884_p777_TCSwingle_7954_contig1884_p777_TCgenetic_marker
Swingle_7954_contig1891_p328_TASwingle_7954_contig1891_p328_TAgenetic_marker
Swingle_7954_contig1891_p711_CGSwingle_7954_contig1891_p711_CGgenetic_marker
Swingle_7954_contig1909_p265_TGSwingle_7954_contig1909_p265_TGgenetic_marker
Swingle_7954_contig1909_p284_GASwingle_7954_contig1909_p284_GAgenetic_marker
Swingle_7954_contig1909_p583_GASwingle_7954_contig1909_p583_GAgenetic_marker
Swingle_7954_contig1909_p96_TGSwingle_7954_contig1909_p96_TGgenetic_marker
Swingle_7954_contig1911_p120_AGSwingle_7954_contig1911_p120_AGgenetic_marker
Swingle_7954_contig1911_p168_CGSwingle_7954_contig1911_p168_CGgenetic_marker
Swingle_7954_contig1911_p181_CGSwingle_7954_contig1911_p181_CGgenetic_marker
Swingle_7954_contig1911_p211_GTSwingle_7954_contig1911_p211_GTgenetic_marker
Swingle_7954_contig1911_p268_TCSwingle_7954_contig1911_p268_TCgenetic_marker
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Pages

Stocks
This publication contains information about 23 stocks:
Stock NameUniquenameType
Alemow pepadaAlemow pepadaaccession
Amakusa tangorAmakusa tangoraccession
Carrizo CitrangeCarrizo Citrangeaccession
ClementineClementineaccession
CleopatraCleopatraaccession
Etrog 861-S1Etrog 861-S1accession
Fortune tangorFortune tangoraccession
Hassaku mandarinHassaku mandarinaccession
Hayata mandarinHayata mandarinaccession
Kankitsu Chukanbohon Nou 6 Gou tangorKankitsu Chukanbohon Nou 6 Gou tangoraccession
MexicanMexicanaccession
Orah tangorOrah tangoraccession
Palestine sweet limePalestine sweet limeaccession
PonkanPonkanaccession
Rangur limeRangur limeaccession
Rixiangxia mandarinRixiangxia mandarinaccession
Rough LemonRough Lemonaccession
Satsuma mandarinSatsuma mandarinaccession
summer orangesummer orangeaccession
Sweet OrangeSweet Orangeaccession
Swingle citrumeloSwingle citrumeloaccession
Tahiti limeTahiti limeaccession
Trifoliate orangeTrifoliate orangeaccession
Properties
Additional details for this publication include:
Property NameValue
URLhttp://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-746