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
aurantium_14584_contig1190_p131_TCaurantium_14584_contig1190_p131_TCgenetic_marker
aurantium_14584_contig122_p329_CGaurantium_14584_contig122_p329_CGgenetic_marker
aurantium_14584_contig122_p380_TCaurantium_14584_contig122_p380_TCgenetic_marker
aurantium_14584_contig122_p617_ACaurantium_14584_contig122_p617_ACgenetic_marker
aurantium_14584_contig16_p451_GTaurantium_14584_contig16_p451_GTgenetic_marker
aurantium_14584_contig242_p307_GCaurantium_14584_contig242_p307_GCgenetic_marker
aurantium_14584_contig242_p479_ATaurantium_14584_contig242_p479_ATgenetic_marker
aurantium_14584_contig254_p166_TCaurantium_14584_contig254_p166_TCgenetic_marker
aurantium_14584_contig254_p464_GAaurantium_14584_contig254_p464_GAgenetic_marker
aurantium_14584_contig254_p482_CTaurantium_14584_contig254_p482_CTgenetic_marker
aurantium_14584_contig254_p515_AGaurantium_14584_contig254_p515_AGgenetic_marker
aurantium_14584_contig26_p218_CTaurantium_14584_contig26_p218_CTgenetic_marker
aurantium_14584_contig282_p229_CTaurantium_14584_contig282_p229_CTgenetic_marker
aurantium_14584_contig295_p274_GAaurantium_14584_contig295_p274_GAgenetic_marker
aurantium_14584_contig297_p148_GAaurantium_14584_contig297_p148_GAgenetic_marker
aurantium_14584_contig297_p221_ACaurantium_14584_contig297_p221_ACgenetic_marker
aurantium_14584_contig297_p309_ACaurantium_14584_contig297_p309_ACgenetic_marker
aurantium_14584_contig297_p379_GTaurantium_14584_contig297_p379_GTgenetic_marker
aurantium_14584_contig297_p466_CGaurantium_14584_contig297_p466_CGgenetic_marker
aurantium_14584_contig30_p144_TGaurantium_14584_contig30_p144_TGgenetic_marker
aurantium_14584_contig30_p297_TCaurantium_14584_contig30_p297_TCgenetic_marker
aurantium_14584_contig30_p72_CAaurantium_14584_contig30_p72_CAgenetic_marker
aurantium_14584_contig322_p415_GAaurantium_14584_contig322_p415_GAgenetic_marker
aurantium_14584_contig322_p430_AGaurantium_14584_contig322_p430_AGgenetic_marker
aurantium_14584_contig322_p770_CTaurantium_14584_contig322_p770_CTgenetic_marker

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