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
clementina_122005_contig10390_p389_GTclementina_122005_contig10390_p389_GTgenetic_marker
clementina_122005_contig10390_p563_TCclementina_122005_contig10390_p563_TCgenetic_marker
clementina_122005_contig10390_p593_GTclementina_122005_contig10390_p593_GTgenetic_marker
clementina_122005_contig10390_p619_ATclementina_122005_contig10390_p619_ATgenetic_marker
clementina_122005_contig10390_p798_TCclementina_122005_contig10390_p798_TCgenetic_marker
clementina_122005_contig10393_p270_GTclementina_122005_contig10393_p270_GTgenetic_marker
clementina_122005_contig10393_p376_CTclementina_122005_contig10393_p376_CTgenetic_marker
clementina_122005_contig10394_p839_ACclementina_122005_contig10394_p839_ACgenetic_marker
clementina_122005_contig10398_p173_AGclementina_122005_contig10398_p173_AGgenetic_marker
clementina_122005_contig10398_p350_TAclementina_122005_contig10398_p350_TAgenetic_marker
clementina_122005_contig1040_p147_TGclementina_122005_contig1040_p147_TGgenetic_marker
clementina_122005_contig1040_p171_GCclementina_122005_contig1040_p171_GCgenetic_marker
clementina_122005_contig1040_p241_CGclementina_122005_contig1040_p241_CGgenetic_marker
clementina_122005_contig1040_p279_GAclementina_122005_contig1040_p279_GAgenetic_marker
clementina_122005_contig1040_p358_GAclementina_122005_contig1040_p358_GAgenetic_marker
clementina_122005_contig1040_p459_TGclementina_122005_contig1040_p459_TGgenetic_marker
clementina_122005_contig1040_p733_AGclementina_122005_contig1040_p733_AGgenetic_marker
clementina_122005_contig1040_p783_TAclementina_122005_contig1040_p783_TAgenetic_marker
clementina_122005_contig10401_p156_ACclementina_122005_contig10401_p156_ACgenetic_marker
clementina_122005_contig10402_p693_GAclementina_122005_contig10402_p693_GAgenetic_marker
clementina_122005_contig10406_p302_ATclementina_122005_contig10406_p302_ATgenetic_marker
clementina_122005_contig10406_p497_ACclementina_122005_contig10406_p497_ACgenetic_marker
clementina_122005_contig10409_p691_TGclementina_122005_contig10409_p691_TGgenetic_marker
clementina_122005_contig10410_p566_CTclementina_122005_contig10410_p566_CTgenetic_marker
clementina_122005_contig10411_p1044_CTclementina_122005_contig10411_p1044_CTgenetic_marker

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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