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_contig14230_p312_GCclementina_122005_contig14230_p312_GCgenetic_marker
clementina_122005_contig14230_p333_CAclementina_122005_contig14230_p333_CAgenetic_marker
clementina_122005_contig14230_p433_GCclementina_122005_contig14230_p433_GCgenetic_marker
clementina_122005_contig14230_p459_CAclementina_122005_contig14230_p459_CAgenetic_marker
clementina_122005_contig14230_p534_GCclementina_122005_contig14230_p534_GCgenetic_marker
clementina_122005_contig14230_p550_GCclementina_122005_contig14230_p550_GCgenetic_marker
clementina_122005_contig14230_p657_GAclementina_122005_contig14230_p657_GAgenetic_marker
clementina_122005_contig14230_p87_GAclementina_122005_contig14230_p87_GAgenetic_marker
clementina_122005_contig14234_p509_T-clementina_122005_contig14234_p509_T-genetic_marker
clementina_122005_contig14239_p207_GAclementina_122005_contig14239_p207_GAgenetic_marker
clementina_122005_contig14239_p362_CTclementina_122005_contig14239_p362_CTgenetic_marker
clementina_122005_contig14239_p382_CGclementina_122005_contig14239_p382_CGgenetic_marker
clementina_122005_contig14239_p410_AGclementina_122005_contig14239_p410_AGgenetic_marker
clementina_122005_contig14242_p261_CGclementina_122005_contig14242_p261_CGgenetic_marker
clementina_122005_contig14242_p88_GTclementina_122005_contig14242_p88_GTgenetic_marker
clementina_122005_contig14266_p1180_CTclementina_122005_contig14266_p1180_CTgenetic_marker
clementina_122005_contig14266_p1213_ACclementina_122005_contig14266_p1213_ACgenetic_marker
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clementina_122005_contig1428_p979_CTclementina_122005_contig1428_p979_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