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_contig12121_p663_TCclementina_122005_contig12121_p663_TCgenetic_marker
clementina_122005_contig12127_p238_GCclementina_122005_contig12127_p238_GCgenetic_marker
clementina_122005_contig12127_p450_CAclementina_122005_contig12127_p450_CAgenetic_marker
clementina_122005_contig12127_p71_TGclementina_122005_contig12127_p71_TGgenetic_marker
clementina_122005_contig12129_p363_CGclementina_122005_contig12129_p363_CGgenetic_marker
clementina_122005_contig12129_p58_ATclementina_122005_contig12129_p58_ATgenetic_marker
clementina_122005_contig12130_p83_ATclementina_122005_contig12130_p83_ATgenetic_marker
clementina_122005_contig12167_p210_TAclementina_122005_contig12167_p210_TAgenetic_marker
clementina_122005_contig12167_p248_ATclementina_122005_contig12167_p248_ATgenetic_marker
clementina_122005_contig12167_p599_CTclementina_122005_contig12167_p599_CTgenetic_marker
clementina_122005_contig1217_p107_CTclementina_122005_contig1217_p107_CTgenetic_marker
clementina_122005_contig1217_p173_TGclementina_122005_contig1217_p173_TGgenetic_marker
clementina_122005_contig1217_p312_GAclementina_122005_contig1217_p312_GAgenetic_marker
clementina_122005_contig1217_p479_CTclementina_122005_contig1217_p479_CTgenetic_marker
clementina_122005_contig12170_p643_GCclementina_122005_contig12170_p643_GCgenetic_marker
clementina_122005_contig1218_p379_GAclementina_122005_contig1218_p379_GAgenetic_marker
clementina_122005_contig1218_p465_TGclementina_122005_contig1218_p465_TGgenetic_marker
clementina_122005_contig1218_p539_AGclementina_122005_contig1218_p539_AGgenetic_marker
clementina_122005_contig1218_p646_ATclementina_122005_contig1218_p646_ATgenetic_marker
clementina_122005_contig1218_p661_CGclementina_122005_contig1218_p661_CGgenetic_marker
clementina_122005_contig12180_p403_TCclementina_122005_contig12180_p403_TCgenetic_marker
clementina_122005_contig12180_p418_TCclementina_122005_contig12180_p418_TCgenetic_marker
clementina_122005_contig12191_p269_GAclementina_122005_contig12191_p269_GAgenetic_marker
clementina_122005_contig12199_p276_CTclementina_122005_contig12199_p276_CTgenetic_marker
clementina_122005_contig12199_p309_G-clementina_122005_contig12199_p309_G-genetic_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