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.
Stocks
This publication contains information about 23 stocks:
Stock NameUniquenameType
Alemow pepadaAlemow pepadacultivar
Amakusa tangorAmakusa tangorcultivar
Carrizo CitrangeCarrizo Citrangebreeding_research_material
ClementineClementinebreeding_research_material
CleopatraCleopatracultivar
Etrog 861-S1Etrog 861-S1breeding_research_material
Fortune tangorFortune tangorcultivar
Hassaku mandarinHassaku mandarincultivar
Hayata mandarinHayata mandarincultivar
Kankitsu Chukanbohon Nou 6 Gou tangorKankitsu Chukanbohon Nou 6 Gou tangorcultivar
MexicanMexicancultivar
Orah tangorOrah tangorcultivar
Palestine sweet limePalestine sweet limebreeding_research_material
PonkanPonkancultivar
Rangur limeRangur limecultivar
Rixiangxia mandarinRixiangxia mandarincultivar
Rough LemonRough Lemoncultivar
Satsuma mandarinSatsuma mandarincultivar
summer orangesummer orangecultivar
Sweet OrangeSweet Orangebreeding_research_material
Swingle citrumeloSwingle citrumelocultivar
Tahiti limeTahiti limecultivar
Trifoliate orangeTrifoliate orangecultivar
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This publication contains information about 25,417 features:
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clementina_122005_contig10182_p90_GTclementina_122005_contig10182_p90_GTgenetic_marker
clementina_122005_contig10187_p153_AGclementina_122005_contig10187_p153_AGgenetic_marker
clementina_122005_contig10187_p284_GCclementina_122005_contig10187_p284_GCgenetic_marker
clementina_122005_contig10187_p387_ACclementina_122005_contig10187_p387_ACgenetic_marker
clementina_122005_contig10195_p277_TCclementina_122005_contig10195_p277_TCgenetic_marker
clementina_122005_contig10195_p312_TAclementina_122005_contig10195_p312_TAgenetic_marker
clementina_122005_contig10195_p333_CGclementina_122005_contig10195_p333_CGgenetic_marker
clementina_122005_contig10195_p360_CTclementina_122005_contig10195_p360_CTgenetic_marker
clementina_122005_contig10195_p718_AGclementina_122005_contig10195_p718_AGgenetic_marker
clementina_122005_contig10199_p263_CTclementina_122005_contig10199_p263_CTgenetic_marker
clementina_122005_contig10199_p505_CTclementina_122005_contig10199_p505_CTgenetic_marker
clementina_122005_contig10199_p579_TGclementina_122005_contig10199_p579_TGgenetic_marker
clementina_122005_contig10199_p613_TCclementina_122005_contig10199_p613_TCgenetic_marker
clementina_122005_contig10199_p715_AGclementina_122005_contig10199_p715_AGgenetic_marker
clementina_122005_contig10199_p802_ATclementina_122005_contig10199_p802_ATgenetic_marker
clementina_122005_contig1021_p368_TAclementina_122005_contig1021_p368_TAgenetic_marker
clementina_122005_contig1021_p439_ATclementina_122005_contig1021_p439_ATgenetic_marker
clementina_122005_contig10218_p169_GTclementina_122005_contig10218_p169_GTgenetic_marker
clementina_122005_contig10224_p195_TAclementina_122005_contig10224_p195_TAgenetic_marker
clementina_122005_contig10224_p209_CTclementina_122005_contig10224_p209_CTgenetic_marker
clementina_122005_contig10224_p225_TGclementina_122005_contig10224_p225_TGgenetic_marker
clementina_122005_contig10224_p333_ATclementina_122005_contig10224_p333_ATgenetic_marker
clementina_122005_contig10224_p384_TCclementina_122005_contig10224_p384_TCgenetic_marker
clementina_122005_contig10224_p444_GAclementina_122005_contig10224_p444_GAgenetic_marker
clementina_122005_contig10224_p471_AGclementina_122005_contig10224_p471_AGgenetic_marker

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URLhttp://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-746