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
Swingle_7954_contig1939_p1107_CGSwingle_7954_contig1939_p1107_CGgenetic_marker
Swingle_7954_contig1939_p1336_TCSwingle_7954_contig1939_p1336_TCgenetic_marker
Swingle_7954_contig1939_p1459_CTSwingle_7954_contig1939_p1459_CTgenetic_marker
Swingle_7954_contig1939_p1517_ATSwingle_7954_contig1939_p1517_ATgenetic_marker
Swingle_7954_contig1951_p186_CASwingle_7954_contig1951_p186_CAgenetic_marker
Swingle_7954_contig1951_p420_AGSwingle_7954_contig1951_p420_AGgenetic_marker
Swingle_7954_contig1966_p1124_TGSwingle_7954_contig1966_p1124_TGgenetic_marker
Swingle_7954_contig1966_p1140_GASwingle_7954_contig1966_p1140_GAgenetic_marker
Swingle_7954_contig1966_p1167_TCSwingle_7954_contig1966_p1167_TCgenetic_marker
Swingle_7954_contig1966_p1329_CTSwingle_7954_contig1966_p1329_CTgenetic_marker
Swingle_7954_contig1976_p202_AGSwingle_7954_contig1976_p202_AGgenetic_marker
Swingle_7954_contig1976_p307_CTSwingle_7954_contig1976_p307_CTgenetic_marker
Swingle_7954_contig1976_p346_GASwingle_7954_contig1976_p346_GAgenetic_marker
Swingle_7954_contig1976_p436_CTSwingle_7954_contig1976_p436_CTgenetic_marker
Swingle_7954_contig1976_p517_TCSwingle_7954_contig1976_p517_TCgenetic_marker
Swingle_7954_contig1976_p535_GASwingle_7954_contig1976_p535_GAgenetic_marker
Swingle_7954_contig1976_p628_GASwingle_7954_contig1976_p628_GAgenetic_marker
Swingle_7954_contig1976_p95_AGSwingle_7954_contig1976_p95_AGgenetic_marker
Swingle_7954_contig1984_p313_GCSwingle_7954_contig1984_p313_GCgenetic_marker
Swingle_7954_contig1984_p457_TCSwingle_7954_contig1984_p457_TCgenetic_marker
Swingle_7954_contig1984_p484_GCSwingle_7954_contig1984_p484_GCgenetic_marker
Swingle_7954_contig1984_p527_TGSwingle_7954_contig1984_p527_TGgenetic_marker
Swingle_7954_contig1984_p560_AGSwingle_7954_contig1984_p560_AGgenetic_marker
Swingle_7954_contig1984_p591_AGSwingle_7954_contig1984_p591_AGgenetic_marker
Swingle_7954_contig1984_p649_ATSwingle_7954_contig1984_p649_ATgenetic_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