Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence
© You et al; licensee BioMed Central Ltd. 2011
Received: 24 August 2010
Accepted: 25 January 2011
Published: 25 January 2011
Many plants have large and complex genomes with an abundance of repeated sequences. Many plants are also polyploid. Both of these attributes typify the genome architecture in the tribe Triticeae, whose members include economically important wheat, rye and barley. Large genome sizes, an abundance of repeated sequences, and polyploidy present challenges to genome-wide SNP discovery using next-generation sequencing (NGS) of total genomic DNA by making alignment and clustering of short reads generated by the NGS platforms difficult, particularly in the absence of a reference genome sequence.
An annotation-based, genome-wide SNP discovery pipeline is reported using NGS data for large and complex genomes without a reference genome sequence. Roche 454 shotgun reads with low genome coverage of one genotype are annotated in order to distinguish single-copy sequences and repeat junctions from repetitive sequences and sequences shared by paralogous genes. Multiple genome equivalents of shotgun reads of another genotype generated with SOLiD or Solexa are then mapped to the annotated Roche 454 reads to identify putative SNPs. A pipeline program package, AGSNP, was developed and used for genome-wide SNP discovery in Aegilops tauschii- the diploid source of the wheat D genome, and with a genome size of 4.02 Gb, of which 90% is repetitive sequences. Genomic DNA of Ae. tauschii accession AL8/78 was sequenced with the Roche 454 NGS platform. Genomic DNA and cDNA of Ae. tauschii accession AS75 was sequenced primarily with SOLiD, although some Solexa and Roche 454 genomic sequences were also generated. A total of 195,631 putative SNPs were discovered in gene sequences, 155,580 putative SNPs were discovered in uncharacterized single-copy regions, and another 145,907 putative SNPs were discovered in repeat junctions. These SNPs were dispersed across the entire Ae. tauschii genome. To assess the false positive SNP discovery rate, DNA containing putative SNPs was amplified by PCR from AL8/78 and AS75 and resequenced with the ABI 3730 xl. In a sample of 302 randomly selected putative SNPs, 84.0% in gene regions, 88.0% in repeat junctions, and 81.3% in uncharacterized regions were validated.
An annotation-based genome-wide SNP discovery pipeline for NGS platforms was developed. The pipeline is suitable for SNP discovery in genomic libraries of complex genomes and does not require a reference genome sequence. The pipeline is applicable to all current NGS platforms, provided that at least one such platform generates relatively long reads. The pipeline package, AGSNP, and the discovered 497,118 Ae. tauschii SNPs can be accessed at (http://avena.pw.usda.gov/wheatD/agsnp.shtml).
Single nucleotide polymorphisms (SNPs) are valuable markers for the construction of genetic and physical maps, genome sequencing, marker-assisted selection, and for other genetic and genomic applications. Resequencing is the most efficient approach for a large scale, genome-wide SNP discovery. For example, resequencing with the Sanger sequencing technology using an annotated genome sequence as a reference has been an effective strategy for genome-wide SNP discovery in low or moderately complex genomes . Compared to Sanger sequencing, massively parallel sequencing technologies, such as the 454 GS FLX Instrument (Roche Applied Science), Solexa (Illumina Inc), and SOLiD (Life Technologies Inc), offer high sequencing throughputs at greatly reduced costs. Each of these sequencing platforms has its own set of advantages and disadvantages. Roche 454 generates longer sequences (200-500 bp or more, depending on the version of the platform) than Solexa (35-150 bp) or SOLiD (25-75 bp), but SOLiD and Solexa have higher throughputs than Roche 454 with the same cost and time investment. Greatly enhanced throughput at reduced cost and time investment is common to all next-generation sequencing (NGS) platforms and allows for deep genome coverage sequencing, a prerequisite for genome-wide SNP discovery in the complex genomes of plants and animals.
Many plants have large and complex genomes with a great abundance of repeated sequences. Polyploidy, a frequent evolutionary strategy in the plant kingdom, further increases genome size and complexity. These attributes are common in the tribe Triticeae, which includes such economically important plants as wheat, barley and rye. These features of the Triticeae genomes present a formidable challenge to genome-wide SNP discovery with NGS platforms, primarily because the abundance of highly repetitive sequences makes alignment and clustering of the short reads generated by some of the NGS platforms difficult.
Strategies are available to ameliorate these difficulties. Reduced representation libraries (RRLs) include only a subset of sequences present in a complex genome. The RRL subset is then used for resequencing, sequence alignment, assembly, and SNP discovery [1, 2]. In plants, RRLs have been used for SNP discovery in maize , rice , soybean [4, 5], and common bean . The use of cDNA libraries for NGS is another and frequently used approach to reduce complexity, avoid repetitive sequences and target coding sequences for SNP discovery. Deep transcriptome resequencing with NGS platforms has been used for SNP discovery in maize  and the polyploid Brassica napus. While both strategies can dramatically reduce sequence complexity, each has limitations. For example, transcriptome sequencing ignores polymorphism in introns and other genic regions absent from mRNA.
An undesirable feature of transcriptome resequencing for SNP discovery is unavailability of potentially useful transposable element (TE)-derived polymorphisms. In contrast to SNPs embedded within repeated sequences (which are notoriously difficult as markers), the junctions of neighbouring repeated sequences are potentially unique [9–11], can be assayed [10–12] and SNPs in them can be treated as single-copy markers. Repeat junctions (RJs) are created by insertions of TEs into each other, into genes, or into other DNA sequences [9, 10]. A high-throughput assay for RJ markers has been reported [9, 11]. Because SNPs at RJs are dispersed over a whole genome, they are well suited for the construction of dense, genome-wide SNP genetic maps. An important application of such maps is in the anchoring and the ordering of contigs of bacterial artificial chromosome (BAC) clones during the construction of physical maps or ordering of scaffolds during genome sequencing. To use RJs in SNP discovery, dedicated annotations of NGS reads are required and relevant computational tools for RJ identification have been developed [10, 11].
A genomic sequence serving as a reference has been the basis of genome-wide SNP discovery utilizing NGS technologies. Tremendous progress has been achieved in the development of algorithms and software tools for mapping short reads from different NGS platforms to a reference genome and then identifying variants between individual sequences and the reference genome sequences [13–16]. However only a few attempts have been reported utilizing NGS to discover SNPs when such a reference is unavailable . A computational pipeline called DIAL (de novo identification of alleles) was recently released for the identification of SNPs between two closely related genotypes without the help of a reference genome sequence . This tool first masks repetitive sequences and then clusters short reads from the genotypes. The clustered reads are assembled with a de novo assembler to identify variants. This tool can be used for the clustering of reads of genome and transcriptome sequences from Roche 454 and Solexa even with a shallow depth of genome coverage. However, the tool has been tested only on relatively low- or moderately-complex genomes. It does not allow SNP discovery in repeat junctions and is applicable only to base-space reads, such as with Roche 454 and Illumina Solexa, but is not applicable to the two-base encoded, color space SOLiD reads.
We report here an annotation-based genome-wide SNP discovery pipeline using NGS data for complex genomes without a reference genome sequence. In this pipeline, Roche 454 shotgun reads with low genome coverage of one genotype are annotated to distinguish single-copy reads covering genes, repeat junctions and other sequences from repetitive sequences and paralogous gene sequences. The annotation dramatically reduces the complexity of the genomic sequences by removing undesirable sequences. Resulting reads are assembled into sequence contigs if possible. The assembled Roche 454 contig and singleton sequences mimic a reference sequence. Shotgun short reads of another genotype with high genome coverage generated with the SOLiD or Solexa NGS platforms are then mapped to the annotated single-copy Roche 454 reads/contigs to identify SNPs in single copy DNA across the entire genome including repeat junctions. Based on this strategy, the pipeline program package, AGSNP, was developed and used for SNP discovery between two accessions of Ae. tauschii (AL8/78 and AS75), the parents of the F2 mapping population used for the construction of an Ae. tauschii genetic map . Aegilops tauschii contains the core genome of the Triticum-Aegilops alliance  and is the diploid source of the wheat D genome [20, 21]. Its genome size is 4.02 Gb  and 90% of its genome is composed of repetitive sequences . It is also an important source of germplasm in wheat breeding and a diploid model for the wheat D-genome.
Next generation sequences used for SNP discovery and for estimation of sequencing error rates
Total size (Mb)
Average Read length (bp)
Roche 454 GS-FLX Titanium
Roche 454 GS-FLX Titanium
AB SOLiD v3.0
AB SOLiD v3.0
Roche 454 GS-FLX Titanium
13 BACs(b), genomic
13 BACs, genomic
AB SOLiD v2.0
13 BACs, genomic
To estimate sequencing error rates intrinsic to each platform and variant calling errors in different sequencing platforms, DNAs of 13 Ae. tauschii (AL8/78) BAC clones were separately fragmented and shotgun sequenced with an ABI 3730 xl (henceforth Sanger sequence). These Sanger sequences were used as a reference in the estimation of sequencing error rates. Pooled DNAs of the 13 Ae. tauschii BAC clones were sequenced on three platforms to depths ranging from 12.9X for Roche 454 to 326.9X for SOLiD (Table 1).
Roche 454 sequencing
Preparation and sequencing of the 454 sequencing library was performed according to the manufacturer's instructions (GS FLX Titanium General library preparation kit/emPCR kit/sequencing kit, Roche Diagnostics, http://www.roche.com). In brief, ten micrograms of Ae. tauschii genomic DNA or pooled DNA of 13 Ae. tauschii BACs were sheared by nebulization and fractionated on agarose gel to isolate 400-750 base fragments. These were used to construct a single-stranded shotgun library that was used as a template for single-molecule PCR. The amplified template beads were recovered after emulsion breaking and selective enrichment. The Genome Sequencer FLX Titanium flows 200 cycles of four solutions containing either dTTP, αSdATP, dCTP and dGTP reagents, in that order, over the cell.
Illumina Solexa sequencing
The AS75 library of genomic DNA or the AL8/78 library of pooled DNA of 13 BACs was quantified by analysis on an Agilent Bioanalyzer (Agilent Technologies, Inc.), using the instrument software to select a region comprising the main library peak. Based on the calculated value, the library was applied to an Illumina single read flow cell at 5 pM concentration and clusters were generated according to manufacturer's instructions. Sequencing was carried out on an Illumina Genome Analyzer GAIIX for 85 cycles. Two, version 3, 36 cycle, kits were used. Data was generated following completion of the run using the Illumina Pipeline 1.4 from the sequencing images. A phix control lane was used to generate phasing and matrix values that were then applied to the experimental samples for basecalling analyses.
ABI SOLiD sequencing
DNA was isolated from nuclei of Ae. tauschii accession AS75 as described in Dvorak et al. 1988 . A fragment library was constructed according to manufacturers' instructions using the Applied Biosystems Fragment Library Construction Kit (Life Technologies, Inc.). In brief, 5 ug of DNA was sheared using the CovarisTM S2 system (Covaris, Inc.), the sheared DNA was end-repaired, adaptors P1 and P2 were ligated to the end-repaired DNA, and the DNA was size-selected on a gel. The size-selected DNA was nick translated and then amplified for 3 cycles to generate the fragment library. The fragment library was quantified using the Agilent DNA high-sensitivity kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).
To construct a cDNA library, Ae. tauschii line AS75 was grown in a solution culture containing 0.5X Hoagland solution and total RNA was isolated from both roots and shoots according to manufacturer's instructions using the Ambion RNAqueous kit and the Ambion Plant RNA Isolation Aid (Life Technologies, Inc.). mRNA was isolated from total RNA according to manufacturer's instructions using the Applied Biosystems Poly(A) Purist Kit (Life Technologies, Inc.). The transcriptome library was constructed according to manufacturers' instructions using the Whole Trascriptome Anaysis Kit from Applied Biosystems (Life Technologies, Inc.). In brief, mRNA was fragmented using RNase III and size-selected. The size-selected RNA was reverse transcribed, and the cDNA size selected. The size-selected cDNA was amplified using 15 cycles to create the transcriptome library. This library was quantified using the Agilent DNA high-sensitivity kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). The root and shoot cDNAs were combined.
Templated beads were prepared from both the fragment library and the transcriptome library according to manufacturer's instructions using the ePCR kit v.2 and the Bead Enrichment Kit from Applied Biosystems (Life Technologies, Inc.) for SOLiD3. Workflow Analysis was done after the first round of templated bead preparation for each library according to manufacturer's instructions using the Workflow Analysis kit from Applied Biosystems (Life Technologies, Inc.) to check library quality and the amount of templated beads generated per ePCR. An additional Workflow Analysis was done for both libraries after it was estimated that a sufficient number of templated beads were produced. Templated beads were deposited on slides according to manufacturers' instructions using the Bead Deposition kit from Applied Biosystems (Life Technologies, Inc.). One full slide was run for the transcriptome library, while 5 full slides (2.5 full runs) were run for the fragment genomic library.
Sequencing errors of NGS platforms and variant calling error
Single read based sequencing errors
The single read sequencing error rate of the Roche 454 GS-FLX Titanium platform was estimated by comparing the single read alignment of AL8/78 reads in a pool of 13 BAC clones previously sequenced with the Sanger method. Because Sanger BAC sequences were based on the shotgun sequencing method they had a negligible error rate. Alignments were obtained using BLASTN of Roche 454 reads against 13 AL8/78 BAC sequences. Insertion and deletion (INDEL), and single base substitutions were counted. The sequencing error rate was calculated as total erroneous bases divided by the total length in bp of Roche 454 reads.
Consensus-based sequencing errors
AL8/78 reads from Roche 454, SOLiD or Solexa were mapped to the 13 BAC sequences generated by the Sanger method using the bwa package [15, 16] at default parameters and consensus sequence of mapped reads were generated using SAMTools . INDEL and single substitutions were counted by comparing Sanger sequences and mapped read consensus sequences. A consensus sequencing error rate of a sequencing platform was calculated as the total erroneous bases divided by the total mapped bases.
Variant calling errors based on Roche 454 single reads as a reference sequence
AL8/78 reads from SOLiD, Solexa or Roche 454 were mapped to Roche 454 genomic contigs or singletons using the bwa package [15, 16] at default parameters. Consensus sequences of mapped reads were generated using SAMtools . The same method was used to count INDEL errors and single-base substitutions and to calculate variant calling error rates.
SNP discovery pipeline
Rationale and strategy
Genome-wide SNP discovery involves two basic steps: (1) the alignment of sequences of two or more genotypes and (2) variant calling in the aligned sequences. Alignment of NGS on a reference genome sequence is called read mapping to the reference sequence. When a reference genome sequence is available, even short reads can be relatively easily mapped and aligned for the purpose of variant calling. In the absence of a genome sequence, long reads (such as those produced by Sanger or Roche 454 sequencing) from different genotypes can be clustered and aligned via multiple alignment algorithms . Difficulties emerge if no reference sequence is available, especially if only short reads generated by the SOLiD or Solexa sequencing platforms are available and genome is highly repetitive. In the strategy used here and similarly reported by Hyten et al. (2010) , the relatively long Roche 454 reads are substituted for the reference genome sequence. Roche 454 reads are annotated, i.e., they are classified on the basis of their sequence homology and copy number in the genome. Single-copy sequences and unique repeat junction sequences are subsequently used as a reference sequence for the alignment of the SOLiD or Solexa reads and for SNP discovery.
The following rationale is used to identify (annotate) Roche 454 single-copy sequences. It is assumed that most genes are in a single-copy dose in a genome and sequences of duplicated genes are usually diverged to such an extent that most of their reads do not cluster together. Therefore, the read depth (number of reads of the same nucleotide position) mapped to coding sequences of known genes estimates the expected read depth of all single-copy sequences in a genome. Sequences showing greater read depth are assumed to be from duplicated or repeated sequences. To implement this rationale, shallow genome coverage by long Roche 454 sequences is used to identify genic sequences by homology search against gene databases. Multiple genome coverages of short SOLiD or Solexa sequences are then used to estimate the read depth of genic sequences in a population of SOLiD or Solexa reads. The estimate is in turn used to identify (annotate) the remaining single-copy Roche 454 reads. This combination of Roche 454 and SOLiD or Solexa platforms combines the long length of Roche 454 reads with the high coverage of the SOLiD/Solexa sequencing platforms, thus reducing costs associated with the development of reference sequence, as already pointed out by Hyten et al. (2010) . Short SOLiD or Solexa reads are mapped and aligned to the Roche 454 reads and contigs with short-read mapping tools [13–16, 25]. After the annotation of all sequences, SNPs are called and filtered.
Annotation of Roche 454 reads
Pre-processing of Roche 454 reads of Ae. tauschii accession AL8/78
The purpose of pre-processing of reads is to remove the chloroplast and mitochondrial sequences. BLASTN against complete wheat chloroplast and mitochondrial genome sequences (AB042240 and AP008982) was performed at an E value of 1E-10. A total of 14,087,315 Roche 454 reads of the AL8/78 genomic library were processed. After the removal of chloroplast and mitochondrial reads, artificial replicates of reads were filtered out using the cd-hit-454 program  at 98% alignment identity and 90% sequence coverage. Artificial replicates are intrinsic artifacts of 454-based pyrosequencing occurring in all currently available 454 technologies, leading to overpresentation of >10% of the original DNA sequencing templates. Those sequences start at the same position and are identical (duplicates) or vary in length, or contain a sequence discrepancy [28, 29].
The first annotation step is to identify reads of known (characterized) repeats. To extract all characterized repetitive reads, all possible plant repeat databases used in RJPrimers , including RepBase14.07, MIPS REdat v4.3 , the complete TREP (release 10), the maize transposable element database (maize TEDB) (July 2009), and 12 TIGR repeat databases , were adopted to perform a BLAST search at an E-value of 1E-10. The extracted characterized repeat reads were further annotated using the repeat junction annotation pipeline (Table S1 in Additional file 1) to identify unique RJs, which are used for SNP identification.
Homology search against known genes is a fundamental approach to identify genes among the sequences generated. The reads remaining after removing repetitive reads were used to search for homology against databases of genes, proteins and unigenes in all species evolutionally related to the targeted genome, Ae. tauschii, including the following: complete genome gene databases of Brachypodium (v1.0), rice (RAP-DB) (build 5) [31–33], sorghum (bicolor-79), and maize; the unigene database of wheat (build #57), rice (build #82), sorghum (build #29), sugarcane (build #14), barley (build #56), maize (build #71) and Arabidopsis (build #79); the UniProt protein database (plant only, release 2010-07), and the Brachypodium protein database (v1.0). An E value of 1E-10 was used for both BLASTN and BLASTX searches. Reads related to transposable elements existing in protein or unigene databases were also removed. Some unknown gene reads were further identified using SOLiD cDNA reads of AS75 (~22X gene coverage) mapping to the Roche 454 reads of AL8/78 with the pipeline program (bwa_mapping_pipeline.pl, Table S1 in Additional file 1). All known and uncharacterized gene reads of Roche 454 were assembled at a higher stringency (95% of alignment identity) using gsAssembler (Roche Applied Science) (batch_gsassembly.pl, Table S1 in Additional file 1).
Single-copy read annotation
SNP filtering criteria
SNP filtering criteria used in this study
Criteria of putative SNPs
Reference sequence length
≥ 200 bp
Minimum mapped read depth to the reference
Maximum mapped read depth to the reference
Roche 454: ≤ 5
SOLiD genomic reads: ≤ 50
SOLiD cDNA: ≤ 100
Consensus base ratio
Mapping quality score in SAMTools
Reference SNP base quality score and neighborhood quality standard (NQS) score
SNP base ≥30
NQS 11 bases: ≥ 20
Removing homopolymer SNPs
SNP base string length ≥ 3 bp
Removing very close SNPs
> 3 bp between two contiguous SNPs
Removing SNPs at the right side of 454 reads
> 30 bp away from the right side
Illumina genotyping quality (optional for SNP discovery but recommended for SNPs intended for Illumina GoldenGate assays )
≥ 60 bp between two contiguous SNPs
In addition, Illumina's GoldenGate or Infinium assays require a minimum of 50 bp (60 bp preferred) of sequence on either side of each SNP and a minimum of 60 bp between two contiguous SNPs. These requirements for Illumina genotyping are optionally applied in the pipeline program.
More stringent SNP filtering criteria are imposed for uncharacterized reads because most of them should be unknown low-copy repetitive sequences. We set the maximum mapped read depth cut-off to 5 reads instead of 8 for both Roche 454 and Solexa reads, and 25 instead of 53 for SOLiD with the aim to eliminate SNPs in potentially low-copy repetitive sequences. In addition, reads with only one SNP are retained.
All annotated AL8/78 single-copy gene-related sequences, RJs, and uncharacterized single-copy sequences were used as a reference sequence in mapping reads from Roche 454, Illumina Solexa and ABI SOLiD of Ae. tauschii accession AS75 (Table 1). Variants (short INDEL and SNP) were called using the read mapping and SNP calling pipeline (bwa_snp_pipeline) with the bwa [15, 16] and SAMTools package . All called variants from different sequencing platforms and DNA sources (genomic or transcriptome) were merged and filtered using the SNP filter pipeline program (summarize_bwa_snp_calls.pl and snp_filter_pipeline.pl, Table S1 in Additional file 1). All short INDELs were excluded and only high-quality SNPs were retained.
A total of 192 gene-related sequences, 96 repeat junction sequences and 95 uncharacterized sequences with at least one SNP were randomly selected among the identified SNPs for PCR validation. Primers flanking SNPs were designed with BatchPrimer3 . DNA targets in both Ae. tauschii AL8/78 and AS75 were PCR amplified. Amplicons were sequenced using the PCR primers as sequencing primers with an ABI 3730 xl DNA Analyzer as described by Choi et al. (2007) .
Estimation of NGS error rates
Sequencing and variant calling errors of next-generation sequencing based on the data set of Sanger sequences of 13 AL8/78 BAC clones
Overall error rate
INDEL error rate
Substitution error rate
Sequencing error compared with Sanger sequences
Single read error
Roche 454 GS-FLX Titanium
7.4 × 10-3
6.2 × 10-3
1.2 × 10-3
Roche 454 GS-FLX Titanium
1.3 × 10-3
1.0 × 10-3
3.0 × 10-4
4.4 × 10-4
9.0 × 10-5
3.5 × 10-4
AB SOLiD v2.0
4.3 × 10-4
2.5 × 10-4
1.8 × 10-4
Variant calling errors using Roche 454 sequence as reference
Roche 454 GS-FLX Titanium
3.79 × 10-3
1.12 × 10-3
2.67 × 10-3
1.87 × 10-3
4.1 × 10-4
1.46 × 10-3
AB SOLiD v2.0
5.9 × 10-4
2.7 × 10-4
3.2 × 10-4
To estimate SNP errors, a random half of Roche 454 reads constructed for the 13 Ae. tauschii BACs were used as references. Then SOLiD and Solexa BAC reads or another half of Roche 454 BAC reads were compared with Roche 454 reference sequences. In this case, errors on both sides contributed to error rates. The consensus base substitution error rates were 0.032%, 0.146% and 0.267% for SOLiD, Solexa and Roche 454, respectively (Table 3). Because SNPs with low quality scores (< 30 for SNP base and < 20 for NQS 11 bases) are filtered out in the SNP filtering pipeline (Table 2), ~70% of SNP errors can be eliminated (Figure 4). Therefore, much lower SNP error rates are expected (30% of the consensus base substitution error rate), about 0.01% for SOLiD, 0.04% for Solexa and 0.08% for Roche 454 (Table 3).
Annotation of Roche 454 reads of Ae. tauschii accession AL8/78
Annotation and SNP discovery using Roche 454 reads of genomic DNA of Ae. tauschi i AL8/78 as reference sequences
No. of reads(a)
Length in Mb (%)
Predicted single-copy reads
Length in Mb
No. of contigs and singletons
Length in Mb
No. of SNPs
No. of annotated genes
4,772. 5 (100%)
Comparison of single-copy read predictions by different sequencing platforms mapped to characterized gene contigs (including singletons) of Ae. tauschi i accession AL8/78 sequenced with Roche 454
Sequencing platform and DNA source
Roche 454 contigs mapped
Contigs shared with SOLiD(a)
Cut-off value for single-copy prediction
Single- copy Roche 454 contigs (% of mapped contigs)
Single-copy contigs shared(a)
Contingency χ2test P value
Roche 454 (~1.6X)
Genome-wide SNP discovery and characterization
SNPs were discovered with the SNP discovery pipeline using the predicted Roche 454 single-copy reads in genes, RJs and uncharacterized regions as a reference sequence (Figure 4 and Table S1 in Additional file 1). A total of 195,631 SNPs were discovered in gene regions, which included 153,787 and 41,844 SNPs in characterized and uncharacterized gene regions, respectively (Table 4 and 6). In addition, 145,907 SNPs were discovered in repeat junctions and 155,580 in uncharacterized regions (Table 4). Relatively more SNPs were in repeat junctions (one SNP per 612 bp) than in genes (one SNP per 876 bp). The SNP frequency in uncharacterized regions cannot be compared with those in repeat junctions and genes because more stringent criteria were applied to SNP discovery in those regions (see Materials and Methods).
SNP discovery in Ae. tauschi i genes using different sequencing platforms and DNA sources
Sequencing platform(DNA source)(a)
Number of reference sequences with SNPs (AL8/78)
Reference sequences with SNPs %
Group by combinations of sequencing platforms and DNA sources (SNP filtered with merged SNPs discovered by three sequencing platforms)
Group by single sequencing platform or DNA source (SNP filtered with merged SNPs discovered by three sequencing platforms)
SOLiD(genomic) (~10.7 X)(b)
Roche 454(genomic) (~1.6X)
SNPs filtered by individual sequencing platforms
SOLiD(genomic) (~10.7 X)(b)
Roche 454(genomic) (~1.6X)
The same SNPs identified by two or more sequencing platforms account for 3.3% (6,422 SNPs) of all putative gene-related SNPs (Table 6). The percentage of the same SNPs identified by two sequencing platforms should be associated with overlapping percentage of reads between two sequencing platforms, which depends on genome coverage of reads obtained from sequencing. Simulation results showed that if the percentage of the same SNPs in two sequencing platforms is 3.3%, the overlapping percentage of reads generated from two sequencing platforms must be over 12%. If this overlapping percentage reaches to 80%, the percentage of the same SNPs will be 79% (Figure S1 in Additional file 1). Twice as many SNPs were identified using SOLiD sequencing of genomic DNA than cDNA, which is not surprising since SNP discovery in cDNA is limited by the number of genes sampled by the cDNA library.
Validation of Ae. tauschii SNPs
PCR validation of Ae. tauschi i SNPs
False positive SNPs
False positive SNPs due to reference
False positive SNPs due to mapped reads
SNP validation rate %
A total of 96 RJ sequences were randomly chosen from the predicted single-copy RJ sequences with a SNP within 50 bp of RJ location. Target DNA at 24 RJ sequences did not amplify in PCR. Of the remaining 72 RJ targets, 20 amplified either only the AL8/78 DNA target (15 out of 20) or had no alignments in the SNP locations (5 out of 20) reflecting diversity between AL8/78 and AS75 in repeated sequences. The remaining 52 RJ targets could be amplified in both DNAs and were expected to contain 67 putative SNPs in the aligned regions. Of these 67 putative SNPs, 59 (88%) were present (Table 7). The SNP validation success rate in RJs was similar to that in gene sequences, showing that single-copy RJs are a productive source of useful SNPs.
Similarly SNPs discovered in uncharacterized sequences were also verified. A subset of 95 uncharacterized sequences were randomly sampled from the reference sequences with 155,580 uncharacterized SNPs. Out of 95 sequences, 18 sequences did not amplify in both accessions (AL8/78 and AS75) and 34 sequences amplified only in one of two accessions or their target sequences had no alignments in the SNP locations. The high failure rate of PCR amplification is likely due to diversity between AL8/78 and AS75 in uncharacterized regions because most of SNPs in uncharacterized sequences should be located in non-coding regions. The remaining 43 sequences amplified in both DNAs were expected to have 48 putative SNPs in the aligned regions. Of these 48 putative SNPs, 39 (81%) were validated (Table 7). The SNP validation rate in the uncharacterized regions was slightly lower than that in gene and RJ sequences.
SNP validation rates associated with individual NGS platforms were assessed (Table 7). SOLiD and Solexa had similar SNP validation rates (88.2% and 85.4%, respectively). Validation of putative SNPs discovered by mapping Roche 454 reads to Roche 454 reference sequence revealed a 71% SNP validation rate. The most likely cause of the lower rate associated with Roche 454 was the shallow depth of Roche 454 read mapping.
A set of SNPs between Ae. tauschii accessions AL8/78 and AS75 was previously discovered by Sanger sequencing of single-copy genes . A total of 1,212 SNPs located in 641 genes were genotyped with the Illumina GoldenGate SNP assays and mapped on an Ae. tauchii genetic map . Of the 641 genes, 192 shared sequence with NGS genic sequences generated here. There were 223 SNPs in these 192 genes, of which 161 (72.2%) were shared by both data sets, indicating they can be genotyped with Illumina GoldenGate assays and mapped.
Annotation-based genome-wide SNP discovery pipeline, AGSNP
We report here the development of a pipeline for large-scale, genome-wide SNP discovery in large and complex genomes with NGS platforms. This pipeline does not require a reference genome sequence, and its utility is illustrated using the 4.02 Gb genome of Ae. tauschii. The large volume of NGS data that must be processed places great demands on computer resources. The pipeline was therefore split into multiple sub-pipelines to perform individual tasks and accomplish its two principal objectives. The first objective is the assignment (annotation) of Roche 454 reads of a single genotype to three categories: (1) characterized gene reads, (2) characterized repeats, and (3) uncharacterized reads. The second objective is predicting single-copy reads and identifying the putative SNPs by mapping multiple genome equivalents of SOLiD, Solexa or Roche 454 reads to the annotated, single-copy Roche 454 reads. The use of single-copy reads in the reference sequence dramatically reduces data processing and computation time to a manageable amount during the SNP discovery phase.
An asset of the pipeline is that it employs computational tools for read mapping and SNP calling that are applicable to any NGS platform. The pipeline is consequently of a universal utility with the existing and future NGS platforms. The Roche 454 platform used here to generate long reads for the construction of the reference sequence can be replaced by any platform that produces reads of a comparable or greater length, particularly if it would have higher throughput than the Roche 454. Flexible and stringent SNP filtering criteria implemented in the pipeline result in the discovery of large numbers of SNPs and low false-positive SNP rates. A total of 497,118 SNPs was identified, of which 195,631 were in genes. SNPs in genes had an 84% validation rate, those in RJs had an 88% validation rate, and those in uncharacterized sequences had 81% validation.
In the pipeline, a reference sequence of relatively shallow genome coverage of one genotype is compared with reads of another genotype with deep coverage. The latter reads can be short, and although any of the current NGS platforms can in theory be used, the overriding requirement is that the platform has a very high throughput to minimize sequencing costs. This requirement is particularly critical for large and complex genomes, such as that of Ae. tauschii or related wheat.
The pipeline can be used to discover SNPs in both genomic DNA and cDNA. Because genomic DNA is more complex than most cDNA resources, more than twice as many SNPs were identified in genomic DNA than cDNA here. Genomic DNA is therefore preferable for SNP discovery over cDNA. Even for a genome as large as that of Ae. tauschii, only 2.5 runs with the SOLiD v3 were needed to generate a sufficient number of genomic reads to control error during SNP discovery. A single run of SOLiD v4 would be needed to achieve the same coverage. An additional disadvantage of using data of cDNA alone, in addition to the labour associated with the construction of a cDNA library, is that it does not facilitate the annotation of uncharacterized single-copy sequences in the reference sequence; only genes can be used for SNP discovery. Therefore, the use of cDNA for SNP discovery limits the total amount of DNA used for SNP discovery and hence the total number of SNPs discovered.
Another advantage of using genomic DNA for SNP discovery is access to RJs, which are an important source of polymorphisms. SNPs were 1.7 times more frequent per kb in RJ than in genic regions, while having equally high validation rate. Higher polymorphism in RJ makes them particularly valuable for plants with generally low levels of SNP. The RJPrimers program used in one of the sub-pipelines in the AGSNP pipeline, facilitates the identification of single-copy repeat junctions. SNPs in repeat junction regions can by genotyped in a high-throughput mode, e.g., with Illumina's GoldenGate assay , which makes them a valuable marker system.
Error sources during SNP discovery with NGS platforms
Errors in SNP discovery have two major sources: (1) sequencing errors and (2) errors in mapping of short reads to Roche 454 reference sequence. The sequencing errors for NGS platforms are less than 1%. The vast number of sequencing errors in all three NGS platforms is INDELs . Filtering INDELs and homopolymers and the use of multiple genome equivalents can reduce sequencing error rate . The base substitution error rates in consensus sequences of Solexa and SOLiD were very low, about four bases in 10,000. The combined error rate of the Roche 454 reference sequence and mapped reads were 0.03%, 0.15% and 0.27% for SOLiD, Solexa, and Roche 454. Therefore, since sequencing errors are an insignificant source of false-positive SNP rates, the major source of SNP errors is mapping errors. The use of single-copy reads in the pipeline helps to reduce those errors.
The validation rate of RJ SNPs (88%) was as high as that of gene SNPs (84%). All RJ SNPs used for validation were randomly selected from a set of the predicted single-copy RJ sequences with a SNP within 50 bp of RJ locations, which are Illumina genotyping-ready. Previous study indicated that in the Illumina GoldenGate genotyping assays the success rate was higher when a repeat junction was in the vicinity of the target SNP as compared with RJ SNPs without a repeat junction . RJ SNPs in vicinity of repeat junctions must also have a high SNP validation rate and should therefore be selected as a first priority for RJ SNP markers.
The 84%, 88% and 81% SNP validation rate for genes, RJs and uncharacterized regions achieved here with genomic DNA is comparable to that reported by others with NGS of cDNA libraries; an 83% SNP validation rate was reported for Eucalyptus grandis cDNA sequenced with Roche 454 , an 85% validation rate was achieved in maize cDNA sequenced with Roche 454 , and an 87.4% validation rate was reported in Brassica napus cDNA sequenced with Solexa . Our validation rate was somewhat lower than those reported for SNPs discovered in RRL. Validation rates of 79%-92.5% were reported in soybean RRL sequenced with Solexa , 96.4% and 97.0% validation rates were respectively reported in rice and soybean RRL sequenced with Solexa , and an 86% validation rate was reported for RRL library in common bean sequenced with a combination of Roche 454 and Solexa . However, complete reference genomes were used in those SNP discovery projects. In addition, none of these genomes is equal in size and complexity to the genome of Ae. tauschii, which underscores the general utility of the AGSNP pipeline, its high SNP discovery rate, and its particular utility for SNP discovery in large and complex genomes, such as those of many plants.
SNP discovery in Ae. tauschii
A total of 195,631 SNPs in genes and 145,907 SNPs in repeat junctions were discovered in this study. The SNP frequencies were one SNP per 876 bp for genes, and one SNP per 612 bp for repeat junctions, respectively. Repeat junctions have a higher SNP frequency than genes, which is consistent with the results from Paux et al. (2010) . But this is still lower than the frequency observed previously in coding regions of wheat with ranges from one SNP per 267 bp  to one SNP per 540 bp , or in the coding region of Ae. tauschii with one SNP per 202 bp . In the genic regions of Ae. tauschii, nucleotide polymorphism was estimated to be 2.44 × 10-3, which is equivalent to one SNP every 409 bp between two randomly selected haplotypes. The expected SNP frequency in genes is therefore at least 2.1-fold higher than that obtained in the SNP discovery here (one SNP every 876 bp in genes). Taking into account the fact that the accession AL8/78 and AS75 were not selected in random - they were selected because they differed greatly on the basis of RFLP  - the number of SNPs discovered in this project, although very high, is fully realistic for these two accessions.
Several major factors impact genome-wide SNP discovery in the Ae. tauschii genome using next generation sequencing and account for the fact that only about one half of genic SNPs expected were discovered. (1) Low genome coverage (~1.35X) of Roche 454 sequences of one genotype AL8/78 was used as reference sequences. According to simulation results from 13 Ae. tauschii BACs (Figure S2 in Additional file 1), ~70% of gene sequences are covered at ~1.5X genome coverage of Roche 454 reads. At least 3X coverage genome equivalents are required for over 90% coverage of gene sequences (Figure S2 in Additional file 1). (2) The second factor is genome coverage of mapping reads sequenced in another genotype (AS75). The total number of discovered SNPs is significantly correlated with genome coverage of mapping reads (Figure 7). Increasing genomic coverage of mapping reads can increase coverage percentage and mapped read depth to a reference sequence, resulting in the increase in SNP discovery rate. (3) The last factor, which is of general significance, is the number of diverse lines used for SNP discovery. In this study, only two genotypes were used. Simulation results with simplified assumptions showed that over 90% of expected number of SNPs can be discovered when more than 5 genotypes are sequenced (Figure S3 in Additional file 1). This fact should be taken into account in projects targeting species-wide SNP discovery.
We demonstrated here that high numbers of genome-wide SNPs can be discovered by sequencing total genomic DNA of a complex genome with NGS platforms without a reference genome sequence. Using the AGSNP pipeline, 195,631 putative SNPs in genes, 145,907 putative SNPs in repeat junctions and 155,580 putative SNPs in uncharacterized reads were discovered in genomic sequences of two accessions of Ae. tauschii. The SNP validation rates obtained here were comparable to those obtained with the cDNAs of less complex plant genomes. The strategy described here and the associated pipeline yielded more SNPs while being otherwise comparable to cDNA or RRL approaches.
Availability and requirements
Project name: Annotation-based genome-wide SNP discovery pipeline
Project home page: http://avena.pw.usda.gov/wheatD/agsnp.shtml
Availability: Freely available
Operating systems: Linux
Programming language: Perl and Java
Other requirements: bwa, SAMTools, gsAssembler (Newbler), cd-hit-454
License: GNU PGL
Any restrictions to use by non-academics: None
This work is supported in part by US National Science Foundation (grant numbers IOS 0701916 and IOS 0822100). Authors thank Charles M. Nicolet for performing Solexa sequencing and Dawei Lin and Joseph Fass for their collaboration in the physical mapping project.
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