SNP markers retrieval for a non-model species: a practical approach

Area of Science:

• Genomics
• Bioinformatics
• Plant Breeding

Background:

• Next-generation sequencing (NGS) drives the use of Single Nucleotide Polymorphism (SNP) markers in breeding.
• Accurate assembly of large sequence datasets is crucial for SNP development.
• Assembler performance in complex, heterogeneous genomes and its impact on SNP retrieval remain understudied.

Purpose of the Study:

• To evaluate and compare the performance of two assemblers, CAP3 and CLC, for SNP retrieval.
• To assess the consequences of different assembly strategies on SNP discovery in highly heterogeneous genomes.
• To propose a practical SNP retrieval scheme for non-model species.

Main Methods:

• Assembly of 454 sequencing data from four lily genotypes using CAP3 and CLC assemblers.
• Comparison of assembly outputs based on contig number, reads per contig, and read length.
• BLAST analysis to assess contig redundancy and identify chimeric contigs.
• Evaluation of SNP marker retrieval efficiency from each assembly.

Main Results:

• CLC assembler produced fewer contigs with longer average read lengths compared to CAP3.
• CAP3 assemblies exhibited high redundancy, while CLC occasionally combined paralogs.
• Redundant and chimeric contigs can lead to erroneous SNP identification.
• A filtering strategy effectively removed most erroneous SNPs originating from chimeric contigs.

Conclusions:

• CLC assembler demonstrates superior performance for assembling highly heterogeneous genomes over CAP3.
• Consequently, CLC facilitates more efficient SNP marker retrieval.
• A practical, universally applicable flow scheme for SNP marker retrieval in non-model species is proposed.