Comparing Genome-Guided Assembly and Phased Variants Based Assembly Approach to Separate the Homoeolog Transcripts in Tetraploid Peanut (Arachis hypogaea L.)

Homoeologous copies of transcripts are abundant in many self-pollinating species including tetraploid peanut, and can impose a challenge to build a transcriptome reference without the merging of homoeologs. De novo transcriptome assembly of tetraploid cultivar OLin with single kmer and multiple kmer approaches has helped in reducing homoeolog collapse to an extent, but requires further efforts. In this study, we have compared the genome-guided transcriptome assembly approach using diploid progenitor species sequences and separation of phased transcripts from de novo transcriptome assembly approach to generate reference transcriptome assemblies. On aligning the raw reads back to each of the generated assembly along with the de novo assembly, we observed that the de novo assembly had 37% of transcripts with more than one SNP whereas the genome-guided approach had 16.5% and the phased approach had 21% of transcripts with more than one SNP respectively. Transcripts with variants on aligning reads back to the reference are a potential indicator of merged of sequences. One hundred transcripts classified as collapsed from OLin de novo assembly were compared to the genome-guided and phased transcriptome assemblies, and it was observed that the collapsed contigs were separated into two or more new transcripts. Thus genome-guided and phased transcriptome assembly approaches will be useful to avoid homoeolog collapse. The genome-guided approach may have an advantage over phased approach due to better representation of genes in a genome, but this requires the genome sequences of the diploid progenitor species.