Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris.

ABSTRACT: Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of

SUBMITTER: Ojeda DI 

PROVIDER: S-EPMC6778806 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature