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 …