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• W2969821207 endingPage "3421" @default.
• W2969821207 startingPage "3409" @default.
• W2969821207 abstract "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 paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity." @default.
• W2969821207 created "2019-08-29" @default.
• W2969821207 creator A5008249059 @default.
• W2969821207 creator A5016901520 @default.
• W2969821207 creator A5022975449 @default.
• W2969821207 creator A5034833941 @default.
• W2969821207 creator A5048972561 @default.
• W2969821207 creator A5057266923 @default.
• W2969821207 creator A5066184470 @default.
• W2969821207 date "2019-10-01" @default.
• W2969821207 modified "2023-09-28" @default.
• W2969821207 title "Utilization of Tissue Ploidy Level Variation in <i>de Novo</i> Transcriptome Assembly of <i>Pinus sylvestris</i>" @default.
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