A multi-tissue transcriptome strategy for genomic resource development in Pinus edulis

In a significant advancement for conifer genomic research, a multi-tissue transcriptome strategy has been developed for piñon pine (Pinus edulis). This approach, which assembles a reference transcriptome from four diploid tissues (needle, phloem, root, vegetative bud) and one haploid tissue (megagametophyte), could prove valuable for other non-model plants with large genomes.

The strategy was designed to enhance probe design and address the challenge of selecting loci without a reference genome, a common barrier in targeted exon-capture methods. By prioritizing highly expressed P. edulis transcripts and those matching a conifer exon database, the researchers were able to design a probe-set that recovered 76% of conserved plant genes, with minimal duplication.

Further filtering resulted in a total of 15,664 transcripts, spanning approximately 31.4 Mb, which is less than 0.1% of the genome. These transcripts were found to exhibit tissue-specific expression, with 27.4% occurring exclusively in non-needle tissues. Functional annotation revealed that the transcriptome includes complementary contributions from various tissues, such as seed-desiccation and germination genes from megagametophytes, as well as defense- and stress-associated genes from roots and phloem.

This multi-tissue approach not only provides a comprehensive view of the P. edulis transcriptome but also serves as a roadmap for future studies on other non-model plants with large genomes.