Comparative transcriptomes of four Elm species provide insights into the genetic features and adaptive evolution of Ulmus spp.

Abstract

Ulmus spp. have a wide distribution, strong adaptability, and high application value. However, due to the outbreak of Dutch elm disease and a lack of nuclear genome data, studies on Ulmus spp. are lacking. In this study, we obtained full-length transcriptomes from four elm species, with an average of 64,529 transcripts per species. Among these transcripts, an average of 6410 long noncoding RNAs were obtained per species. We performed SSR site detection and primer design and obtained an average of 20,650 SSR primer pairs per elm species. Fisher’s exact test revealed a large difference in the enrichment of functional genes shared between Ulmus parvifolia and three other elms, which represented 31 Gene Ontology terms, four Kyoto Encyclopedia of Genes and Genomes pathways, and two transcription factors. Phylogenetic evolution and divergence time analyses indicated that U. parvifolia diverged from the three other elms ca. 13.98 Mya; the divergence time of Ulmus macrocarpa, Ulmus davidiana, and Ulmus pumila was ca. 10.84–7.25 Mya. Furthermore, we identified 22 genes that were positively selected, and transcriptional profiling analysis showed that the expression levels of those genes showed marked changes under high temperature. These positively selected genes are widely involved in the ubiquitin system, nucleotide excision repair, protein modification, circadian rhythm regulation, light stimulus response, abiotic stimulus response, MAPK signaling, and plant pathogenicity interactions; they may play an important role in the adaptation of elms to environmental changes. This study provides a basis for the study of adaptive evolution, genetic diversity and functional gene development in Ulmus spp.