Is Phylotranscriptomics as Reliable as Phylogenomics?

Abstract

Phylogenomics, the study of phylogenetic relationships among taxa based on their genome sequences, has emerged as the preferred phylogenetic method because of the wealth of phylogenetic information contained in genome sequences. Genome sequencing, however, can be prohibitively expensive, especially for taxa with huge genomes and when many taxa need sequencing. Consequently, the less costly phylotranscriptomics has seen an increased use in recent years. Phylotranscriptomics reconstructs phylogenies using DNA sequences derived from transcriptomes, which are often orders of magnitude smaller than genomes. However, in the absence of corresponding genome sequences, comparative analyses of transcriptomes can be challenging and it is unclear whether phylotranscriptomics is as reliable as phylogenomics. Here we respectively compare the phylogenomic and phylotranscriptomic trees of 22 mammals and 15 plants that have both sequenced nuclear genomes and publicly available RNA sequencing data from multiple tissues. We found that phylotranscriptomic analysis can be sensitive to orthologous gene identification. When a rigorous method for identifying orthologs is employed, phylogenomic and phylotranscriptomic trees are virtually identical to each other, regardless of the tissue of origin of the transcriptomes and whether the same tissue is used across species. These findings validate phylotranscriptomics, brighten its prospect, and illustrate the criticality of reliable ortholog detection in such practices.

The frequency and topology of pseudoorthologs

“…Multiple studies have attempted to assess the influence of pseudoorthologs on phylogenetic inference, though they have generally done so by comparing results filtered using different ortholog detection methods (3). The results of these analyses have been mixed, with some studies finding substantial differences in inferred species trees (13)(14)(15) and others finding minimal differences (14,16,17). Furthermore, and in contrast to the long-held opinion that orthologs, not paralogs, should be used to infer species relationships, recent methodological developments explicitly allow for the inclusion of paralogs in phylogenetic inference (reviewed in 18).…”

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline forde novotranscriptome assembly

“…Another major disadvantage of keeping false isoforms is in phylogenomic analyses. Due to the relative ease of generation and affordability, many phylogenomic studies analyse multi-gene alignments based on transcriptome data instead of full genome data to estimate phylogenies (Lozano-Fernandez et al, 2019; Cheon et al, 2020). By using TransPi, the automation of large-scale phylogenomic approaches, focusing on thousands of proteins from many taxa, can be attained with ease in a scalable and reproducible way.…”

Smelling in the dark: phylogenomic insights on the chemosensory system of a subterranean beetle

“…With this approach, we aim to infer diversity patterns of the chemosensory repertoire of S. longicornis and to characterize each gene family more specifically, indicating with a higher confidence the putative function of these genes compared to analysis merely based on homology. Since no reference genome is available for the focus species, we inferred a deeplysequenced de novo transcriptome which resulted in a high completeness based on our assessment of BUSCO genes (see Results), indicating that we recovered a mostly complete reference gene set and hence it is of enough quality to explore gene family evolution (Cheon et al 2020). This approach has been successfully applied in other studies with non-model organisms through the combination of genomic and high quality transcriptomic data (e.g., Fernández and Gabaldón 2020;Vizueta et al 2020).…”