RNAseq‐based phylogenetic reconstruction of Taxaceae and Cephalotaxaceae

Abstract

Taxaceae and Cephalotaxaceae are the two economically important conifer families. Over the years there has been much controversy over the issue of merging these families. The position of Amentotaxus and Torreya is also ambiguous. Some authors consider them closer to Taxaceae while others deemed them to fit within Cephalotaxaceae. Still, others prefer to raise them to their own tribe. Different morphological, anatomical, embryological and phylogenetic evidence supports one or the other view, making the precise delineation between them unresolved. Here we used an RNAseq-based approach to obtain orthologous genes across the selected species to reconstruct a more robust phylogeny of these families. A total of 233.123 million raw reads were de novo assembled to generate nine different transcript assemblies for the corresponding species. Of the 940 191 assembled transcripts across nine species, we generated 409 734 unigenes, which were clustered into orthologous groups. A total of 331 singlecopy complete orthologous groups were selected for phylogenetic analysis. Maximum-likelihood, maximum-parsimony and Bayesian phylogenetic trees showed a sister relationship between Taxaceae and Cephalotaxaceae. Our analysis supports their distinctiveness at the family level and also shows that Amentotaxus and Torreya fit within Cephalotaxaceae.

Plastome phylogenomics ofCephalotaxus(Cephalotaxaceae) and allied genera

“…Although the sister relationship between Torreya and Amentotaxus has been commonly revealed by previous studies ( Chaw et al , 1997 ; Cheng et al , 2000 ; Wang and Shu, 2000 ; Quinn et al , 2002 ; Hao et al , 2008 ; Lu et al , 2014 ; Majeed et al , 2018 ; Ran et al , 2018 ; X. Zhang et al , 2019 ), the position of these two genera remains unresolved.…”

“… Zhang et al , 2019 ), the position of these two genera remains unresolved. For instance, the phylogenetic analyses based on 18S ribosomal DNA ( Chaw et al , 1997 ), ribosomal ITS regions ( Cheng et al , 2000 ; Hao et al , 2008 ), LFY and NLY genes ( Lu et al , 2014 ) and RNA sequencing ( Majeed et al , 2018 ) revealed that they are closer to Cephalotaxus (Cephalotaxaceae) than to Taxaceae. However, phylogenetic reconstruction using plastid matK ( Cheng et al , 2000 ), a combination of plastid matK , rbcL , trnL–F and psbA–trnH ( Hao et al , 2008 ), transcriptomic data ( Ran et al , 2018 ) and plastomes (X.…”

“…Notably, those studies that reconstructed phylogeny based on nuclear sequence data, i.e. Chaw et al (1997) , Cheng et al (2000) , Lu et al (2014) and Majeed et al (2018) , had limited taxonomic sampling from Cephalotaxaceae and Taxaceae. Accordingly, phylogenetic errors or uncertainty in the tree topology resulting from limited taxon sampling seem inevitable ( Rokas and Carroll, 2005 ; Philippe et al , 2011 ).…”

“…Although the analyses by Ran et al (2018) and X. Zhang et al (2019) showed that these two genera are closer to Taxaceae, Cheng et al (2000) , Hao et al (2008) , Lu et al (2014) and Majeed et al (2018) proposed to include them within Cephalotaxaceae. These conflicts necessitate that the relationships between Cephalotaxus and its relatives require further investigation.…”

“…For instance, cladistic analysis based on morphological characters ( Ghimire and Heo, 2014 ) as well as phylogenetic inference utilizing 18S ribosomal DNA sequences ( Chaw et al , 1997 ) and plastid rbcL and matK regions ( Quinn et al , 2002 ) suggest that Cephalotaxaceae should be merged into Taxaceae. However, phylogenetic analyses using a combination of plastid matK and nuclear ribosomal internal transcribed spacer (ITS) regions ( Cheng et al , 2000 ), plastid matK , rbcL , trnL–trnF , psbA–trnH and nuclear ITS ( Hao et al , 2008 ), nuclear LFY and NLY ( Lu et al , 2014 ), and transcriptomic data ( Majeed et al , 2018 ; Ran et al , 2018 ) support the sister relationship between Cephalotaxaceae and Taxaceae. Nevertheless, a clear-cut delineation between the two families remains unresolved due to the ambiguous position of Amentotaxus and Torreya .…”