Abstract
WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification.
Highlights
We constructed a high-confidence phylogenetic tree and estimated the divergence times of 15 plant species using genes extracted from a total of 439 single-copy families (Fig. 1 and Extended Data Fig. 2)
We identified B-AP3 genes from the transcriptomes of species of each of the orchid subfamilies and the B-class MADS-box genes from the floral transcriptome data of Molineria capitulata, a member of Hypoxidaceae that possesses a flower with petaloid tepals and powdery pollen
Type I MADS-box genes are important for the initiation of endosperm development[22], and transcripts of type I Mαand MγMADS-box genes were found in developing seeds of A. shenzhenica, P. equestris, and M. capitulata (Extended Data Fig. 10 and Supplementary Fig. 11)
Summary
We constructed a high-confidence phylogenetic tree and estimated the divergence times of 15 plant species using genes extracted from a total of 439 single-copy families (Fig. 1 and Extended Data Fig. 2). Analyses of gene trees that contained at least one paralogue pair from co-linear regions from one of the three orchid genomes placed the younger A. shenzhenica WGD and the P. equestris and D. catenatum WGDs on the orchid stem branch, and provided additional evidence for the monocot τWGD13,14 (Fig. 3 and Supplementary Note 2.3).
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