DOI: 10.5061/dryad.g84g5
title: Data from: Complete plastome sequence of Thalictrum coreanum (Ranunculaceae) and transfer of the rpl32 gene to the nucleus in the ancestor of the subfamily Thalictroideae

description: Background: Plastids originated from cyanobacteria and the majority of the
 ancestral genes were lost or functionally transferred to the nucleus after
 endosymbiosis. Comparative genomic investigations have shown that gene
 transfer from plastids to the nucleus is an ongoing evolutionary process
 but molecular evidence for recent functional gene transfers among seed
 plants have only been documented for the four genes accD, infA, rpl22, and
 rpl32. Results: The complete plastid genome of Thalictrum coreaum, the
 first from the subfamily Thalictroideae (Ranunculaceae), was sequenced and
 revealed the losses of two genes, infA and rpl32. The functional transfer
 of these two genes to the nucleus in Thalictrum was verified by
 examination of nuclear transcriptomes. A survey of the phylogenetic
 distribution of the rpl32 loss was performed using 17 species of
 Thalictrum and representatives of related genera in the subfamily
 Thalictroideae. The plastid-encoded rpl32 gene is likely nonfunctional in
 members of the subfamily Thalictroideae (Aquilegia, Enemion, Isopyrum,
 Leptopyrum, Paraquilegia, and Semiaquilegia) including 17 Thalictrum
 species due to the presence of indels that disrupt the reading frame. A
 nuclear-encoded rpl32 with high sequence identity was identified in both
 Thalictrum and Aquilegia. The phylogenetic distribution of this gene
 loss/transfer and the high level of sequence similarity in transit
 peptides suggest a single transfer of the plastid-encoded rpl32 to the
 nucleus in the ancestor of the subfamily Thalictroideae approximately
 20-32 Mya. Conclusions: The genome sequence of Thalictrum coreanum
 provides valuable information for improving the understanding of the
 evolution of plastid genomes within Ranunculaceae and across angiosperms.
 Thalictrum is unusual among the three sequenced Ranunculaceae plastid
 genomes in the loss of two genes infA and rpl32, which have been
 functionally transferred to the nucleus. In the case of rpl32 this
 represents the third documented independent transfer from the plastid to
 the nucleus with the other two transfers occurring in the unrelated
 angiosperm families Rhizophoraceae and Salicaceae. Furthermore, the
 transfer of rpl32 provides additional molecular evidence for the monophyly
 of the subfamily Thalictroideae.
description: Align_39Thalictroideae_treenucleotide sequence alignment for phylogenetic relationships among 39 species of the subfamily ThalictroideaeAlign_22rpl32nucleotide sequence alignment of rpl32 gene/pseudogenes for RanunculaceaeAlign_52rpl32only_treenucleotide sequence alignment of rpl32 gene for maximum likelihood phylogenetic tree of 52 taxaAlign_51angiosperms_constraint_treenucleotide sequence alignment of 16 genes for maximum likelihood phylogenetic tree of 51 taxa from angiospermsAlign_nc_rpl32_Thalictrum_Aquilegianucleotide sequence alignment of the nuclear-encoded rpl32 copies from Thalictrum and AquilegiaAlign_7amino_rpl32amino acid sequence alignment of the nuclear-encoded rpl32 copies from Thalictrum, Aquilegia, and Populus with three plastid-encoded copies from related speciesAlign_infA_Aquilegianucleotide sequence alignment of nuclear and transcript copies from AquilegiaAlign_nc_infA_Thalictrum_Aquilegiaamino acid sequence alignment of the nuclear copies of rpl32 of Thalictrum and Aquilegia