Data from: Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae)

We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa).

Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6–7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a ‘ghost lineage’ of a now-extinct North American poplar.

Usage notes

Populus-aligned plastome sequence alignments WGS short reads were aligned to the Nisqually-1 chloroplast reference genome (GenBank: EF489041.1) using BWA version 0.6.2. For each position in the reference plastome, bases were called only if the coverage was greater than 1000 reads, as the average read depth for each base pair was 7000 or greater. To improve accuracy, bases were only called if the 1000+ calls agreed for either the reference or alternate base for at least 80% of the reads.

Any position not meeting these criteria was called as missing data. Indels were excluded for all analyses. populus_sal.phy Manihot-aligned plastome sequence alignments Using the same protocol as the Populus-aligned dataset, but aligned to the Manihot esculenta reference plastome (NCBI Reference Sequence: NC_010433.1). manihot.phy pop_to_manihot_beauti.xml XML file generated by BEAUTi for use by BEAST for dating analyses. pop_to_manihot_gtr.xml pop_to_manihot.log BEAST log file pop_to_manihot_4.log pop_to_manihot.trees NEXUS tree file containing trees generated by BEAST. pop_to_manihot_4.trees ns_vs_s Divergence statistics for the four species that were de novo assembled (P. trichocarpa, P. balsamifera, P. fremontii, Salix interior).

These were calculated using scripts "parse_fasta_to_genes.pl" and "diffs.pl" from github.com/daisieh/phylogenomics/releases/tag/v1.01-nph