Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies

Abstract

Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in plastomes is important to characterize the nature of evolutionary processes in nuclear and cytoplasmic genomes with the different selection pressures, population structures and breeding systems.

New chromosome counts and genome size estimates for 28 species of Taraxacum sect. Taraxacum

“…In our study, we aimed to either find variation in ploidy or confirm the prevailing triploid level. Our findings confirmed previously published records of 2n = 3x = 24 for T.diastematicum and T.obtusifrons (Uhlemann 2001, Salih et al 2017); the chromosome numbers for all other 26 species are new findings. The ploidy level measured by flow cytometry was previously documented for 11 species ( T.atrox , T.baeckiiforme , T.corynodes , T.crassum , T.glossodon , T.guttigestans , T.ingens , T.laticordatum , T.ohlsenii , T.sertatum and T.valens ; Trávníček et al 2010); we now provide exact information on chromosome numbers and genome size estimations.…”

Plastome phylogenomics of Saussurea (Asteraceae: Cardueae)

“…The 20 Saussurea plastomes in our analyses indicated that plastome evolution has been conservative within this genus. All Saussurea plastomes possessed the typical plastome structure of most Asteraceae, including both LSC inversions that are present in nearly all Asteraceae, as for example in Lactuca [27], Artemisia [29], Lasthenia [28], Taraxacum [39] and Mikania [40]. The expansion and contraction of the IR region has been demonstrated to be a significant source of length variation in some plastomes, e.g.…”

Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors

“…The sequencing here was carried out in two multiplex NextSeq500 mid-throughput 2x150bp runs, with two sheep and three samples of plants, and three sheep and three plant samples, respectively. The plant reads gave c. 40-fold coverage of the cytoplasmic chloroplast genome of Taraxacum (Salih et al 2017) which was assembled with a similar approach to that described here. The overall error rate in the sequence calls (<1%) was identical to that in the sheep data omitting the alternative calls, and in particular, no systematic alternative reads were seen in other high-coverage assemblies, suggesting that the multiple reads of different sequences here are not sequencing artefacts.…”