Phylogenomics of Salvia L. subgenus Calosphace (Lamiaceae)

The evolutionary relationships of Salvia have been difficult to estimate. In this study, we used the Next Generation Sequencing method Hyb-Seq to evaluate relationships among 90 Lamiaceae samples, including representatives of Mentheae, Ocimeae, Salvia subgenera Audibertia, Leonia, Salvia, and 69 species of subgenus Calosphace, representing 32 of Epling's sections. A bait set was designed in MarkerMiner using available transcriptome data to enrich 119 variable nuclear loci. Nuclear and chloroplast loci were assembled with hybphylomaker (HPM), followed by coalescent approach analyses for nuclear data (ASTRAL, BEAST) and a concatenated Maximum Likelihood analysis of chloroplast loci. The HPM assembly had an average of 1,314,368 mapped reads for the sample and 527 putative exons. Phylogenetic inferences resolved strongly supported relationships for the deep-level nodes, agreeing with previous hypotheses which assumed that subgenus Audibertia is sister to subgenus Calosphace. Within subgenus Calosphace, we recovered eight monophyletic sections sensu Epling, Cardinalis, Hastatae, Incarnatae, and Uricae in all the analyses (nDNA and cpDNA), Biflorae, Lavanduloideae, and Sigmoideae in nuclear analyses (ASTRAL, BEAST) and Curtiflorae in ASTRAL trees. Network analysis supports deep node relationships, some of the main clades, and recovers reticulation within the core Calosphace. The chloroplast phylogeny resolved deep nodes and four monophyletic Calosphace sections. Placement of S. axillaris is distinct in nuclear evidence and chloroplast, as sister to the rest of the S. subg. Calosphace in chloroplast and a clade with “Hastatae clade” sister to the rest of the subgenus in nuclear evidence. We also tested the monophyly of S. hispanica, S. polystachia, S. purpurea, and S. tiliifolia, including two samples of each, and found that S. hispanica and S. purpurea are monophyletic. Our baits can be used in future studies of Lamiaceae phylogeny to estimate relationships between genera and among species. In this study, we presented a Hyb-Seq phylogeny for complex, recently diverged Salvia, which could be implemented in other Lamiaceae.

Phylogeny, Biogeography, and Classification of the Elms (Ulmus)

A RAD-seq phylogeny is presented for the genus Ulmus, and a revised infrageneric classification is given, with keys, descriptions, and range maps for the subgenera and sections. The previously accepted classification was based on a cpDNA phylogeny, but several well-marked clades in the chloroplast phylogeny are not recovered in the RAD-seq phylogeny and do not seem to represent valid clades in the organismal phylogeny. Ordination and STRUCTURE analysis support a broad species concept in Ulmus sect. Foliaceae and demonstrate interspecific hybridization in the section. Several sections of the genus are disjunct between Asia, Europe, and North America, indicating dispersals between the northern continents with inferred dates from ca. 20 Ma to ca. 3 Ma. Morphological variation is discussed, and some characterspreviously considered characteristic of Ulmus subg. Oreoptelea (narrowly winged achenes, ciliate achene margin) are shared with the unrelated U. villosa. A new subgenus, Ulmus subg. Indoptelea, is described. It can be recognized morphologically by its combination of compact inflorescences with very short pedicels, and samaras with narrow, strongly ciliate wings. It is sister to Ulmus subg. Ulmus, but has a smaller genome than either of the other subgenera.

Hybridization history and repetitive element content in the genome of a homoploid hybrid, Yucca gloriosa (Asparagaceae)

Hybridization in plants results in phenotypic and genotypic perturbations that can have dramatic effects on hybrid physiology, ecology, and overall fitness. Hybridization can also perturb epigenetic control of transposable elements, resulting in their proliferation. Understanding the mechanisms that maintain genomic integrity after hybridization is often confounded by changes in ploidy that occur in hybrid plant species. Homoploid hybrid species, which have no change in chromosome number relative to their parents, offer an opportunity to study the genomic consequences of hybridization in the absence of change in ploidy. Yucca gloriosa (Asparagaceae) is a young homoploid hybrid species, resulting from a cross between Yucca aloifolia and Yucca filamentosa. Previous analyses of ~11kb of the chloroplast genome and nuclear-encoded microsatellites implicated a single Y. aloifolia genotype as the maternal parent of Y. gloriosa. Using whole genome resequencing, we assembled chloroplast genomes from multiple accessions of all three species to re-assess the hybrid origins of Y. gloriosa. We further used re-sequencing data to annotate transposon abundance in the three species and mRNA-seq to analyze transcription of transposons. The chloroplast phylogeny and haplotype analysis suggest multiple hybridization events contributing to the origin of Y. gloriosa, with both parental species acting as the maternal donor. Transposon abundance at the superfamily level was significantly different between the three species; the hybrid was frequently intermediate to the parental species in TE superfamily abundance or appeared more similar to one or the other parent. In only one case – Copia LTR transposons – did Y. gloriosa have a significantly higher abundance relative to either parent. Expression patterns across the three species showed little increased transcriptional activity of transposons, suggesting that either no transposon release occurred in Y. gloriosa upon hybridization, or that any transposons that were activated via hybridization were rapidly silenced. Further work will assess the degree to which transposon abundance and location has affected the epigenomic landscape, gene expression, and ecophysiology in Y. gloriosa.

Phylogenomics of 42 tomato chloroplasts using assembly and alignment-free method

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filter out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.

Phylogenomics of 42 tomato chloroplasts using assembly and alignment-free method

Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on the comparison of single DNA sequences, or a concatenation of a number of these. However, with the advent of next-generation DNA sequencing technologies, the approaches that consider large genomic data sets are of growing importance for the elucidation of evolutionary relationships among species. Among these approaches, the assembly and alignment-free methods which allow an efficient distance computation and phylogeny reconstruction are of great importance. However, it is not yet clear under what quality conditions and abundance of genomic data such methods are able to infer phylogenies accurately. In the present study we assess the method originally proposed by Fan et al. for whole genome data, in the elucidation of Tomatoes' chloroplast phylogenetics using short read sequences. We find that this assembly and alignment-free method is capable of reproducing previous results under conditions of high coverage, given that low frequency k-mers (i.e. error prone data) are effectively filter out. Finally, we present a complete chloroplast phylogeny for the best data quality candidates of the recently published 360 tomato genomes.

Sistemática y evolución del género Yucca (Agavaceae): evidencias de análisis nunfológicos y moleculares

Yucca L. (the Desert Soaptree, Agavaceae) consists of 45 perennial species distributed primarily in the deserts of Mexico and the United States. Although several taxonomic treatments of yuccas exist; the-phylogeny of the group is poorly known. It is unclear which taxa retain primitive characters and how characters have evolved. In addition, relationships of taxa within the genus are uncertain. We compare our phylogeny based upon reproductive characters with a chloroplast phylogeny (Hanson and Rieseberg, 1991 ; Hanson, 1993) and with data from the ITS region of the nuclear genome (Bogler, this volume). The molecular analyses of the chloroplast genome by Hanson and Rieseberg (1991) led to a phylogeny only partially congruent with the traditional morphology-based phylogeny (McKelvey, 1938, 1947) because the cpDNA analysis indicated that chloroplast capture among distantly related, sympatric/parapatric species has been a factor in the evolution of the group. Our results indicate that Yucca in the traditional sense is paraphyletic, that sect. Chaenocarpa is more basal than sect. Yucca ( =Sarcocarpa), and that Yucca (=Hesperoyucca) whipplei falls outside of Yucca.