The genome of the model species Anthoceros agrestis

The monophyletic group of hornworts is believed to represent the immediate sister group of all vascular land plants. However, this traditional view is still debated and cannot be satisfactorily resolved owing to the lack of detailed knowledge on the general biology and genomic features of hornworts. Until now, advancement in this field was primarily hindered by the lack of genomic resources for a hornwort model species. Here we provide the first insight into the major features of the draft genome sequence of the model hornwort, Anthoceros agrestis. We show that A. agrestis has a remarkably small genome, with few recent paralogues, which makes it appropriate for genetic analysis. Finally, we also report on the genomic features of the chloroplast, mitochondrion and nuclear genomes and compare those with algal and vascular land plant genomes. At the very end of the chapter we summarize our achievements and provide a list of issues that need to be resolved in the future

Sequence capture using RAD probes clarifies phylogenetic relationships and species boundaries in Primula sect. Auricula

Species-rich evolutionary radiations are a common feature of mountain floras worldwide. However, the frequent lack of phylogenetic resolution in species-rich alpine plant groups hampers progress towards clarifying the causes of diversification in mountains. In this study, we use the largest plant group endemic to the European Alpine system, Primula sect. Auricula, as a model system. We employ a newly developed next-generation-sequencing protocol, involving sequence capture with RAD probes, and map reads to the reference genome of Primula veris to obtain DNA matrices with thousands of SNPs. We use these data-rich matrices to infer phylogenetic relationships in Primula sect. Auricula and examine species delimitations in two taxonomically difficult subgroups: the clades formed by the close relatives of P. auricula and P. pedemontana, respectively. Our molecular dataset enables us to resolve most phylogenetic relationships in the group with strong support, and in particular to infer four well-supported clades within sect. Auricula. Our results support existing species delimitations for P. auricula, P. lutea, and P. subpyrenaica, while they suggest that the group formed by P. pedemontana and close relatives might need taxonomic revision. Finally, we discuss preliminary implications of these findings on the biogeographic history of Primula sect. Auricula

Selfing in haploid plants and efficacy of selection: codon usage bias in the model moss Physcomitrella patens

Long term reduction in effective population size will lead to major shift in genome evolution. In particular, when effective population size is small, genetic drift becomes dominant over natural selection. The onset of self-fertilization is one evolutionary event considerably reducing effective size of populations. Theory predicts that this reduction should be more dramatic in organisms capable for haploid than for diploid selfing. Although theoretically well-grounded, this assertion received mixed experimental support. Here we test this hypothesis by analyzing synonymous codon usage bias of genes in the model moss Physcomitrella patens frequently undergoing haploid selfing. In line with population genetic theory, we found that the effect of natural selection on synonymous codon usage bias is very weak. Our conclusion is supported by four independent lines of evidence: a) Very weak or nonsignificant correlation between gene expression and codon usage bias; b) No increased codon usage bias in more broadly expressed genes; c) No evidence that codon usage bias would constrain synonymous and nonsynonymous divergence; d) Predominant role of genetic drift on synonymous codon usage predicted by a model-based analysis. These findings show striking similarity to those observed in AT-rich genomes with weak selection for optimal codon usage and GC content overall. Our finding is in contrast to a previous study reporting adaptive codon usage bias in the moss P. patens

The Ceratodon purpureus transcriptome ushers in the era of moss comparative genomics

This chapter outlines the scope of the ongoing Ceratodon purpureus genome project and provides an overview of the C. purpureus transcriptome, the evolution of the C. purpureus UV sex chromosomes, and the patterns of polymorphism in the species. Comparative analyses of the transcriptomes of a male and a female isolate showed that C. purpureus and the moss model Physcomitrella patens had highly overlapping gene sets, and that most of the genes shared between these two species evolve under strong purifying selection. However, the differences between the C. purpureus and P. patens genomes refined our understanding of the timing of gene family gain and loss across the land plants and the heterogeneity in rate of molecular evolution across the genome of these two species. Ceratodon purpureus showed a slightly greater codon usage bias compared to P. patens, which may be explained by the contrasting mating system of the two species. The C. purpureus transcriptomes also showed evidence of a genome doubling event ∼65–76 MYA that was independent of the contemporaneous polyploidy event inferred for P. patens. These data also suggested considerable physiological and developmental divergence between the two species. Genetic mapping and molecular evolutionary analysis showed that the nonrecombining UV chromosomes of C. purpureus are actively capturing new genes, illustrating that at least this part of the genome is highly dynamic. Moreover, patterns of polymorphism were highly variable across the genome, suggesting that sexual recombination in other parts of the genome decouples even genes on the same chromosome, and they experience different patterns of natural selection. The forthcoming C. purpureus genome will build on these existing resources and enable us to answer definitively many questions regarding the evolution of land plant gene families, genome structure, and the genetic basis of adaptive variation

Ingroup Dataset

Fasta file as exported from STACKS software. This file includes sequences for all populations of Primula farinosa and was used for all subsequent molecular analysis except for the phylogenomic (RAxML) analysis

How Do Cold-Adapted Plants Respond to Climatic Cycles? Interglacial Expansion Explains Current Distribution and Genomic Diversity in Primula farinosa L

Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model. We first approximate the time and extent of demographic contractions and expansions during the Late Quaternary by projecting species distribution models across the last 72 ka. We also generate genome-wide sequence data using a Reduced Representation Library approach to reconstruct the spatial structure, genetic diversity, and phylogenetic relationships of lineages within P. farinosa. Finally, by integrating the results of climatic and genomic analyses in an Approximate Bayesian Computation framework, we propose the most likely model for the extent and direction of population-size changes in $P$. farinosa through the Late Quaternary. Our results support the interglacial expansion of $P$. farinosa, differing from the prevailing paradigm that the observed distribution of cold-adapted species currently fragmented in high altitude and latitude regions reflects the consequences of postglacial contraction processes

How do cold-adapted plants respond to climatic cycles? Interglacial expansion explains current distribution and genomic diversity in Primula farinosa L

Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model. We first approximate the time and extent of demographic contractions and expansions during the Late Quaternary by projecting species distribution models across the last 72 ka. We also generate genome-wide sequence data using a Reduced Representation Library approach to reconstruct the spatial structure, genetic diversity, and phylogenetic relationships of lineages within P. farinosa. Finally, by integrating the results of climatic and genomic analyses in an Approximate Bayesian Computation framework, we propose the most likely model for the extent and direction of population-size changes in P. farinosa through the Late Quaternary. Our results support the interglacial expansion of P. farinosa, differing from the prevailing paradigm that the observed distribution of cold-adapted species currently fragmented in high altitude and latitude regions reflects the consequences of postglacial contraction processes. [Approximate Bayesian computation; climate change; hindcasting; Late Quaternary glacial cycles; paleoclimate; Reduced Representation Library; species distribution models.

Resolution 1964-08-20 Wildlife Habitat Research Program of U.S. Forest Service

Understanding the effects of past climatic fluctuations on the distribution and population-size dynamics of cold-adapted species is essential for predicting their responses to ongoing global climate change. In spite of the heterogeneity of cold-adapted species, two main contrasting hypotheses have been proposed to explain their responses to Late Quaternary glacial cycles, namely, the interglacial contraction versus the interglacial expansion hypotheses. Here, we use the cold-adapted plant Primula farinosa to test two demographic models under each of the two alternative hypotheses and a fifth, null model. We first approximate the time and extent of demographic contractions and expansions during the Late Quaternary by projecting species distribution models across the last 72 ka. We also generate genome-wide sequence data using a Reduced Representation Library approach to reconstruct the spatial structure, genetic diversity, and phylogenetic relationships of lineages within P. farinosa. Finally, by integrating the results of climatic and genomic analyses in an Approximate Bayesian Computation framework, we propose the most likely model for the extent and direction of population-size changes in P. farinosa through the Late Quaternary. Our results support the interglacial expansion of P. farinosa, differing from the prevailing paradigm that the observed distribution of cold-adapted species currently fragmented in high altitude and latitude regions reflects the consequences of postglacial contraction processes

The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data

High‐throughput RNA sequencing (RNA‐seq) has recently become the method of choice to define and analyze transcriptomes. For the model moss Physcomitrella patens, although this method has been used to help analyze specific perturbations, no overall reference dataset has yet been established. In the framework of the Gene Atlas project, the Joint Genome Institute selected P. patens as a flagship genome, opening the way to generate the first comprehensive transcriptome dataset for this moss. The first round of sequencing described here is composed of 99 independent libraries spanning 34 different developmental stages and conditions. Upon dataset quality control and processing through read mapping, 28 509 of the 34 361 v3.3 gene models (83%) were detected to be expressed across the samples. Differentially expressed genes (DEGs) were calculated across the dataset to permit perturbation comparisons between conditions. The analysis of the three most distinct and abundant P. patens growth stages – protonema, gametophore and sporophyte – allowed us to define both general transcriptional patterns and stage‐specific transcripts. As an example of variation of physico‐chemical growth conditions, we detail here the impact of ammonium supplementation under standard growth conditions on the protonemal transcriptome. Finally, the cooperative nature of this project allowed us to analyze inter‐laboratory variation, as 13 different laboratories around the world provided samples. We compare differences in the replication of experiments in a single laboratory and between different laboratories