Development of an Arabis alpina genomic contig sequence data set and application to single nucleotide polymorphisms discovery

Arabis alpina: A perennial model plant for ecological genomics and life-history evolution

Many model organisms were chosen and achieved prominence because of an advantageous combination of their life‐history characteristics, genetic properties and also practical considerations. Discoveries made in Arabidopsis thaliana, the most renowned noncrop plant model species, have markedly stimulated studies in other species with different biology. Within the family Brassicaceae, the arctic–alpine Arabis alpina has become a model complementary to Arabidopsis thaliana to study the evolution of life‐history traits, such as perenniality, and ecological genomics in harsh environments. In this review, we provide an overview of the properties that facilitated the rapid emergence of A. alpina as a plant model. We summarize the evolutionary history of A. alpina, including genomic aspects, the diversification of its mating system and demographic properties, and we discuss recent progress in the molecular dissection of developmental traits that are related to its perennial life history and environmental adaptation. From this published knowledge, we derive open questions that might inspire future research in A. alpina, other Brassicaceae species or more distantly related plant families.

Identification of Arabis alpina genomic regions associated with climatic variables along an elevation gradient through whole genome scan

We performed a pooled whole-genome sequencing on samples of the alpine plant Arabis alpina, harvested in ten populations along an elevation gradient in the French Alps. A large dataset of genetic variations was produced as single nucleotide polymorphisms (SNPs). A combined genome scan approach enabled detecting genomic regions associated with a synthetic environmental variable characterizing the climate at each sampling location. Positive loci detected by two methods were retained and belong to 19 regions in the Arabis alpina genome. The most significant region harbors an ortholog of the AtNAC062 gene, encoding a membrane-bound transcription factor described as linking the cold response and pathogen resistance that may confer protection to plants under extended snow coverage at high elevations. Other genes involved in the stress response or in flowering regulation were also detected. Altogether, our results indicated that Arabis alpina represent a suitable model for studying genomic adaptation in alpine perennial plants.

The complete mitochondrial genome sequence of an alpine plant Arabis alpina

Arabis alpina (A. alpina) is an arctic-alpine flowering plant in the family Brassicaceae, naturally growing in the tundra of arctic regions and in mountains at southern latitudes. In this study, we first report the assembly of the complete A. alpina mitochondrial (mt) genome using the next-generation sequencing technologies. The A. alpina mt circular genome is 323,159 bp in length and contains 33 protein-coding genes, 18 tRNA genes and 3 rRNA genes. To analyze the phylogenic and evolutional relationship of A. alpina, a neighbour-joining phylogenetic tree was reconstructed based on the mt genome of A. alpina and other 27 plants. The complete A. alpina mt genome will be helpful in population studies or investigations of mt functions of these alpine plant species.

Comparative analysis of molecular and physiological traits between perennial Arabis alpina Pajares and annual Arabidopsis thaliana Sy-0

Annual plants complete life cycle in a year while perennial plants maintain growth for several years. Arabis alpina, a polycarpic perennial, is a close relative of monocarpic annual Arabidopsis. Pajares is an accession of A. alpina requiring vernalization, a long-term cold for flowering. Arabidopsis shows holistic flowering whereas Pajares shows idiographic flowering, producing axillary branches under variable developmental phases from juvenile, adult vegetative to reproductive phases. To understand the molecular mechanism behind diverse phases of axillary branches, we analyzed the levels of primary miR156 expressions because miR156-SPL module is a key regulator for developmental phase transition. We found that in Pajares, miR156 levels were highly variable among the axillary branches, which causes differential sensitivity to vernalization. Thus, the axillary branches expressing high levels of miR156 remain in juvenile phase even after vernalization, whereas the axillary branches expressing low levels of miR156 produce flowers after vernalization. In contrast, every axillary branches of Arabidopsis winter annual Sy-0 expressed similar levels of miR156 and synchronously responded to vernalization, which causes holistic flowering. Therefore, we suggest that variable miR156 expression levels and the resulting differential response to vernalization among axillary branches are distinctive features determining polycarpic perenniality of A. alpina Pajares.

Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

Gene model annotations are important community resources that ensure comparability and reproducibility of analyses and are typically the first step for functional annotation of genomic regions. Without up-to-date genome annotations, genome sequences cannot be used to maximum advantage. It is therefore essential to regularly update gene annotations by integrating the latest information to guarantee that reference annotations can remain a common basis for various types of analyses. Here, we report an improvement of the Arabidopsis lyrata gene annotation using extensive RNA-seq data. This new annotation consists of 31,132 protein coding gene models in addition to 2,089 genes with high similarity to transposable elements. Overall, ~87% of the gene models are corroborated by evidence of expression and 2,235 of these models feature multiple transcripts. Our updated gene annotation corrects hundreds of incorrectly split or merged gene models in the original annotation, and as a result the identification of alternative splicing events and differential isoform usage are vastly improved.

Evolution of the Selfing Syndrome in Arabis alpina (Brassicaceae)

Introduction

The transition from cross-fertilisation (outcrossing) to self-fertilisation (selfing) frequently coincides with changes towards a floral morphology that optimises self-pollination, the selfing syndrome. Population genetic studies have reported the existence of both outcrossing and selfing populations in Arabis alpina (Brassicaceae), which is an emerging model species for studying the molecular basis of perenniality and local adaptation. It is unknown whether its selfing populations have evolved a selfing syndrome.

Methods

Using macro-photography, microscopy and automated cell counting, we compared floral syndromes (size, herkogamy, pollen and ovule numbers) between three outcrossing populations from the Apuan Alps and three selfing populations from the Western and Central Alps (Maritime Alps and Dolomites). In addition, we genotyped the plants for 12 microsatellite loci to confirm previous measures of diversity and inbreeding coefficients based on allozymes, and performed Bayesian clustering.

Results and Discussion

Plants from the three selfing populations had markedly smaller flowers, less herkogamy and lower pollen production than plants from the three outcrossing populations, whereas pistil length and ovule number have remained constant. Compared to allozymes, microsatellite variation was higher, but revealed similar patterns of low diversity and high Fis in selfing populations. Bayesian clustering revealed two clusters. The first cluster contained the three outcrossing populations from the Apuan Alps, the second contained the three selfing populations from the Maritime Alps and Dolomites.

Conclusion

We conclude that in comparison to three outcrossing populations, three populations with high selfing rates are characterised by a flower morphology that is closer to the selfing syndrome. The presence of outcrossing and selfing floral syndromes within a single species will facilitate unravelling the genetic basis of the selfing syndrome, and addressing which selective forces drive its evolution.