Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

Rawat, Vimal; Abdelsamad, Ahmed; Pietzenuk, Björn; Seymour, Danelle K.; Koenig, Daniel; Weigel, Detlef; Pečinka, Aleš; Schneeberger, Korbinian

doi:10.1371/journal.pone.0137391

Cited by 85 publications

(74 citation statements)

References 38 publications

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“…Since finalizing this work, a newer annotation has been published (Rawat et al, 2015) that recognizes two FLC genes in A. lyrata. Because of the very close similarity between the two genes, we could not use our coverage estimates from read alignments to A. lyrata or to the A. arenosa bacterial artificial chromosome (BAC) to differentiate the expression of the two copies.…”

Section: Abrogated Vernalization Responsiveness and Loss Of Flc Exprementioning

confidence: 99%

Habitat-Associated Life History and Stress-Tolerance Variation in Arabidopsis arenosa

et al. 2016

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Weediness in ephemeral plants is commonly characterized by rapid cycling, prolific all-in flowering, and loss of perenniality. Many species made transitions to weediness of this sort, which can be advantageous in high-disturbance or human-associated habitats. The molecular basis of this shift, however, remains mostly mysterious. Here, we use transcriptome sequencing, genome resequencing scans for selection, and stress tolerance assays to study a weedy population of the otherwise nonweedy Arabidopsis arenosa, an obligately outbreeding relative of Arabidopsis thaliana. Although weedy A. arenosa is widespread, a single genetic lineage colonized railways throughout central and northern Europe. We show that railway plants, in contrast to plants from sheltered outcrops in hill/mountain regions, are rapid cycling, have lost the vernalization requirement, show prolific flowering, and do not return to vegetative growth. Comparing transcriptomes of railway and mountain plants across time courses with and without vernalization, we found that railway plants have sharply abrogated vernalization responsiveness and high constitutive expression of heat-and cold-responsive genes. Railway plants also have strong constitutive heat shock and freezing tolerance compared with mountain plants, where tolerance must be induced. We found 20 genes with good evidence of selection in the railway population. One of these, LATE ELONGATED HYPOCOTYL, is known in A. thaliana to regulate many stress-response genes that we found to be differentially regulated among the distinct habitats. Our data suggest that, beyond life history regulation, other traits like basal stress tolerance also are associated with the evolution of weediness in A. arenosa.Life history traits differ between and within plant species and commonly reflect the requirements of the habitats in which they are found (Baker, 1974;Weinig et al., 2003;Grime, 2006). Depending on abiotic and biotic conditions, a variety of strategies can be favored, and accordingly, weeds are phenotypically diverse. In environments that are unpredictable, with frequent occurrences of stresses like drought, temperature fluctuations, or human-associated perturbations, rapid cycling and early flowering are common (Hall and Willis, 2006;Sherrard and Maherali, 2006;Franks et al., 2007;Wu et al., 2010). Life history adaptations can help mediate tradeoffs between resource accumulation and stress avoidance and are important for wild species as well as for crops (Jung and Müller, 2009). Comparing results among species, as well as the correlates of these traits with other fitness-related traits, promises new insights into the mechanisms of adaptation to unpredictable habitats.A common phenotype of plants in unpredictable habitats is early and prolific flowering relative to related populations in more stable habitats (Baker, 1965; Grotkopp et al

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Section: Abrogated Vernalization Responsiveness and Loss Of Flc Exprementioning

confidence: 99%

Habitat-Associated Life History and Stress-Tolerance Variation in Arabidopsis arenosa

et al. 2016

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“…This conservative approach led to 40 unique genes specific for Ler and 63 genes specific for Col-0. Using the genome of the close relative A. lyrata (36,40) as outgroup, we found that the majority of these polymorphic genes (77%) evolved via deletions within the genome in which they are absent, rather than by a spontaneous appearance in the genome in which they are present (Fig. 4A).…”

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Chromosome-level assembly ofArabidopsis thalianaLerreveals the extent of translocation and inversion polymorphisms

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et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Resequencing or reference-based assemblies reveal large parts of the small-scale sequence variation. However, they typically fail to separate such local variation into colinear and rearranged variation, because they usually do not recover the complement of large-scale rearrangements, including transpositions and inversions. Besides the availability of hundreds of genomes of diverse Arabidopsis thaliana accessions, there is so far only one full-length assembled genome: the reference sequence. We have assembled 117 Mb of the A. thaliana Landsberg erecta (Ler) genome into five chromosome-equivalent sequences using a combination of short Illumina reads, long PacBio reads, and linkage information. Whole-genome comparison against the reference sequence revealed 564 transpositions and 47 inversions comprising ∼3.6 Mb, in addition to 4.1 Mb of nonreference sequence, mostly originating from duplications. Although rearranged regions are not different in local divergence from colinear regions, they are drastically depleted for meiotic recombination in heterozygotes. Using a 1.2-Mb inversion as an example, we show that such rearrangement-mediated reduction of meiotic recombination can lead to genetically isolated haplotypes in the worldwide population of A. thaliana. Moreover, we found 105 single-copy genes, which were only present in the reference sequence or the Ler assembly, and 334 single-copy orthologs, which showed an additional copy in only one of the genomes. To our knowledge, this work gives first insights into the degree and type of variation, which will be revealed once complete assemblies will replace resequencing or other reference-dependent methods.

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“…Our finding that plants from sandy substrates show faster root growth in length and a higher number of primary side roots is consistent with physiological predictions that sand‐dwelling plants should grow faster and deeper roots to increase their water‐extraction capability (Jackson, Sperry, & Dawson, ). Changes in root growth are likely to be polygenic with 399 genes in A. lyrata being annotated with GO terms linked to root morphology (Rawat et al, ). In addition to root morphology , GO terms were also associated with plant growth and stress responses in all data sets (Supporting Information Tables –S10).…”

Section: Discussionmentioning

confidence: 99%

Postglacial ecotype formation under outcrossing and self‐fertilization inArabidopsis lyrata

Hohmann

Willi

2019

Molecular Ecology

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The formation of ecotypes has been invoked as an important driver of postglacial biodiversity, because many species colonized heterogeneous habitats and experienced divergent selection. Ecotype formation has been predominantly studied in outcrossing taxa, while far less attention has been paid to the implications of mating system shifts. Here, we addressed whether substrate‐related ecotypes exist in selfing and outcrossing populations of Arabidopsis lyrata subsp. lyrata and whether the genomic footprint differs between mating systems. The North American subspecies colonized both rocky and sandy habitats during postglacial range expansion and shifted the mating system from predominantly outcrossing to predominantly selfing in a number of regions. We performed an association study on pooled whole‐genome sequence data of 20 selfing or outcrossing populations, which suggested genes involved in adaptation to substrate. Motivated by enriched gene ontology terms, we compared root growth between plants from the two substrates in a common environment and found that plants originating from sand grew roots faster and produced more side roots, independent of mating system. Furthermore, single nucleotide polymorphisms associated with substrate‐related ecotypes were more clustered among selfing populations. Our study provides evidence for substrate‐related ecotypes in A. lyrata and divergence in the genomic footprint between mating systems. The latter is the likely result of selfing populations having experienced divergent selection on larger genomic regions due to higher genome‐wide linkage disequilibrium.

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Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data

Cited by 85 publications

References 38 publications

Habitat-Associated Life History and Stress-Tolerance Variation in Arabidopsis arenosa

Habitat-Associated Life History and Stress-Tolerance Variation in Arabidopsis arenosa

Chromosome-level assembly ofArabidopsis thalianaLerreveals the extent of translocation and inversion polymorphisms

Postglacial ecotype formation under outcrossing and self‐fertilization inArabidopsis lyrata

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