8 research outputs found
Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch
Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.Peer reviewe
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Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.
In the version of this article initially published, there was a mistake in the calculation of the nucleotide mutation rate per site per generation: 1 × 10−9 mutations per site per generation was used, whereas 9.5 × 10−9 was correct. This error affects the interpretation of population-size changes over time and their possible correspondence with known geological events, as shown in the original Fig. 4 and supporting discussion in the text, as well as details in the Supplementary Note. Neither the data themselves nor any other results are affected. Figure 4 has been revised accordingly. Images of the original and corrected figure panels are shown in the correction notice
Gene Expression Differences between <i>Noccaea caerulescens</i> Ecotypes Help to Identify Candidate Genes for Metal Phytoremediation
Populations of <i>Noccaea caerulescens</i> show tremendous
differences in their capacity to hyperaccumulate and hypertolerate
metals. To explore the differences that could contribute to these
traits, we undertook SOLiD high-throughput sequencing of the root
transcriptomes of three phenotypically well-characterized <i>N. caerulescens</i> accessions, <i>i.e.</i>, Ganges,
La Calamine, and Monte Prinzera. Genes with possible contribution
to zinc, cadmium, and nickel hyperaccumulation and hypertolerance
were predicted. The most significant differences between the accessions
were related to metal ion (di-, trivalent inorganic cation) transmembrane
transporter activity, iron and calcium ion binding, (inorganic) anion
transmembrane transporter activity, and antioxidant activity. Analysis
of correlation between the expression profile of each gene and the
metal-related characteristics of the accessions disclosed both previously
characterized (<i>HMA4</i>, <i>HMA3</i>) and new
candidate genes (<i>e.g.</i>, for nickel <i>IRT1</i>, <i>ZIP10</i>, and <i>PDF2.3</i>) as possible
contributors to the hyperaccumulation/tolerance phenotype. A number
of unknown <i>Noccaea</i>-specific transcripts also showed
correlation with Zn<sup>2+</sup>, Cd<sup>2+</sup>, or Ni<sup>2+</sup> hyperaccumulation/tolerance. This study shows that <i>N. caerulescens</i> populations have evolved great diversity in the expression of metal-related
genes, facilitating adaptation to various metalliferous soils. The
information will be helpful in the development of improved plants
for metal phytoremediation
Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch
Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A
Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch
Abstract
Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A