| 1. |
- Ahola, Virpi, et al.
(författare)
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The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera
- 2014
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 5, s. 4737-
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n = 31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n = 31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.
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| 2. |
- Jarvi, Sari, et al.
(författare)
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Photosystem II Repair and Plant Immunity : Lessons Learned from Arabidopsis Mutant Lacking the THYLAKOID LUMEN PROTEIN 18.3
- 2016
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Ingår i: Frontiers in Plant Science. - : Frontiers Media SA. - 1664-462X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Chloroplasts play an important role in the cellular sensing of abiotic and biotic stress. Signals originating from photosynthetic light reactions, in the form of redox and pH changes, accumulation of reactive oxygen and electrophile species or stromal metabolites are of key importance in chloroplast retrograde signaling. These signals initiate plant acclimation responses to both abiotic and biotic stresses. To reveal the molecular responses activated by rapid fluctuations in growth light intensity, gene expression analysis was performed with Arabidopsis thaliana wild type and the tlp18.3 mutant plants, the latter showing a stunted growth phenotype under fluctuating light conditions (Biochem. J, 406, 415-425). Expression pattern of genes encoding components of the photosynthetic electron transfer chain did not differ between fluctuating and constant light conditions, neither in wild type nor in tlp18.3 plants, and the composition of the thylakoid membrane protein complexes likewise remained unchanged. Nevertheless, the fluctuating light conditions repressed in wild-type plants a broad spectrum of genes involved in immune responses, which likely resulted from shade-avoidance responses and their intermixing with hormonal signaling. On the contrary, in the tlp18.3 mutant plants there was an imperfect repression of defense-related transcripts upon growth under fluctuating light, possibly by signals originating from minor malfunction of the photosystem II (PSII) repair cycle, which directly or indirectly modulated the transcript abundances of genes related to light perception via phytochromes. Consequently, a strong allocation of resources to defense reactions in the tlp18.3 mutant plants presumably results in the stunted growth phenotype under fluctuating light.
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| 3. |
- Leal, Luis J., et al.
(författare)
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Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences
- 2023
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Ingår i: Systematic Biology. - : Oxford University Press. - 1063-5157 .- 1076-836X. ; 72:2, s. 372-390
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Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic analysis of polyploid hybrid species has long posed a formidable challenge as it requires the ability to distinguish between alleles of different ancestral origins in order to disentangle their individual evolutionary history. This problem has been previously addressed by conceiving phylogenies as reticulate networks, using a two-step phasing strategy that first identifies and segregates homoeologous loci and then, during a second phasing step, assigns each gene copy to one of the subgenomes of an allopolyploid species. Here, we propose an alternative approach, one that preserves the core idea behind phasing-to produce separate nucleotide sequences that capture the reticulate evolutionary history of a polyploid-while vastly simplifying its implementation by reducing a complex multistage procedure to a single phasing step. While most current methods used for phylogenetic reconstruction of polyploid species require sequencing reads to be pre-phased using experimental or computational methods-usually an expensive, complex, and/or time-consuming endeavor-phasing executed using our algorithm is performed directly on the multiple-sequence alignment (MSA), a key change that allows for the simultaneous segregation and sorting of gene copies. We introduce the concept of genomic polarization that, when applied to an allopolyploid species, produces nucleotide sequences that capture the fraction of a polyploid genome that deviates from that of a reference sequence, usually one of the other species present in the MSA. We show that if the reference sequence is one of the parental species, the polarized polyploid sequence has a close resemblance (high pairwise sequence identity) to the second parental species. This knowledge is harnessed to build a new heuristic algorithm where, by replacing the allopolyploid genomic sequence in the MSA by its polarized version, it is possible to identify the phylogenetic position of the polyploid's ancestral parents in an iterative process. The proposed methodology can be used with long-read and short-read high-throughput sequencing data and requires only one representative individual for each species to be included in the phylogenetic analysis. In its current form, it can be used in the analysis of phylogenies containing tetraploid and diploid species. We test the newly developed method extensively using simulated data in order to evaluate its accuracy. We show empirically that the use of polarized genomic sequences allows for the correct identification of both parental species of an allotetraploid with up to 97% certainty in phylogenies with moderate levels of incomplete lineage sorting (ILS) and 87% in phylogenies containing high levels of ILS. We then apply the polarization protocol to reconstruct the reticulate histories of Arabidopsis kamchatica and Arabidopsis suecica, two allopolyploids whose ancestry has been well documented. [Allopolyploidy; Arabidopsis; genomic polarization; homoeologs; incomplete lineage sorting; phasing; polyploid phylogenetics; reticulate evolution.]
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| 4. |
- Salojarvi, Jarkko, et al.
(författare)
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Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch
- 2017
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Ingår i: Nature Genetics. - : NATURE PUBLISHING GROUP. - 1061-4036 .- 1546-1718. ; 49:6, s. 904-912
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Tidskriftsartikel (refereegranskat)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.
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| 5. |
- Simola, Jaana, et al.
(författare)
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Using hidden Markov model to uncover processing states from eye movements in information search tasks
- 2008
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Ingår i: Cognitive Systems Research. - : Elsevier BV. - 1389-0417. ; 9:4, s. 237-251
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Tidskriftsartikel (refereegranskat)abstract
- We study how processing states alternate during information search tasks. Inference is carried out with a discriminative hidden Markov model (dHMM) learned from eye movement data, measured in an experiment consisting of three task types: (i) simple word search, (ii) finding a sentence that answers a question and (iii) choosing a subjectively most interesting title from a list of ten titles. The results show that eye movements contain necessary information for determining the task type. After training, the dHMM predicted the task for test data with 60.2% accuracy (pure chance 33.3%). Word search and subjective interest conditions were easier to predict than the question-answer condition. The dHMM that best fitted our data segmented each task type into three hidden states. The three processing states were identified by comparing the parameters of the dHMM states to literature on eye movement research. A scanning type of eye behavior was observed in the beginning of the tasks. Next, participants tended to shift to states reflecting reading type of eye movements, and finally they ended the tasks in states which we termed as the decision states. (C) 2008 Elsevier B.V. All rights reserved.
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| 6. |
- Vaattovaara, Aleksia, et al.
(författare)
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High-throughput sequencing data and the impact of plant gene annotation quality
- 2019
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Ingår i: Journal of Experimental Botany. - : Oxford University Press. - 0022-0957 .- 1460-2431. ; 70:4, s. 1069-1076
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Tidskriftsartikel (refereegranskat)abstract
- The use of draft genomes of different species and re-sequencing of accessions and populations are now common tools for plant biology research. The de novo assembled draft genomes make it possible to identify pivotal divergence points in the plant lineage and provide an opportunity to investigate the genomic basis and timing of biological innovations by inferring orthologs between species. Furthermore, re-sequencing facilitates the mapping and subsequent molecular characterization of causative loci for traits, such as those for plant stress tolerance and development. In both cases high-quality gene annotation-the identification of protein-coding regions, gene promoters, and 5'- and 3'-untranslated regions-is critical for investigation of gene function. Annotations are constantly improving but automated gene annotations still require manual curation and experimental validation. This is particularly important for genes with large introns, genes located in regions rich with transposable elements or repeats, large gene families, and segmentally duplicated genes. In this opinion paper, we highlight the impact of annotation quality on evolutionary analyses, genome-wide association studies, and the identification of orthologous genes in plants. Furthermore, we predict that incorporating accurate information from manual curation into databases will dramatically improve the performance of automated gene predictors.
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| 7. |
- Wrzaczek, Michael, et al.
(författare)
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Transcriptional regulation of the CRK/DUF26 group of Receptor-like rotein kinases by ozone and plant hormones in Arabidopsis
- 2010
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Ingår i: BMC Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 10, s. 95-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Plant Receptor-like/Pelle kinases (RLK) are a group of onserved signalling components that regulate developmental programs and esponses to biotic and abiotic stresses. One of the largest RLK groups s formed by the Domain of Unknown Function 26 (DUF26) RLKs, also called ysteine-rich Receptor-like Kinases (CRKs), which have been suggested to lay important roles in the regulation of pathogen defence and rogrammed cell death. Despite the vast number of RLKs present in lants, however, only a few of them have been functionally haracterized. esults: We examined the transcriptional regulation of all Arabidopsis RKs by ozone (O(3)), high light and pathogen/ elicitor reatment-conditions known to induce the production of reactive oxygen pecies (ROS) in various subcellular compartments. Several CRKs were ranscriptionally induced by exposure to O(3) but not by light stress. (3) induces an extracellular oxidative burst, whilst light stress leads o ROS production in chloroplasts. Analysis of publicly available icroarray data revealed that the transcriptional responses of the CRKs o O(3) were very similar to responses to microbes or athogen-associated molecular patterns (PAMPs). Several mutants altered n hormone biosynthesis or signalling showed changes in basal and (3)-induced transcriptional responses. onclusions: Combining expression analysis from multiple treatments with utants altered in hormone biosynthesis or signalling suggest a model in hich O(3) and salicylic acid (SA) activate separate signaling pathways hat exhibit negative crosstalk. Although O(3) is classified as an biotic stress to plants, transcriptional profiling of CRKs showed trong similarities between the O(3) and biotic stress responses.
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