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1. A synopsis of genus pogonatum (Polytrichaceae, Musci)
by Hyvönen, Jaakko and Societas pro Fauna et Flora Fennica
1989, ISBN 9789519469324, Volume 138., 87
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2. Full Text The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae
by Amiryousefi, Ali and Hyvönen, Jaakko and Poczai, Péter
PLoS ONE, ISSN 1932-6203, 04/2018, Volume 13, Issue 4, p. e0196069
Bittersweet (Solanum dulcamara) is a native Old World member of the nightshade family. This European diploid species can be found from marshlands to high... 
ORGANIZATION | PHYLOGENETIC ANALYSIS | LATE BLIGHT | DNA | ANNOTATION | MULTIDISCIPLINARY SCIENCES | GENES | ANGIOSPERMS | RIBOSOMAL-RNA | COMPLETE NUCLEOTIDE-SEQUENCE | Botanical research | Evolutionary genetics | Genetic aspects | Research | Chloroplasts | Plant genetics | Plastomes | Post-transcription | Genes | Synteny | Genomes | Phylogeny | Gene sequencing | Annotations | Evolutionary conservation | Blight | Phylogenetics | Evolution | Plant sciences | Deoxyribonucleic acid--DNA | tRNA | Nucleotide sequence | rRNA | Museums | RNA polymerase | Gene expression | Environmental science | Evolutionary biology | Spacer | Late blight | Marshlands | Genetic engineering | Genetic testing | Deoxyribonucleic acid
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3. Full Text Advances in plant gene-targeted and functional markers: A review
by Poczai, Péter and Varga, Ildikó and Laos, Maarja and Cseh, András and Bell, Neil and Valkonen, Jari P.T and Hyvönen, Jaakko
Plant Methods, ISSN 1746-4811, 02/2013, Volume 9, Issue 1, pp. 6 - 6
Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used... 
Functional markers | Molecular markers | Gene targeting | Genomic database | DNA fingerprinting | RETROTRANSPOSON-BASED SSAP | AUTOMATED DNA SEQUENCER | BIOCHEMICAL RESEARCH METHODS | REGION AMPLIFICATION POLYMORPHISM | EUKARYOTIC TRANSPOSABLE ELEMENTS | EXPRESSED SEQUENCE TAGS | PLANT SCIENCES | FRAGMENT-LENGTH POLYMORPHISM | POLYMERASE-CHAIN-REACTION | DISEASE RESISTANCE GENES | EST-DERIVED SSR | CDNA-AFLP ANALYSIS | Genetic markers | Transposons | Promoters (Genetics) | RNA | Genes | Genomics | Plant genetics | DNA testing | Nucleotide sequencing | Genetic polymorphisms | DNA sequencing | Studies | Phylogenetics
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4. Full Text Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects
by Poczai, Péter and Poczai, Péter and Hyvönen, Jaakko and Hyvönen, Jaakko
Molecular Biology Reports, ISSN 0301-4851, 4/2010, Volume 37, Issue 4, pp. 1897 - 1912
The nuclear ribosomal locus coding for the large subunit is represented in tandem arrays in the plant genome. These consecutive gene blocks, consisting of... 
Life Sciences | Internal transcribed spacer (ITS) | External transcribed spacer (ETS) | Animal Biochemistry | Intergenic spacer (IGS) | Phylogenetics | Nuclear ribosomal DNA (rDNA) | Animal Anatomy / Morphology / Histology | DNA-SEQUENCES | RNA GENES | INTERNAL TRANSCRIBED SPACER | BIOCHEMISTRY & MOLECULAR BIOLOGY | MOLECULAR EVOLUTION | IN-SITU HYBRIDIZATION | SACCHAROMYCES-CEREVISIAE | CONCERTED EVOLUTION | RDNA INTERGENIC SPACER | MULTIGENE FAMILIES | SECONDARY STRUCTURE | Repetitive Sequences, Nucleic Acid - genetics | Cell Nucleus - genetics | DNA, Ribosomal Spacer - genetics | Plants - genetics | DNA, Ribosomal Spacer - chemistry | Phylogeny | Nucleic Acid Conformation | Sequence Homology, Nucleic Acid | Evolution, Molecular | Universities and colleges | RNA | Analysis | Plant genetics | Plant biology | Molecular biology | Ribonucleic acid--RNA | Genomics | Deoxyribonucleic acid--DNA
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5. Full Text The complete chloroplast genome sequence of the CAM epiphyte Spanish moss (Tillandsia usneoides, Bromeliaceae) and its comparative analysis
by Poczai, Péter and Hyvönen, Jaakko
PLoS ONE, ISSN 1932-6203, 11/2017, Volume 12, Issue 11, p. e0187199
Spanish moss (Tillandsia usneoides) is an epiphytic bromeliad widely distributed throughout tropical and warm temperate America. This plant is highly adapted... 
SYNONYMOUS CODON USAGE | EVOLUTIONARY RATE | PLASTID GENOMES | AMPLIFICATION | GENE | PHYLOGENETIC-RELATIONSHIPS | DNA | GRASSES | MULTIDISCIPLINARY SCIENCES | ACETYL-COA CARBOXYLASE | IDENTIFICATION | Bromeliaceae - genetics | Bromeliaceae - classification | Bromeliaceae - physiology | Phylogeny | Photosynthesis | Genome, Chloroplast | Crassulacean acid metabolism | Bromeliaceae | Genetic aspects | Research | Chloroplasts | Analysis | Biodegradation | Enzymes | Nucleotide sequence | Introns | Genes | Mosses | Inversion | Genomes | Museums | Grasses | Metabolism | Environmental conditions | Studies | Phylogenetics | Nutrients | Trichomes | Shoots | Plant sciences | Comparative analysis | Deoxyribonucleic acid--DNA | Deoxyribonucleic acid
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6. Full Text Phylogeny of the moss class Polytrichopsida (BRYOPHYTA): Generic-level structure and incongruent gene trees
by Bell, Neil E and Hyvönen, Jaakko
Molecular Phylogenetics and Evolution, ISSN 1055-7903, 2010, Volume 55, Issue 2, pp. 381 - 398
Analysis of an extensive new molecular dataset for the moss class Polytrichopsida provides convincing support for many traditionally recognised genera and... 
Polytrichastrum | Phytogeography | Polytrichales | Polytrichaceae | Polysporangiophyte | Phylogeny | 18S | Reticulate evolution | Consensus network | Incongruence | Bayes factors | Hybridization network | Embryophyte | Oligotrichum | Polytrichopsida | Pogonatum | SEQUENCES | CHLOROPLAST | INFERENCE | POLYTRICHASTRUM POLYTRICHACEAE | MOLECULAR PHYLOGENY | ORIGIN | GENETICS & HEREDITY | BIOCHEMISTRY & MOLECULAR BIOLOGY | DESICCATION TOLERANCE | 185 | LAND PLANTS | EVOLUTIONARY BIOLOGY | EVOLUTION | MODELS | Geography | Bryophyta - genetics | RNA, Ribosomal, 18S - genetics | Bryophyta - classification | Sequence Analysis, DNA | Sequence Alignment | DNA, Mitochondrial - genetics | Cell Nucleus - genetics | Bayes Theorem | Models, Genetic | DNA, Plant - genetics | Evolution, Molecular | Evolution | RNA | Analysis | Trees | Molecular structure | Chloroplasts | Genes | Moss | Topology | Cladding
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7. Full Text iMEC: Online Marker Efficiency Calculator
by Amiryousefi, Ali and Hyvönen, Jaakko and Poczai, Péter
Applications in Plant Sciences, ISSN 2168-0450, 06/2018, Volume 6, Issue 6, pp. e01159 - n/a
Premise of the Study To accurately design plant genetic studies, the information content of utilized markers and primers must be calculated. Plant genotyping... 
arbitrarily amplified dominant markers (AADs) | polymorphism | multi‐locus fingerprinting | molecular marker | DNA band | multi-locus fingerprinting | MOLECULAR MARKERS | IDENTIFICATION | PLANT SCIENCES | Mathematics | Heterozygosity | Germplasm | Genetic markers | Genotyping | Primers | Efficiency | Information processing | Population | Software | Internet | DNA fingerprinting | Deoxyribonucleic acid--DNA | Polymorphism
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8. Full Text IRscope: an online program to visualize the junction sites of chloroplast genomes
by Amiryousefi, Ali and Hyvönen, Jaakko and Poczai, Peter
Bioinformatics, ISSN 1367-4803, 09/2018, Volume 34, Issue 17, pp. 3030 - 3031
Abstract Motivation Genome plotting is performed using a wide range of visualizations tools each with emphasis on a different informative dimension of the... 
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DNA | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY
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9. Full Text Organellar genomes of the four-toothed moss, Tetraphis pellucida
by Bell, Neil E and Boore, Jeffrey L and Mishler, Brent D and Hyvönen, Jaakko
BMC Genomics, ISSN 1471-2164, 05/2014, Volume 15, Issue 1, pp. 383 - 383
Background: Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods.... 
Tetraphis pellucida | nad7 | Moss | Organellar genomes | petN | Phylogeny | Peristome | Sequencing | NAD7 GENE | MITOCHONDRIAL GENOME | CHLOROPLAST GENOME | CLASSIFICATION | BRYOPHYTA | EVOLUTION | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | PHYLOGENETIC-RELATIONSHIPS | SEQUENCE | GENETICS & HEREDITY | PHYSCOMITRELLA-PATENS | MARCHANTIOPHYTA | Sequence Analysis, RNA | Bryophyta - genetics | Base Sequence | Genome, Chloroplast | Molecular Sequence Data | Chromosome Mapping | Genome, Mitochondrial | Genome, Plant | Bryophyta - classification | Physiological aspects | Evolution | Genomes | Genetic aspects | Research | Plants | Nucleotide sequencing | Comparative analysis | DNA sequencing
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10. Estimating storm damage with the help of low-altitude photographs and different sampling designs and estimators
by Pekka Hyvönen and Jaakko Heinonen
Silva Fennica, ISSN 0037-5330, 01/2018, Volume 52, Issue 3, p. 1
Climate change has been estimated to increase the risk of storm damage in forests in Finland. There is a growing need for methods to obtain information on the... 
Trees | Wind | Forests | Random sampling | Computer simulation | Flight | Harvesting | Sampling designs | Estimation | Storm damage | Estimates | Climate change | Low altitude | Photographs | Statistical sampling | Estimators | Altitude
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11. Full Text Exploring phylogeny of the microsoroid ferns (Polypodiaceae) based on six plastid DNA markers
by Chen, Chi-Chuan and Hyvönen, Jaakko and Schneider, Harald
Molecular Phylogenetics and Evolution, ISSN 1055-7903, 02/2020, Volume 143, p. 106665
The microsoroid ferns are one of the largest subfamilies of the Polypodiaceae with over 180 species mainly found in the humid forests of tropical Australasia.... 
Polypodiaceae | matK | atpA | Microsoroid ferns | Phylogeny
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12. Full Text Sequencing the Plastid Genome of Giant Ragweed (Ambrosia trifida, Asteraceae) From a Herbarium Specimen
by Sablok, G and Amiryousefi, A and He, XL and Hyvonen, J and Poczai, P
FRONTIERS IN PLANT SCIENCE, ISSN 1664-462X, 02/2019, Volume 10, p. 218
We report the first plastome sequence of giant ragweed (Ambrosia trifida); with this new genome information, we assessed the phylogeny of Asteraceae and the... 
noxious weeds | COMPLETE CHLOROPLAST GENOME | RECURRENT SELECTION | COMMON RAGWEED | GLYPHOSATE RESISTANCE | ragweed | NATIVE RANGE | PLANT SCIENCES | invasive plants | GENETIC DIVERSITY | ARTEMISIIFOLIA L | herbicide resistance | Ambrosia trifida | INVERSION VARIATION | chloroplast genome | genome skimming | glyphosate | EARLY EVOLUTION | Genetic aspects | Compositae | Identification and classification | Plastids | Analysis | Plant genetics
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13. Full Text Will bryophytes survive in a warming world?
by He, Xiaolan and He, Kate S and Hyvönen, Jaakko
Perspectives in Plant Ecology, Evolution and Systematics, ISSN 1433-8319, 04/2016, Volume 19, pp. 49 - 60
Understanding how plant species respond to climate change is one of the great challenges in biodiversity conservation and sustainable ecosystem planning.... 
Climate change | Species diversity | Temperature | Ecosystem | Photosynthesis | Bryophyte | Embryophyte | PHYSIOLOGICAL ECOLOGY | TEMPERATURE RESPONSES | CLIMATE-CHANGE | CO2 EXCHANGE | GLOBAL CHANGE | PLANT SCIENCES | CARBON-DIOXIDE EXCHANGE | NITROGEN DEPOSITION | SIMULATED ENVIRONMENTAL-CHANGE | DESICCATION-TOLERANCE | ECOLOGY | DICRANUM-FUSCESCENS | Global temperature changes | Ecosystems | Phytochemistry | Ecosystem components | Biological diversity conservation | Physiological aspects | Biomes | Global warming | Plants | Biological diversity | Nutrients | Plants (organisms) | Bryophytes | Acclimation
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