Insights into phylogeny, age and evolution of Allium (Amaryllidaceae) based on the whole plastome sequences

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude

(2019) Ticao Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Dissection of Three Giant Genomes: Allium cepa, Allium sativum, and Allium ursinum

(2019) Vratislav Peška et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The complete chloroplast genome of a wild onion species Allium monanthum (Alliaceae)

(2019) Deng-Feng Xie et al.   Mitochondrial DNA Part B-Resources

Characterization of the complete chloroplast genome of Allium kingdonii

(2019) Xin Yang et al.   Mitochondrial DNA Part B-Resources

Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome

(2019) Deng-Feng Xie et al.   Frontiers in Plant Science

Comparative Analysis of the Chloroplast Genomes of the Chinese Endemic Genus Urophysa and Their Contribution to Chloroplast Phylogeny and Adaptive Evolution

(2018) Deng-Feng Xie et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Paleoallium billgenseli gen. et sp. nov.: Fossil Monocot Remains from the Latest Early Eocene Republic Flora, Northeastern Washington State, USA

(2018) Kathleen B. Pigg et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Patterns of phenotypic plasticity and local adaptation in the wide elevation range of the alpine plant Arabis alpina

(2018) Pierre de Villemereuil et al.   JOURNAL OF ECOLOGY

Plastome organization, genome-based phylogeny and evolution of plastid genes in Podophylloideae (Berberidaceae)

(2018) Wen-Qing Ye et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Strong phenotypic plasticity limits potential for evolutionary responses to climate change

(2018) Vicencio Oostra et al.   Nature Communications

Comparative Genomics and Phylogenetic Analysis Revealed the Chloroplast Genome Variation and Interspecific Relationships of Corylus (Betulaceae) Species

(2018) Zhen Yang et al.   Frontiers in Plant Science

Comparative Chloroplast Genomics of Gossypium Species: Insights Into Repeat Sequence Variations and Phylogeny

(2018) Ying Wu et al.   Frontiers in Plant Science

Comparative Chloroplast Genomics of Dipsacales Species: Insights Into Sequence Variation, Adaptive Evolution, and Phylogenetic Relationships

(2018) Wei-Bing Fan et al.   Frontiers in Plant Science

Characterization of the complete plastid genome of lop-sided onion Allium obliquum L. (Amaryllidaceae)

(2018) Mikhail A. Filyushin et al.   Mitochondrial DNA Part B-Resources

Characterization of the complete chloroplast genome of Allium prattii

(2018) Fang-Yu Jin et al.   Mitochondrial DNA Part B-Resources

The effect of Hengduan Mountains Region (HMR) uplift to environmental changes in the HMR and its eastern adjacent area: Tracing the evolutionary history of Allium section Sikkimensia (Amaryllidaceae)

(2018) Chuan Xie et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Spatially heterogeneous selection in nature favors phenotypic plasticity in anuran larvae

(2017) Josh Van Buskirk   EVOLUTION

Molecular adaptation in the world's deepest-living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas

(2017) Yi Lan et al.   MOLECULAR ECOLOGY

Insights into the historical assembly of East Asian subtropical evergreen broadleaved forests revealed by the temporal history of the tea family

(2017) Xiang-Qin Yu et al.   NEW PHYTOLOGIST

Evolution of phenotypic plasticity in extreme environments

(2017) Luis-Miguel Chevin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cytotaxonomy of Allium (Amaryllidaceae) subgenera Cyathophora and Amerallium sect. Bromatorrhiza

(2017) MIN-JIE LI et al.   Phytotaxa

Chloroplast Genome Analysis of Resurrection Tertiary Relict Haberlea rhodopensis Highlights Genes Important for Desiccation Stress Response

(2017) Zdravka Ivanova et al.   Frontiers in Plant Science

Assessment of Genetic Diversity and Structure of Large Garlic (Allium sativum) Germplasm Bank, by Diversity Arrays Technology “Genotyping-by-Sequencing” Platform (DArTseq)

(2017) Leticia A. Egea et al.   Frontiers in Genetics

Phylogeny of Allium L. subgenus Anguinum (G. Don. ex W.D.J. Koch) N. Friesen (Amaryllidaceae)

(2016) Tobias Herden et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Revisiting the evolutionary events in Allium subgenus Cyathophora (Amaryllidaceae): Insights into the effect of the Hengduan Mountains Region (HMR) uplift and Quaternary climatic fluctuations to the environmental changes in the Qinghai-Tibet Plateau

(2016) Min-Jie Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Chromosome diversity and evolution in Allium (Allioideae, Amaryllidaceae)

(2016) L. Peruzzi et al.   PLANT BIOSYSTEMS

Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice

(2016) Zheng-Feng Zhang et al.   Scientific Reports

Molecular phylogeny, divergence time estimates and historical biogeography within one of the world's largest monocot genera

(2016) Qin-Qin Li et al.   AoB Plants

Taxonomy, phylogenetics and biogeography of Chesneya (Fabaceae), evidenced from data of three sequences, ITS, trnS-trnG, and rbcL

(2015) Ming-Li Zhang et al.   BIOCHEMICAL SYSTEMATICS AND ECOLOGY

Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats

(2015) Shiliang Hu et al.   BMC GENOMICS

The Plastomes of Two Species in the Endoparasite GenusPilostyles(Apodanthaceae) Each Retain Just Five or Six Possibly Functional Genes

(2015) Sidonie Bellot et al.   Genome Biology and Evolution

A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the GenusCitrus

(2015) Jose Carbonell-Caballero et al.   MOLECULAR BIOLOGY AND EVOLUTION

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity

(2015) Susana Magallón et al.   NEW PHYTOLOGIST

Orchid phylogenomics and multiple drivers of their extraordinary diversification

(2015) Thomas J. Givnish et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

ycf1, the most promising plastid DNA barcode of land plants

(2015) Wenpan Dong et al.   Scientific Reports

Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: The tortoise and the hare IV

(2014) Joey Shaw et al.   AMERICAN JOURNAL OF BOTANY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification

(2014) Steven A Yates et al.   BMC GENOMICS

Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus

(2014) Liandong Yang et al.   Genome Biology and Evolution

Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia

(2014) Xiao Gou et al.   GENOME RESEARCH

Comparative transcriptome resources of elevenPrimulinaspecies, a group of ‘stone plants’ from a biodiversity hot spot

(2014) Bin Ai et al.   Molecular Ecology Resources

Phylogeny and historical biogeography of Isodon (Lamiaceae): Rapid radiation in south-west China and Miocene overland dispersal into Africa

(2014) Xiang-Qin Yu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times

(2014) Liping Zeng et al.   Nature Communications

Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates

(2013) Susana Magallón et al.   AMERICAN JOURNAL OF BOTANY

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

(2013) Craig F. Barrett et al.   ANNALS OF BOTANY

Polyploidy and b chromosomes in Alium flavum from Serbia

(2013) Vujosevic M. et al.   Archives of Biological Sciences

Chloroplast genome analysis of Australian eucalypts – Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae)

(2013) Michael J. Bayly et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q–T plateau and the Hengduan Mountains

(2013) Yun-Dong Gao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation

(2013) Jizeng Jia et al.   NATURE

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

(2013) Marc Lohse et al.   NUCLEIC ACIDS RESEARCH

Phylogeographic Evidence for a Link of Species Divergence of Ephedra in the Qinghai-Tibetan Plateau and Adjacent Regions to the Miocene Asian Aridification

(2013) Ai-Li Qin et al.   PLoS One

Complete Chloroplast Genome of Sedum sarmentosum and Chloroplast Genome Evolution in Saxifragales

(2013) Wenpan Dong et al.   PLoS One

Cytology as an Important Tool for Solving Evolutionary Problems in Angiosperms

(2013) Geeta Sharma et al.   Proceedings of the National Academy of Sciences, India. Section B

Transcriptome sequencing to produce SNP-based genetic maps of onion

(2013) J. Duangjit et al.   THEORETICAL AND APPLIED GENETICS

Intraspecific differentiation ofAllium wallichii(Amaryllidaceae) inferred from chloroplast DNA and internal transcribed spacer fragments

(2013) De-Qing HUANG et al.   Journal of Systematics and Evolution

Draft genome sequence of the Tibetan antelope

(2013) Ri-Li Ge et al.   Nature Communications

Genetics of Climate Change Adaptation

(2012) Steven J. Franks et al.   Annual Review of Genetics

The yak genome and adaptation to life at high altitude

(2012) Qiang Qiu et al.   NATURE GENETICS

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

DAC Is Involved in the Accumulation of the Cytochrome b6/f Complex in Arabidopsis

(2012) J. Xiao et al.   PLANT PHYSIOLOGY

Current challenges in de novo plant genome sequencing and assembly

(2012) Michael C Schatz et al.   GENOME BIOLOGY

A partial revision of Allium (Amaryllidaceae) in Korea and north-eastern China

(2011) HYEOK JAE CHOI et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Adaptation to Climate Across the Arabidopsis thaliana Genome

(2011) A. M. Hancock et al.   SCIENCE

A structural phylogenetic map for chloroplast photosynthesis

(2011) John F. Allen et al.   TRENDS IN PLANT SCIENCE

The age and diversification of the angiosperms re-revisited

(2010) Charles D. Bell et al.   AMERICAN JOURNAL OF BOTANY

Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China

(2010) Q.-Q. Li et al.   ANNALS OF BOTANY

Phylogeography and allopatric divergence of cypress species (Cupressus L.) in the Qinghai-Tibetan Plateau and adjacent regions

(2010) Tingting Xu et al.   BMC EVOLUTIONARY BIOLOGY

Broad-scale amplification of matK for DNA barcoding plants, a technical note

(2010) LUKE T. DUNNING et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Comparison of mitochondrial and chloroplast genome segments from three onion (Allium cepa L.) cytoplasm types and identification of a trans-splicing intron of cox2

(2010) Sunggil Kim et al.   CURRENT GENETICS

Statistical Properties of the Branch-Site Test of Positive Selection

(2010) Z. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic Variations in Tibetan Populations and High-Altitude Adaptation at the Himalayas

(2010) Y. Peng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiple autopolyploidizations and range expansion ofAllium przewalskianumRegel. (Alliaceae) in the Qinghai-Tibetan Plateau

(2010) LI-LI WU et al.   MOLECULAR ECOLOGY

Evolutionary response of Caragana (Fabaceae) to Qinghai–Tibetan Plateau uplift and Asian interior aridification

(2010) Ming-Li Zhang et al.   PLANT SYSTEMATICS AND EVOLUTION

An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants

(2010) S. A. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural selection on EPAS1 (HIF2 ) associated with low hemoglobin concentration in Tibetan highlanders

(2010) C. M. Beall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

(2010) M. J. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Evidence for High-Altitude Adaptation in Tibet

(2010) T. S. Simonson et al.   SCIENCE

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

Plant phenotypic plasticity in a changing climate

(2010) A.B. Nicotra et al.   TRENDS IN PLANT SCIENCE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci

(2009) Yuan Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

The velocity of climate change

(2009) Scott R. Loarie et al.   NATURE

Probabilistic Models of Chromosome Number Evolution and the Inference of Polyploidy

(2009) Itay Mayrose et al.   SYSTEMATIC BIOLOGY

Orchids

(2008) David L. Roberts et al.   CURRENT BIOLOGY

Adaptation, migration or extirpation: climate change outcomes for tree populations

(2008) Sally N. Aitken et al.   Evolutionary Applications

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

A molecular phylogeny of the wild onions (Allium; Alliaceae) with a focus on the western North American center of diversity

(2008) Nhu H. Nguyen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Meta-Analysis of Local Adaptation in Plants

(2008) Roosa Leimu et al.   PLoS One