Chloroplast DNA Structural Variation, Phylogeny, and Age of Divergence among Diploid Cotton Species

Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes

(2015) Mingyong Tang et al.   BMC GENOMICS

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

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

(2015) Fuguang Li et al.   NATURE BIOTECHNOLOGY

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

The complete chloroplast genome of colchicine plants (Colchicum autumnale L. and Gloriosa superba L.) and its application for identifying the genus

(2015) Pham Anh Thi Nguyen et al.   PLANTA

Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites

(2015) Xia Liu et al.   Scientific Reports

The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

(2015) Daojun Yuan et al.   Scientific Reports

Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae)

(2014) Joseph F. Walker et al.   AMERICAN JOURNAL OF BOTANY

jmodeltest.org: selection of nucleotide substitution models on the cloud

(2014) J. M. Santorum et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum Wittmack

(2014) C. E. Grover et al.   GENETIC RESOURCES AND CROP EVOLUTION

Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants

(2014) Peter Civáň et al.   Genome Biology and Evolution

Alignathon: a competitive assessment of whole-genome alignment methods

(2014) Dent Earl et al.   GENOME RESEARCH

Genome sequence of the cultivated cotton Gossypium arboreum

(2014) Fuguang Li et al.   NATURE GENETICS

Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses

(2013) Jun-Bo Yang et al.   BMC EVOLUTIONARY BIOLOGY

Cytoplasmic diversity of the cotton genus as revealed by chloroplast microsatellite markers

(2013) Pengbo Li et al.   GENETIC RESOURCES AND CROP EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Complete Chloroplast Genome of Banana (Musa acuminata, Zingiberales): Insight into Plastid Monocotyledon Evolution

(2013) Guillaume Martin et al.   PLoS One

The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes

(2013) Guozheng Liu et al.   PLoS One

Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)

(2012) Peng-tao Luan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing

(2012) Wambui Njuguna et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

The draft genome of a diploid cotton Gossypium raimondii

(2012) Kunbo Wang et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Analysis of Complete Nucleotide Sequences of 12 Gossypium Chloroplast Genomes: Origin and Evolution of Allotetraploids

(2012) Qin Xu et al.   PLoS One

Paleocene Malvaceae from northern South America and their biogeographical implications

(2011) Mónica R. Carvalho et al.   AMERICAN JOURNAL OF BOTANY

Use of the Chloroplast Gene ycf1 for the Genetic Differentiation of Pine Nuts Obtained from Consumers Experiencing Dysgeusia

(2011) Sara M. Handy et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Exceptionally Large Chloroplast Genome of the Green Alga Floydiella terrestris Illuminates the Evolutionary History of the Chlorophyceae

(2010) J. S. Brouard et al.   Genome Biology and Evolution

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Phylogenetic network of Linum species as revealed by non-coding chloroplast DNA sequences

(2009) Yong-Bi Fu et al.   GENETIC RESOURCES AND CROP EVOLUTION

Next-generation DNA sequencing techniques

(2009) Wilhelm J. Ansorge   New Biotechnology

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

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

Complete Sequence of the Duckweed (Lemna minor) Chloroplast Genome: Structural Organization and Phylogenetic Relationships to Other Angiosperms

(2008) Andrey V. Mardanov et al.   JOURNAL OF MOLECULAR EVOLUTION

A Phylogenetic Analysis of Indel Dynamics in the Cotton Genus

(2008) C. E. Grover et al.   MOLECULAR BIOLOGY AND EVOLUTION

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Sequencing breakthroughs for genomic ecology and evolutionary biology

(2007) MATTHEW E. HUDSON   Molecular Ecology Resources