Results 31 to 40 of about 17,366 (243)

Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes

Frontiers in Plant Science, 2022
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets ...
Prakash Raj Timilsena, Eric K. Wafula, Craig F. Barrett, Saravanaraj Ayyampalayam, Saravanaraj Ayyampalayam, Joel R. McNeal, Jeremy D. Rentsch, Michael R. McKain, Karolina Heyduk, Alex Harkess, Matthieu Villegente, John G. Conran, Nicola Illing, Bruno Fogliani, Cécile Ané, Cécile Ané, J. Chris Pires, Jerrold I. Davis, Wendy B. Zomlefer, Dennis W. Stevenson, Sean W. Graham, Thomas J. Givnish, James Leebens-Mack, Claude W. dePamphilis   +23 more
doaj   +1 more source

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

Systematic Biology, 2020
AbstractMolecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid ...
Hime, Paul M., Lemmon, Alan R., Lemmon, Emily C. Moriarty, Prendini, Elizabeth, Brown, Jeremy M., Thomson, Robert C., Kratovil, Justin D., Noonan, Brice P., Pyron, R. Alexander, Peloso, Pedro L. V., Kortyna, Michelle L., Keogh, J. Scott, Donnellan, Stephen C., Mueller, Rachel Lockridge, Raxworthy, Christopher J., Kunte, Krushnamegh, Ron, Santiago R., Das, Sandeep, Gaitonde, Nikhil, Green, David M., Labisko, Jim, Che, Jing, Weisrock, David W.   +22 more
openaire   +4 more sources

The complete mitochondrial genome of a mangrove plant: Bruguiera sexangula (Lour.) Poir. var. rhynchopetala Ko

Mitochondrial DNA. Part B. Resources, 2020
The complete mitochondrial genome of mangrove plant: Bruguiera sexangula (Lour.) Poir. var. rhynchopetala Ko was analyzed in this paper, which is the first for the genus within the family Rhizophoraceae.
Shijie Zhang, He Bai, Qiang Liu, Ying Zhang   +3 more
doaj   +1 more source

Anchored phylogenomics illuminates the skipper butterfly tree of life [PDF]

BMC Evolutionary Biology, 2018
Butterflies (Papilionoidea) are perhaps the most charismatic insect lineage, yet phylogenetic relationships among them remain incompletely studied and controversial. This is especially true for skippers (Hesperiidae), one of the most species-rich and poorly studied butterfly families.To infer a robust phylogenomic hypothesis for Hesperiidae, we ...
Emmanuel F. A. Toussaint, Jesse W. Breinholt, Chandra Earl, Andrew D. Warren, Andrew V. Z. Brower, Masaya Yago, Kelly M. Dexter, Marianne Espeland, Naomi E. Pierce, David J. Lohman, Akito Y. Kawahara   +10 more
openaire   +5 more sources

Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics

BMC Bioinformatics, 2008
Background The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible.
Lee Ernest K, Coruzzi Gloria, Egan Mary G, Sarkar Indra, DeSalle Rob   +4 more
doaj   +1 more source

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

Scientific Reports, 2021
Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes.
Maria Alejandra Serna-Sánchez, Oscar A. Pérez-Escobar, Diego Bogarín, María Fernanda Torres-Jimenez, Astrid Catalina Alvarez-Yela, Juliana E. Arcila-Galvis, Climbie F. Hall, Fábio de Barros, Fábio Pinheiro, Steven Dodsworth, Mark W. Chase, Alexandre Antonelli, Tatiana Arias   +12 more
doaj   +1 more source

Phylogenomic Analyses and Molecular Signatures Elucidating the Evolutionary Relationships amongst the Chlorobia and Ignavibacteria Species: Robust Demarcation of Two Family-Level Clades within the Order Chlorobiales and Proposal for the Family Chloroherpetonaceae fam. nov

Microorganisms, 2022
Evolutionary relationships amongst Chlorobia and Ignavibacteria species/strains were examined using phylogenomic and comparative analyses of genome sequences.
Sarah Bello, Mohammad Howard-Azzeh, Herb E. Schellhorn, Radhey S. Gupta   +3 more
doaj   +1 more source

Phylogenomic Models from Tree Symmetries

SIAM Journal on Applied Algebra and Geometry
A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting. Chifman and Kubatko initiated the study of such models, leading to the development of the SVDquartets methods of ...
Elizabeth S. Allman, Colby Long, John A. Rhodes   +2 more
openaire   +4 more sources

Phylogenetic and Phylogenomic Definition of Rhizopus Species

G3: Genes, Genomes, Genetics, 2018
Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life.
Andrii P. Gryganskyi, Jacob Golan, Somayeh Dolatabadi, Stephen Mondo, Sofia Robb, Alexander Idnurm, Anna Muszewska, Kamil Steczkiewicz, Sawyer Masonjones, Hui-Ling Liao, Michael T. Gajdeczka, Felicia Anike, Antonina Vuek, Iryna M. Anishchenko, Kerstin Voigt, G. Sybren de Hoog, Matthew E. Smith, Joseph Heitman, Rytas Vilgalys, Jason E. Stajich   +19 more
doaj   +1 more source

The complete mitochondrial genome of the Kandelia obovata Sheue, H.Y.Liu & J.W.H.Yong (Rhizophoraceae)

Mitochondrial DNA. Part B. Resources, 2023
Kandelia obovata Sheue, H.Y.Liu & J.W.H.Yong is one of the most cold-resistant true mangrove species, and it is widely distributed from the South China Sea to southern Japan. In the current study, the complete mitochondrial genome sequence of K.
Xiuming Xu, Chengcheng Hou, Yingjia Shen
doaj   +1 more source