scholarly journals The Utility of Genome Skimming for Phylogenomic Analyses as Demonstrated for Glycerid Relationships (Annelida, Glyceridae)

2015 ◽  
Vol 7 (12) ◽  
pp. 3443-3462 ◽  
Author(s):  
Sandy Richter ◽  
Francine Schwarz ◽  
Lars Hering ◽  
Markus Böggemann ◽  
Christoph Bleidorn
Keyword(s):  
Genome Skimming ◽  
Phylogenomic Analyses

scholarly journals Proposal to recognise the tribes Adinobotryeae and Glycyrrhizeae (Leguminosae subfamily Papilionoideae) based on chloroplast phylogenomic evidence

PhytoKeys ◽  
2021 ◽  
Vol 181 ◽  
pp. 65-77
Author(s):  
Lei Duan ◽  
Li-Na Han ◽  
Yotsawate Sirichamorn ◽  
Jun Wen ◽  
James A. Compton ◽  
...  
Keyword(s):  
Inverted Repeat ◽  
Taxonomic Status ◽  
Sister Relationship ◽  
New Tribe ◽  
Genome Skimming ◽  
Phylogenomic Analyses

Within the legume family, the taxonomic status of subtribe Glycyrrhizinae of tribe Galegeae and of the genus Adinobotrys has been re-assessed. Based on genome skimming data, we conducted phylogenomic analyses of the inverted repeat-lacking clade within subfamily Papilionoideae. The results support the sister relationship between Glycyrrhizeae and Adinobotrys. Glycyrrhizeae is resurrected based on Glycyrrhiza and Glycyrrhizopsis, and a new tribe, Adinobotryeae, is proposed to accommodate Adinobotrys.

Phylogenomic analyses based on genome-skimming data reveal cyto-nuclear discordance in the evolutionary history of Cotoneaster (Rosaceae)

2021 ◽  
Vol 158 ◽  
pp. 107083
Author(s):  
Kai-Kai Meng ◽  
Su-Fang Chen ◽  
Ke-Wang Xu ◽  
Ren-Chao Zhou ◽  
Ming-Wan Li ◽  
...  
Keyword(s):  
Evolutionary History ◽  
History Of ◽  
Genome Skimming ◽  
Phylogenomic Analyses

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

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maria Alejandra Serna-Sánchez ◽  
Oscar A. Pérez-Escobar ◽  
Diego Bogarín ◽  
María Fernanda Torres-Jimenez ◽  
Astrid Catalina Alvarez-Yela ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Times ◽  
Molecular Clocks ◽  
Phylogenetic Placement ◽  
Plastid Genomes ◽  
Phylogenetic Reconstructions ◽  
A Genome ◽  
Tree Models ◽  
Phylogenomic Analyses ◽  
First Time

AbstractRecent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To address these knowledge-gaps, we here provide the most extensively sampled analysis of the orchid family to date, based on 78 plastid coding genes representing 264 species, 117 genera, 18 tribes and 28 subtribes. Divergence times are also provided as inferred from strict and relaxed molecular clocks and birth–death tree models. Our taxon sampling includes 51 newly sequenced plastid genomes produced by a genome skimming approach. We focus our sampling efforts on previously unplaced clades within tribes Cymbidieae and Epidendreae. Our results confirmed phylogenetic relationships in Orchidaceae as recovered in previous studies, most of which were recovered with maximum support (209 of the 262 tree branches). We provide for the first time a clear phylogenetic placement for Codonorchideae within subfamily Orchidoideae, and Podochilieae and Collabieae within subfamily Epidendroideae. We also identify relationships that have been persistently problematic across multiple studies, regardless of the different details of sampling and genomic datasets used for phylogenetic reconstructions. Our study provides an expanded, robust temporal phylogenomic framework of the Orchidaceae that paves the way for biogeographical and macroevolutionary studies.

Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture

2021 ◽  
pp. 107232
Author(s):  
Ying-Ying Yang ◽  
Xiao-Jian Qu ◽  
Rong Zhang ◽  
Gregory W. Stull ◽  
Ting-Shuang Yi
Keyword(s):  
Chloroplast Capture ◽  
Phylogenomic Analyses

scholarly journals Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles

2021 ◽  
Author(s):  
Gitta Szabó ◽  
Frederik Schulz ◽  
Alejandro Manzano-Marín ◽  
Elena Rebecca Toenshoff ◽  
Matthias Horn
Keyword(s):  
Defense Mechanisms ◽  
Amino Acid Production ◽  
Evolutionary Transition ◽  
Evolutionary Time ◽  
Evolutionary Trajectories ◽  
Host Infection ◽  
Phylogenomic Analyses ◽  
Time Specific ◽  
High Level ◽  
Metagenomic Approach

AbstractAdelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelgestardus species complex containing betaproteobacterial (“Candidatus Vallotia tarda”) and gammaproteobacterial (“Candidatus Profftia tarda”) symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other’s role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

scholarly journals Naive binning improves phylogenomic analyses

2013 ◽  
Vol 29 (18) ◽  
pp. 2277-2284 ◽  
Author(s):  
Md Shamsuzzoha Bayzid ◽  
Tandy Warnow
Keyword(s):  
Phylogenomic Analyses
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