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Phylogenomics

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https://www.readbyqxmd.com/read/29456146/a-comprehensive-and-dated-phylogenomic-analysis-of-butterflies
#1
Marianne Espeland, Jesse Breinholt, Keith R Willmott, Andrew D Warren, Roger Vila, Emmanuel F A Toussaint, Sarah C Maunsell, Kwaku Aduse-Poku, Gerard Talavera, Rod Eastwood, Marta A Jarzyna, Robert Guralnick, David J Lohman, Naomi E Pierce, Akito Y Kawahara
Butterflies (Papilionoidea), with over 18,000 described species [1], have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species representing 98% of tribes, a 35-fold increase in gene sampling and 3-fold increase in taxon sampling over previous studies [4]...
February 14, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29453332/step-wise-evolution-of-complex-chemical-defenses-in-millipedes-a-phylogenomic-approach
#2
Juanita Rodriguez, Tappey H Jones, Petra Sierwald, Paul E Marek, William A Shear, Michael S Brewer, Kevin M Kocot, Jason E Bond
With fossil representatives from the Silurian capable of respiring atmospheric oxygen, millipedes are among the oldest terrestrial animals, and likely the first to acquire diverse and complex chemical defenses against predators. Exploring the origin of complex adaptive traits is critical for understanding the evolution of Earth's biological complexity, and chemical defense evolution serves as an ideal study system. The classic explanation for the evolution of complexity is by gradual increase from simple to complex, passing through intermediate "stepping stone" states...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29449857/plastid-genome-comparative-and-phylogenetic-analyses-of-the-key-genera-in-fagaceae-highlighting-the-effect-of-codon-composition-bias-in-phylogenetic-inference
#3
Yanci Yang, Juan Zhu, Li Feng, Tao Zhou, Guoqing Bai, Jia Yang, Guifang Zhao
Fagaceae is one of the largest and economically important taxa within Fagales. Considering the incongruence among inferences from plastid and nuclear genes in the previous Fagaceae phylogeny studies, we assess the performance of plastid phylogenomics in this complex family. We sequenced and assembled four complete plastid genomes ( Fagus engleriana, Quercus spinosa, Quercus aquifolioides , and Quercus glauca ) using reference-guided assembly approach. All of the other 12 published plastid genomes in Fagaceae were retrieved for genomic analyses (including repeats, sequence divergence and codon usage) and phylogenetic inference...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29442617/assembly-of-highly-repetitive-genomes-using-short-reads-the-genome-of-discrete-typing-unit-iii-trypanosoma-cruzi-strain-231
#4
Rodrigo P Baptista, Joao Luis Reis-Cunha, Jeremy D DeBarry, Egler Chiari, Jessica C Kissinger, Daniella C Bartholomeu, Andrea M Macedo
Next-generation sequencing (NGS) methods are low-cost high-throughput technologies that produce thousands to millions of sequence reads. Despite the high number of raw sequence reads, their short length, relative to Sanger, PacBio or Nanopore reads, complicates the assembly of genomic repeats. Many genome tools are available, but the assembly of highly repetitive genome sequences using only NGS short reads remains challenging. Genome assembly of organisms responsible for important neglected diseases such as Trypanosoma cruzi, the aetiological agent of Chagas disease, is known to be challenging because of their repetitive nature...
February 14, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29440651/reconstruction-of-the-sialylation-pathway-in-the-ancestor-of-eukaryotes
#5
Daniel Petit, Elin Teppa, Ugo Cenci, Steven Ball, Anne Harduin-Lepers
The biosynthesis of sialylated molecules of crucial relevance for eukaryotic cell life is achieved by sialyltransferases (ST) of the CAZy family GT29. These enzymes are widespread in the Deuterostoma lineages and more rarely described in Protostoma, Viridiplantae and various protist lineages raising the question of their presence in the Last eukaryotes Common Ancestor (LECA). If so, it is expected that the main enzymes associated with sialic acids metabolism are also present in protists. We conducted phylogenomic and protein sequence analyses to gain insights into the origin and ancient evolution of ST and sialic acid pathway in eukaryotes, Bacteria and Archaea...
February 13, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29432851/filtering-of-target-sequence-capture-individuals-facilitates-species-tree-construction-in-the-plant-subtribe-iochrominae-solanaceae
#6
Daniel J Gates, Diana Pilson, Stacey D Smith
Advances in sequencing technology have made it possible to produce large multi-locus datasets required for species tree analyses. One challenge with constructing high throughput sequencing datasets, however, is that missing information is propagated at different steps in the sequence preparation process. To date, species tree studies have focused on filtering and removing errors that occur at particular loci. Given the way that high throughput sequencing datasets are constructed, however, large amounts of error or ambiguity may also manifest across individuals...
February 9, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29425128/the-complete-chloroplast-genome-of-catha-edulis-a-comparative-analysis-of-genome-features-with-related-species
#7
Cuihua Gu, Luke R Tembrock, Shaoyu Zheng, Zhiqiang Wu
Qat (Catha edulis, Celastraceae) is a woody evergreen species with great economic and cultural importance. It is cultivated for its stimulant alkaloids cathine and cathinone in East Africa and southwest Arabia. However, genome information, especially DNA sequence resources, for C. edulis are limited, hindering studies regarding interspecific and intraspecific relationships. Herein, the complete chloroplast (cp) genome of Catha edulis is reported. This genome is 157,960 bp in length with 37% GC content and is structurally arranged into two 26,577 bp inverted repeats and two single-copy areas...
February 9, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29421312/discovista-interpretable-visualizations-of-gene-tree-discordance
#8
Erfan Sayyari, James B Whitfield, Siavash Mirarab
Phylogenomics has ushered in an age of discordance. Analyses often reveal abundant discordances among phylogenies of different parts of genomes, as well as incongruences between species trees obtained using different methods or data partitions. Researchers are often left trying to make sense of such incongruences. Interpretive ways of measuring and visualizing discordance are needed, both among alternative species trees and gene trees, especially for specific focal branches of a tree. Here, we introduce DiscoVista, a publicly available tool that creates a suite of simple but interpretable visualizations...
February 5, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29420807/transoceanic-dispersal-and-plate-tectonics-shaped-global-cockroach-distributions-evidence-from-mitochondrial-phylogenomics
#9
Thomas Bourguignon, Tang Qian, Simon Y W Ho, Frantisek Juna, Zongqing Wang, Daej A Arab, Stephen L Cameron, James Walker, David Rentz, Theodore A Evans, Nathan Lo
Following the acceptance of plate tectonics theory in the latter half of the 20th century, vicariance became the dominant explanation for the distributions of many plant and animal groups. In recent years, however, molecular-clock analyses have challenged a number of well-accepted hypotheses of vicariance. As a widespread group of insects with a fossil record dating back 300 million years, cockroaches provide an ideal model for testing hypotheses of vicariance through plate tectonics vs transoceanic dispersal...
February 6, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29418041/intrageneric-variability-between-the-chloroplast-genomes-of-trachelomonas-grandis-and-trachelomonas-volvocina-and-phylogenomic-analysis-of-phototrophic-euglenoids
#10
Nadja Dabbagh, Angelika Preisfeld
The latest studies of chloroplast genomes of phototrophic euglenoids yielded different results according to intrageneric variability such as cluster arrangement or diversity of introns. Whereas the genera Euglena and Monomorphina in those studies show high syntenic arrangements at the intrageneric level, the two investigated Eutreptiella species comprise low synteny. Furthermore T. volvocina show low synteny to the chloroplast genomes of the sister genera Monomorphina aenigmatica, M. parapyrum, Cryptoglena skujae, Euglenaria anabaena, Strombomonas acuminata, all of which were highly syntenic...
February 8, 2018: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/29416954/a-250-plastome-phylogeny-of-the-grass-family-poaceae-topological-support-under-different-data-partitions
#11
Jeffery M Saarela, Sean V Burke, William P Wysocki, Matthew D Barrett, Lynn G Clark, Joseph M Craine, Paul M Peterson, Robert J Soreng, Maria S Vorontsova, Melvin R Duvall
The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses...
2018: PeerJ
https://www.readbyqxmd.com/read/29402211/phylogenomics-of-a-rapid-radiation-the-australian-rainbow-skinks
#12
Jason G Bragg, Sally Potter, Ana C Afonso Silva, Conrad J Hoskin, Benjamin Y H Bai, Craig Moritz
BACKGROUND: The application of target capture with next-generation sequencing now enables phylogenomic analyses of rapidly radiating clades of species. But such analyses are complicated by extensive incomplete lineage sorting, demanding the use of methods that consider this process explicitly, such as the multispecies coalescent (MSC) model. However, the MSC makes strong assumptions about divergence history and population structure, and when using the full Bayesian implementation, current computational limits mean that relatively few loci and samples can be analysed for even modest sized radiations...
February 5, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29385718/the-diverging-routes-of-boris-and-ctcf-an-interactomic-and-phylogenomic-analysis
#13
Kamel Jabbari, Peter Heger, Ranu Sharma, Thomas Wiehe
The CCCTC-binding factor (CTCF) is multi-functional, ubiquitously expressed, and highly conserved from Drosophila to human. It has important roles in transcriptional insulation and the formation of a high-dimensional chromatin structure. CTCF has a paralog called "Brother of Regulator of Imprinted Sites" (BORIS) or "CTCF-like" (CTCFL). It binds DNA at sites similar to those of CTCF. However, the expression profiles of the two proteins are quite different. We investigated the evolutionary trajectories of the two proteins after the duplication event using a phylogenomic and interactomic approach...
January 30, 2018: Life
https://www.readbyqxmd.com/read/29374214/phylogenomic-reclassification-of-the-world-s-most-venomous-spiders-mygalomorphae-atracinae-with-implications-for-venom-evolution
#14
Marshal Hedin, Shahan Derkarabetian, Martín J Ramírez, Cor Vink, Jason E Bond
Here we show that the most venomous spiders in the world are phylogenetically misplaced. Australian atracine spiders (family Hexathelidae), including the notorious Sydney funnel-web spider Atrax robustus, produce venom peptides that can kill people. Intriguingly, eastern Australian mouse spiders (family Actinopodidae) are also medically dangerous, possessing venom peptides strikingly similar to Atrax hexatoxins. Based on the standing morphology-based classification, mouse spiders are hypothesized distant relatives of atracines, having diverged over 200 million years ago...
January 26, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29370802/phylogenomics-of-the-olive-tree-olea-europaea-reveals-the-relative-contribution-of-ancient-allo-and-autopolyploidization-events
#15
Irene Julca, Marina Marcet-Houben, Pablo Vargas, Toni Gabaldón
BACKGROUND: Polyploidization is one of the major evolutionary processes that shape eukaryotic genomes, being particularly common in plants. Polyploids can arise through direct genome doubling within a species (autopolyploidization) or through the merging of genomes from distinct species after hybridization (allopolyploidization). The relative contribution of both mechanisms in plant evolution is debated. Here we used phylogenomics to dissect the tempo and mode of duplications in the genome of the olive tree (Olea europaea), one of the first domesticated Mediterranean fruit trees...
January 25, 2018: BMC Biology
https://www.readbyqxmd.com/read/29367699/plastid-phylogenomics-with-broad-taxon-sampling-further-elucidates-the-distinct-evolutionary-origins-and-timing-of-secondary-green-plastids
#16
Christopher Jackson, Andrew H Knoll, Cheong Xin Chan, Heroen Verbruggen
Secondary plastids derived from green algae occur in chlorarachniophytes, photosynthetic euglenophytes, and the dinoflagellate genus Lepidodinium. Recent advances in understanding the origin of these plastids have been made, but analyses suffer from relatively sparse taxon sampling within the green algal groups to which they are related. In this study we aim to derive new insights into the identity of the plastid donors, and when in geological time the independent endosymbiosis events occurred. We use newly sequenced green algal chloroplast genomes from carefully chosen lineages potentially related to chlorarachniophyte and Lepidodinium plastids, combined with recently published chloroplast genomes, to present taxon-rich phylogenetic analyses to further pinpoint plastid origins...
January 24, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29367657/phylogenomics-and-antimicrobial-resistance-of-the-leprosy-bacillus-mycobacterium-leprae
#17
Andrej Benjak, Charlotte Avanzi, Pushpendra Singh, Chloé Loiseau, Selfu Girma, Philippe Busso, Amanda N Brum Fontes, Yuji Miyamoto, Masako Namisato, Kidist Bobosha, Claudio G Salgado, Moisés B da Silva, Raquel C Bouth, Marco A C Frade, Fred Bernardes Filho, Josafá G Barreto, José A C Nery, Samira Bührer-Sékula, Andréanne Lupien, Abdul R Al-Samie, Yasin Al-Qubati, Abdul S Alkubati, Gisela Bretzel, Lucio Vera-Cabrera, Fatoumata Sakho, Christian R Johnson, Mamoudou Kodio, Abdoulaye Fomba, Samba O Sow, Moussa Gado, Ousmane Konaté, Mariane M A Stefani, Gerson O Penna, Philip N Suffys, Euzenir Nunes Sarno, Milton O Moraes, Patricia S Rosa, Ida M F Dias Baptista, John S Spencer, Abraham Aseffa, Masanori Matsuoka, Masanori Kai, Stewart T Cole
Leprosy is a chronic human disease caused by the yet-uncultured pathogen Mycobacterium leprae. Although readily curable with multidrug therapy (MDT), over 200,000 new cases are still reported annually. Here, we obtain M. leprae genome sequences from DNA extracted directly from patients' skin biopsies using a customized protocol. Comparative and phylogenetic analysis of 154 genomes from 25 countries provides insight into evolution and antimicrobial resistance, uncovering lineages and phylogeographic trends, with the most ancestral strains linked to the Far East...
January 24, 2018: Nature Communications
https://www.readbyqxmd.com/read/29366829/a-revised-dated-phylogeny-of-scorpions-phylogenomic-support-for-ancient-divergence-of-the-temperate-gondwanan-family-bothriuridae
#18
Prashant P Sharma, Caitlin M Baker, Julia G Cosgrove, Joanne E Johnson, Jill T Oberski, Robert J Raven, Mark S Harvey, Sarah L Boyer, Gonzalo Giribet
The scorpion family Bothriuridae occupies a subset of landmasses formerly constituting East and West Gondwana, but its relationship to other scorpion families is in question. Whereas morphological data have strongly supported a sister group relationship of Bothriuridae and the superfamily Scorpionoidea, a recent phylogenomic analysis recovered a basal placement of bothriurids within Iurida, albeit sampling only a single exemplar. Here we reexamined the phylogenetic placement of the family Bothriuridae, sampling six bothriurid exemplars representing both East and West Gondwana, using transcriptomic data...
January 20, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29365145/phylochromomap-a-tool-for-mapping-phylogenomic-history-along-chromosomes-reveals-the-dynamic-nature-of-karyotype-evolution-in-plasmodium-falciparum
#19
Mario A Cerón-Romero, Esther Nwaka, Zuliat Owoade, Laura A Katz
The genome of P. falciparum, the causative agent of malaria in Africa, has been extensively studied since it was first fully sequenced in 2002. However, many open questions remain, including understanding the chromosomal context of molecular evolutionary changes (e.g. relationship between chromosome map and phylogenetic conservation, patterns of gene duplication, and patterns of selection). Here we present PhyloChromoMap, a method that generates a phylogenomic map of chromosomes from a custom-built bioinformatics pipeline...
January 22, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29362692/-comparative-spigot-ontogeny-across-the-spider-tree-of-life
#20
Rachael E Alfaro, Charles E Griswold, Kelly B Miller
Spiders are well known for their silk and its varying use across taxa. Very few studies have examined the silk spigot ontogeny of the entire spinning field of a spider. Historically the spider phylogeny was based on morphological data and behavioral data associated with silk. Recent phylogenomics studies have shifted major paradigms in our understanding of silk use evolution, reordering phylogenetic relationships that were once thought to be monophyletic. Considering this, we explored spigot ontogeny in 22 species, including Dolomedes tenebrosus and Hogna carolinensis, reported here for the first time...
2018: PeerJ
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