Novel genome assemblies and Evolutionary Dynamics of North American Anopheles mosquitoes

Anopheles mosquitoes are the principal vectors for malaria and lymphatic filariasis, and evidence for arboviral transmission under laboratory and natural contexts has been demonstrated. Vector management approaches require an understanding of the ecological, epidemiological, and biological context of the species in question, and increased interest in gene drive systems for vector control applications has resulted in an increased need for genome assemblies from understudied mosquito species. While the genomes for many Anopheles species have been sequenced, North American Anopheles taxa have been neglected. In this study we present novel genome assemblies for the North American species An. crucians, An. freeborni, An. albimanus, and An. quadrimaculatus, and examine the evolutionary relationship between these species. We identified 790 shared single copy orthologs between the newly sequenced genomes and created a phylogeny using 673 of the orthologs, identifying 525 orthologs with evidence for positive selection on at least one branch of the phylogeny. Gene ontology terms such as calcium ion signaling, histone binding, and protein acetylation were identified as being biased in the set of selected genes. These novel genome sequences will be useful in developing our understanding of the diverse biological traits that drive vectorial capacity in anophelines.

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Evolution of Old World Equus and origin of the zebra-ass clade

Scientific Reports ◽

10.1038/s41598-021-89440-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Omar Cirilli ◽

Luca Pandolfi ◽

Lorenzo Rook ◽

Raymond L. Bernor

Keyword(s):

North American ◽

Evolutionary Relationship ◽

Cladistic Analysis ◽

Dental Morphology ◽

Old World ◽

The North ◽

Equus Grevyi ◽

Evolutionary Role

AbstractEvolution of the genus Equus has been a matter of long debate with a multitude of hypotheses. Currently, there is no consensus on either the taxonomic content nor phylogeny of Equus. Some hypotheses segregate Equus species into three genera, Plesippus, Allohippus and Equus. Also, the evolutionary role of European Pleistocene Equus stenonis in the origin of the zebra-ass clade has been debated. Studies based on skull, mandible and dental morphology suggest an evolutionary relationship between North American Pliocene E. simplicidens and European and African Pleistocene Equus. In this contribution, we assess the validity of the genera Plesippus, Allohippus and Equus by cladistic analysis combined with morphological and morphometrical comparison of cranial anatomy. Our cladistic analysis, based on cranial and postcranial elements (30 taxa, 129 characters), supports the monophyly of Equus, denies the recognition of Plesippus and Allohippus and supports the derivation of Equus grevyi and members of the zebra-ass clade from European stenonine horses. We define the following evolutionary steps directly relevant to the phylogeny of extant zebras and asses: E. simplicidens–E. stenonis–E. koobiforensis–E. grevyi -zebra-ass clade. The North American Pliocene species Equus simplicidens represents the ancestral stock of Old World Pleistocene Equus and the zebra-ass clade. Our phylogenetic results uphold the most recent genomic outputs which indicate an age of 4.0–4.5 Ma for the origin and monophyly of Equus.

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The salmon louse genome may be much larger than sequencing suggests

10.1101/2022.01.14.476287 ◽

2022 ◽

Author(s):

Grace Wyngaard ◽

Rasmus Skern-Mauritzen ◽

Ketil Malde ◽

Rachel Prendergast ◽

Stefano Peruzzi

Keyword(s):

Genome Size ◽

North Atlantic ◽

Single Copy ◽

Bay Of Fundy ◽

Lepeophtheirus Salmonis ◽

The North ◽

Salmon Lice ◽

The North Atlantic ◽

Genome Assemblies ◽

Chromosome Level

The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding over 92% of expected genes and transcriptome datasets routinely mapping over 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements in the range of 1.3 to 1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up approx. 60% of the genome assemblies.

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Anopheles mosquitoes revealed new principles of 3D genome organization in insects

10.1101/2020.05.26.114017 ◽

2020 ◽

Cited By ~ 5

Author(s):

Varvara Lukyanchikova ◽

Miroslav Nuriddinov ◽

Polina Belokopytova ◽

Jiangtao Liang ◽

Maarten J.M.F. Reijnders ◽

...

Keyword(s):

Genome Organization ◽

Evolutionary Dynamics ◽

Mosquito Species ◽

Cell Nuclei ◽

Functional Importance ◽

Active Chromatin ◽

Anopheles Mosquitoes ◽

3D Genome ◽

Different Levels ◽

Gene Expression Levels

AbstractChromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance and evolutionary dynamics of these hierarchies are poorly defined. Here, we comprehensively profiled genome organizations of five Anopheles mosquito species and showed how different levels of chromatin architecture influence contacts between genomic loci. Patterns observed on Hi-C maps are associated with known cytological structures, epigenetic profiles, and gene expression levels. At the level of individual loci, we identified specific, extremely long-ranged looping interactions, conserved for ~100 million years. We showed that the mechanisms underlying these looping contacts differ from previously described Polycomb-dependent interactions and clustering of active chromatin.

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Herbicide-Resistant Kochia (Bassia scoparia) in North America: A Review

Weed Science ◽

10.1017/wsc.2018.72 ◽

2018 ◽

Vol 67 (1) ◽

pp. 4-15 ◽

Cited By ~ 9

Author(s):

Vipan Kumar ◽

Prashant Jha ◽

Mithila Jugulam ◽

Ramawatar Yadav ◽

Phillip W. Stahlman

Keyword(s):

Great Plains ◽

Herbicide Resistance ◽

Cover Crops ◽

North American ◽

Weed Management ◽

Evolutionary Dynamics ◽

Integrated Weed Management ◽

Herbicide Resistant ◽

The North ◽

Sites Of Action

AbstractKochia [Bassia scoparia(L.) A. J. Scott] is a problematic annual broadleaf weed species in the North American Great Plains.Bassia scopariainherits unique biological characteristics that contribute to its propensity to evolve herbicide resistance. Evolution of glyphosate resistance inB. scopariahas become a serious threat to the major cropping systems and soil conservation practices in the region.Bassia scopariapopulations with resistance to four different herbicide sites of action are a concern for growers. The widespread occurrence of multiple herbicide–resistant (HR)B. scopariaacross the North American Great Plains has renewed research efforts to devise integrated weed management strategies beyond herbicide use. In this review, we aim to compile and document the growing body of literature on HRB. scopariawith emphasis on herbicide-resistance evolutionary dynamics, distribution, mechanisms of evolved resistance, agronomic impacts, and current/future weed management technologies. We focused on ecologically based, non-herbicidal strategies such as diverse crop rotations comprising winter cereals and perennial forages, enhanced crop competition, cover crops, harvest weed seed control (HWSC), and tillage to manage HRB. scopariaseedbanks. Remote sensing using hyperspectral imaging and other sensor-based technologies would be valuable for early detection and rapid response and site-specific herbicide resistance management. We propose research priorities based on an improved understanding of the biology, genetic diversity, and plasticity of this weed that will aid in preserving existing herbicide resources and designing sustainable, integrated HRB. scopariamitigation plans.

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Molecular evolution of chloroplast genomes in subfamily Zingiberoideae (Zingiberaceae)

BMC Plant Biology ◽

10.1186/s12870-021-03315-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Dong-Mei Li ◽

Jie Li ◽

Dai-Rong Wang ◽

Ye-Chun Xu ◽

Gen-Fa Zhu

Keyword(s):

Molecular Markers ◽

Evolutionary Dynamics ◽

Phylogenetic Analyses ◽

Evolutionary Relationship ◽

Single Copy ◽

Rrna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Chloroplast Genomes ◽

Usage Patterns

Abstract Background Zingiberoideae is a large and diverse subfamily of the family Zingiberaceae. Four genera in subfamily Zingiberoideae each possess 50 or more species, including Globba (100), Hedychium (> 80), Kaempferia (50) and Zingiber (150). Despite the agricultural, medicinal and horticultural importance of these species, genomic resources and suitable molecular markers for them are currently sparse. Results Here, we have sequenced, assembled and analyzed ten complete chloroplast genomes from nine species of subfamily Zingiberoideae: Globba lancangensis, Globba marantina, Globba multiflora, Globba schomburgkii, Globba schomburgkii var. angustata, Hedychium coccineum, Hedychium neocarneum, Kaempferia rotunda ‘Red Leaf’, Kaempferia rotunda ‘Silver Diamonds’ and Zingiber recurvatum. These ten chloroplast genomes (size range 162,630–163,968 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 87,172–88,632 bp), a small single copy (SSC, 15,393–15,917 bp) and a pair of inverted repeats (IRs, 29,673–29,833 bp). The genomes contain 111–113 different genes, including 79 protein coding genes, 28–30 tRNAs and 4 rRNA genes. The dynamics of the genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats exhibit similarities, with slight differences observed among the ten genomes. Further comparative analysis of seventeen related Zingiberoideae species, 12 divergent hotspots are identified. Positive selection is observed in 14 protein coding genes, including accD, ccsA, ndhA, ndhB, psbJ, rbcL, rpl20, rpoC1, rpoC2, rps12, rps18, ycf1, ycf2 and ycf4. Phylogenetic analyses, based on the complete chloroplast-derived single-nucleotide polymorphism data, strongly support that Globba, Hedychium, and Curcuma I + “the Kaempferia clade” consisting of Curcuma II, Kaempferia and Zingiber, form a nested evolutionary relationship in subfamily Zingiberoideae. Conclusions Our study provides detailed information on ten complete Zingiberoideae chloroplast genomes, representing a valuable resource for future studies that seek to understand the molecular evolutionary dynamics in family Zingiberaceae. The identified divergent hotspots can be used for development of molecular markers for phylogenetic inference and species identification among closely related species within four genera of Globba, Hedychium, Kaempferia and Zingiber in subfamily Zingiberoideae.

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Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-05-19-0131-r ◽

2020 ◽

Vol 33 (2) ◽

pp. 189-199 ◽

Cited By ~ 3

Author(s):

J. F. Tabima ◽

K. L. Søndreli ◽

S. Keriö ◽

N. Feau ◽

M. L. Sakalidis ◽

...

Keyword(s):

United States ◽

British Columbia ◽

North America ◽

North American ◽

Plant Pathogens ◽

Evolutionary Dynamics ◽

Population Genomics ◽

Plant Domestication ◽

North American Population ◽

The North

Domestication of plant species has affected the evolutionary dynamics of plant pathogens in agriculture and forestry. A model system for studying the consequences of plant domestication on the evolution of an emergent plant disease is the fungal pathogen Sphaerulina musiva. This ascomycete causes leaf spot and stem canker disease of Populus spp. and their hybrids. A population genomics approach was used to determine the degree of population structure and evidence for selection on the North American population of S. musiva. In total, 122 samples of the fungus were genotyped identifying 120,016 single-nucleotide polymorphisms after quality filtering. In North America, S. musiva has low to moderate degrees of differentiation among locations. Three main genetic clusters were detected: southeastern United States, midwestern United States and Canada, and a new British Columbia cluster (BC2). Population genomics suggest that BC2 is a novel genetic cluster from central British Columbia, clearly differentiated from previously reported S. musiva from coastal British Columbia, and the product of a single migration event. Phenotypic measurements from greenhouse experiments indicate lower aggressiveness of BC2 on Populus trichocarpa. In summary, S. musiva has geographic structure across broad regions indicative of gene flow among clusters. The interconnectedness of the North American S. musiva populations across large geographic distances further supports the hypothesis of anthropogenic-facilitated transport of the pathogen.

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