Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes

AbstractLocal adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in the coding sequence of rhodopsin (Tyr261Phe substitution), suggesting local adaptation by C. kiyi to the blue-shifted depths of Lake Superior. Parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

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Nanopore amplicon sequencing reveals molecular convergence and local adaptation of rhodopsin in Great Lakes salmonids

Genome Biology and Evolution ◽

10.1093/gbe/evaa237 ◽

2020 ◽

Author(s):

Katherine M Eaton ◽

Moisés A Bernal ◽

Nathan J C Backenstose ◽

Daniel L Yule ◽

Trevor J Krabbenhoft

Keyword(s):

Amino Acid ◽

Great Lakes ◽

Local Adaptation ◽

Environmental Gradients ◽

Parallel Evolution ◽

Amplicon Sequencing ◽

Species Flock ◽

Ancestral State ◽

Oxford Nanopore ◽

Species Specific

Abstract Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle and MinION. We sequenced five visual opsin genes for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in a key spectral tuning amino acid in rhodopsin (Tyr261Phe substitution), suggesting local adaptation of C. kiyi to the blue-shifted depths of Lake Superior. Ancestral state reconstruction demonstrates that parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

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Excessive Parallelism in Protein Evolution of Lake Baikal Amphipod Species Flock

Genome Biology and Evolution ◽

10.1093/gbe/evaa138 ◽

2020 ◽

Vol 12 (9) ◽

pp. 1493-1503

Author(s):

Valentina Burskaia ◽

Sergey Naumenko ◽

Mikhail Schelkunov ◽

Daria Bedulina ◽

Tatyana Neretina ◽

...

Keyword(s):

Amino Acid ◽

Lake Baikal ◽

Related Species ◽

Parallel Evolution ◽

Amino Acid Level ◽

Species Flock ◽

Amphipod Species ◽

Closely Related Species ◽

Epistatic Interactions ◽

Synonymous Sites

Abstract Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistatic interactions underlying the dynamic nature of the amino acid preferences: The same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 46 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. Strikingly, in genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. At sites of parallel substitutions, the intraspecies polymorphism is low, suggesting that parallelism has been driven by positive selection and is therefore adaptive. By contrast, in cichlids, the rate of nonsynonymous parallel evolution was similar to that at synonymous sites, whereas in vertebrates, this rate was lower than that at synonymous sites, indicating that in these groups of species, parallel substitutions are mainly fixed by drift.

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Landscape genomics and selection signatures of local adaptation of Eritrean indigenous cattle along environmental gradients

Tropical Animal Health and Production ◽

10.1007/s11250-021-02837-6 ◽

2021 ◽

Vol 53 (4) ◽

Author(s):

S. Goitom ◽

Mathew G. Gicheha ◽

Francis K. Njonge ◽

Ngeno Kiplangat

Keyword(s):

Local Adaptation ◽

Environmental Gradients ◽

Selection Signatures ◽

Indigenous Cattle ◽

Landscape Genomics

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A Comparative Study of 5S rDNA Non-Transcribed Spacers in Elaeagnaceae Species

Plants ◽

10.3390/plants10010004 ◽

2020 ◽

Vol 10 (1) ◽

pp. 4

Author(s):

Oleg S. Alexandrov ◽

Olga V. Razumova ◽

Gennady I. Karlov

Keyword(s):

Polymerase Chain Reaction ◽

Molecular Markers ◽

Dna Markers ◽

5S Rdna ◽

Chain Reaction ◽

Closely Related Species ◽

Pcr Products ◽

Polymerase Chain ◽

Species Specific ◽

Shepherdia Canadensis

5S rDNA is organized as a cluster of tandemly repeated monomers that consist of the conservative 120 bp coding part and non-transcribed spacers (NTSs) with different lengths and sequences among different species. The polymorphism in the 5S rDNA NTSs of closely related species is interesting for phylogenetic and evolutional investigations, as well as for the development of molecular markers. In this study, the 5S rDNA NTSs were amplified with universal 5S1/5S2 primers in some species of the Elaeagnaceae Adans. family. The polymerase chain reaction (PCR) products of five Elaeagnus species had similar lengths near 310 bp and were different from Shepherdia canadensis (L.) Nutt. and Sh. argentea (Pusch.) Nutt. samples (260 bp and 215 bp, respectively). The PCR products were cloned and sequenced. An analysis of the sequences revealed that intraspecific levels of NTS identity are high (approximately 95–96%) and similar in the Elaeagnus L. species. In Sh. argentea, this level was slightly lower due to the differences in the poly-T region. Moreover, the intergeneric and intervarietal NTS identity levels were studied and compared. Significant differences between species (except E. multiflora Thunb. and E. umbellata Thunb.) and genera were found. Herein, a range of the NTS features is discussed. This study is another step in the investigation of the molecular evolution of Elaeagnaceae and may be useful for the development of species-specific DNA markers in this family.

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Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing

10.1101/2020.07.17.209346 ◽

2020 ◽

Author(s):

Kimothy L Smith ◽

Howard A Shuman ◽

Douglas Findeisen

Keyword(s):

Microbial Community ◽

16S Rrna ◽

Water Samples ◽

Ad Hoc ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

The Other ◽

Water Usage ◽

16S Rrna Amplicon Sequencing ◽

Oxford Nanopore

AbstractWe conducted two studies of water samples from buildings with normal occupancy and water usage compared to water from buildings that were unoccupied with little or no water usage due to the COVID-19 shutdown. Study 1 had 52 water samples obtained ad hoc from buildings in four metropolitan locations in different states in the US and a range of building types. Study 2 had 36 water samples obtained from two buildings in one metropolitan location with matched water sample types. One of the buildings had been continuously occupied, and the other substantially vacant for approximately 3 months. All water samples were analyzed using 16S rRNA amplicon sequencing with a MinION from Oxford Nanopore Technologies. More than 127 genera of bacteria were identified, including genera with members that are known to include more than 50 putative frank and opportunistic pathogens. While specific results varied among sample locations, 16S rRNA amplicon abundance and the diversity of bacteria were higher in water samples from unoccupied buildings than normally occupied buildings as was the abundance of sequenced amplicons of genera known to include pathogenic bacterial members. In both studies Legionella amplicon abundance was relatively small compared to the abundance of the other bacteria in the samples. Indeed, when present, the relative abundance of Legionella amplicons was lower in samples from unoccupied buildings. Legionella did not predominate in any of the water samples and were found, on average, in 9.6% of samples in Study 1 and 8.3% of samples in Study 2.SynopsisComparison of microbial community composition in the plumbing of occupied and unoccupied buildings during the COVID-19 pandemic shutdown.

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Repeated evolution of asymmetric genitalia and right-sided mating behavior in theDrosophila nannopteraspecies group

10.1101/553024 ◽

2019 ◽

Author(s):

Andrea Acurio ◽

Flor T. Rhebergen ◽

Sarah Paulus ◽

Virginie Courtier-Orgogozo ◽

Michael Lang

Keyword(s):

Related Species ◽

Current Data ◽

The Other ◽

Genital Morphology ◽

Closely Related Species ◽

Outgroup Species ◽

Repeated Evolution ◽

Drosophila Pachea ◽

Species Specific ◽

Group Species

AbstractBackgroundMale genitals have repeatedly evolved left-right asymmetries, and the causes of such evolution remain unclear. TheDrosophila nannopteragroup contains four species, among which three exhibit left-right asymmetries of distinct genital organs. In the most studied species,Drosophila pachea, males display asymmetric genital lobes and they mate right-sided on top of the female. Copulation position of the other species is unknown.ResultsTo assess whether the evolution of genital asymmetry could be linked to the evolution of one-sided mating, we examined phallus morphology and copulation position inD. pacheaand closely related species. The phallus was found to be symmetric in all investigated species exceptD. pachea, which display an asymmetric phallus with a right-sided gonopore, andD. acanthoptera, which harbor an asymmetrically bent phallus. In all examined species, males were found to position themselves symmetrically on top of the female, except inD. pacheaandD. nannoptera, where males mated right-sided, in distinctive, species-specific positions. In addition, the copulation duration was found to be increased innannopteragroup species compared to closely related outgroup species.ConclusionOur study shows that gains, and possibly losses, of asymmetry in genital morphology and mating position have evolved repeatedly in thenannopteragroup. Current data does not allow us to conclude whether genital asymmetry has evolved in response to changes in mating position, or vice versa.

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Do Differences in Latitudinal Distributions of Species and Organelle Haplotypes Reflect Thermal Reaction Norms Within the Emiliania/Gephyrocapsa Complex?

Frontiers in Marine Science ◽

10.3389/fmars.2021.785763 ◽

2021 ◽

Vol 8 ◽

Author(s):

Peter von Dassow ◽

Paula Valentina Muñoz Farías ◽

Sarah Pinon ◽

Esther Velasco-Senovilla ◽

Simon Anguita-Salinas

Keyword(s):

Local Adaptation ◽

Coastal Upwelling ◽

Environmental Gradients ◽

Reaction Norm ◽

Emiliania Huxleyi ◽

Thermal Reaction ◽

Reaction Norms ◽

Thermal Niche ◽

Significant Difference ◽

The Difference

The cosmopolitan phytoplankter Emiliania huxleyi contrasts with its closest relatives that are restricted to narrower latitudinal bands, making it interesting for exploring how alternative outcomes in phytoplankton range distributions arise. Mitochondrial and chloroplast haplogroups within E. huxleyi are shared with their closest relatives: Some E. huxleyi share organelle haplogroups with Gephyrocapsa parvula and G. ericsonii which inhabit lower latitudes, while other E. huxleyi share organelle haplogroups with G. muellerae, which inhabit high latitudes. We investigated whether the phylogeny of E. huxleyi organelles reflects environmental gradients, focusing on the Southeast Pacific where the different haplogroups and species co-occur. There was a high congruence between mitochondrial and chloroplast haplogroups within E. huxleyi. Haplogroup II of E. huxleyi is negatively associated with cooler less saline waters, compared to haplogroup I, both when analyzed globally and across temporal variability at the small special scale of a center of coastal upwelling at 30° S. A new mitochondrial haplogroup Ib detected in coastal Chile was associated with warmer waters. In an experiment focused on inter-species comparisons, laboratory-determined thermal reaction norms were consistent with latitudinal/thermal distributions of species, with G. oceanica exhibiting warm thermal optima and tolerance and G. muellerae exhibiting cooler thermal optima and tolerances. Emiliania huxleyi haplogroups I and II tended to exhibit a wider thermal niche compared to the other Gephyrocapsa, but no differences among haplogroups within E. huxleyi were found. A second experiment, controlling for local adaptation and time in culture, found a significant difference between E. huxleyi haplogroups. The difference between I and II was of the expected sign, but not the difference between I and Ib. The differences were small (≤1°C) compared to differences reported previously within E. huxleyi by local adaptation and even in-culture evolution. Haplogroup Ib showed a narrower thermal niche. The cosmopolitanism of E. huxleyi might result from both wide-spread generalist phenotypes and specialist phenotypes, as well as a capacity for local adaptation. Thermal reaction norm differences can well explain the species distributions but poorly explain distributions among mitochondrial haplogroups within E. huxleyi. Perhaps organelle haplogroup distributions reflect historical rather than selective processes.

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Detection and Quantification of Bremia lactucae by Spore Trapping and Quantitative PCR

Phytopathology ◽

10.1094/phyto-03-16-0143-r ◽

2016 ◽

Vol 106 (11) ◽

pp. 1426-1437 ◽

Cited By ~ 16

Author(s):

Sridhara G. Kunjeti ◽

Amy Anchieta ◽

Frank N. Martin ◽

Young-Joon Choi ◽

Marco Thines ◽

...

Keyword(s):

Quantitative Polymerase Chain Reaction ◽

Amplicon Sequencing ◽

Coefficient Of Determination ◽

Target Sequence ◽

Bremia Lactucae ◽

Cropping Season ◽

Leaf Chlorosis ◽

Salinas Valley ◽

Species Specific ◽

Detection And Quantification

Bremia lactucae is an obligate, oomycete pathogen of lettuce that causes leaf chlorosis and necrosis and adversely affects marketability. The disease has been managed with a combination of host resistance and fungicide applications with success over the years. Fungicide applications are routinely made under the assumption that inoculum is always present during favorable environmental conditions. This approach often leads to fungicide resistance in B. lactucae populations. Detection and quantification of airborne B. lactucae near lettuce crops provides an estimation of the inoculum load, enabling more judicious timing of fungicide applications. We developed a quantitative polymerase chain reaction (qPCR)-based assay using a target sequence in mitochondrial DNA for specific detection of B. lactucae. Validation using amplicon sequencing of DNA from 83 geographically diverse isolates, representing 14 Bremia spp., confirmed that the primers developed for the TaqMan assays are species specific and only amplify templates from B. lactucae. DNA from a single sporangium could be detected at a quantification cycle (Cq) value of 32, and Cq values >35 were considered to be nonspecific. The coefficient of determination (R2) for regression between sporangial density derived from flow cytometry and Cq values derived from the qPCR was 0.86. The assay was deployed using spore traps in the Salinas Valley, where nearly half of U.S. lettuce is produced. The deployment of this sensitive B. lactucae-specific assay resulted in the detection of the pathogen during the 2-week lettuce-free period as well as during the cropping season. These results demonstrate that this assay will be useful for quantifying inoculum load in and around the lettuce fields for the purpose of timing fungicide applications based on inoculum load.

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The Visual Opsin Gene Repertoires of Teleost Fishes: Evolution, Ecology, and Function

Annual Review of Cell and Developmental Biology ◽

10.1146/annurev-cellbio-120219-024915 ◽

2021 ◽

Vol 37 (1) ◽

Author(s):

Zuzana Musilova ◽

Walter Salzburger ◽

Fabio Cortesi

Keyword(s):

Sensory System ◽

Photoreceptor Cells ◽

Opsin Gene ◽

Annual Review ◽

Specific Gene ◽

Publication Date ◽

Teleost Fishes ◽

Opsin Genes ◽

The Rich ◽

Species Specific

Visual opsin genes expressed in the rod and cone photoreceptor cells of the retina are core components of the visual sensory system of vertebrates. Here, we provide an overview of the dynamic evolution of visual opsin genes in the most species-rich group of vertebrates, teleost fishes. The examination of the rich genomic resources now available for this group reveals that fish genomes contain more copies of visual opsin genes than are present in the genomes of amphibians, reptiles, birds, and mammals. The expansion of opsin genes in fishes is due primarily to a combination of ancestral and lineage-specific gene duplications. Following their duplication, the visual opsin genes of fishes repeatedly diversified at the same key spectral-tuning sites, generating arrays of visual pigments sensitive from the ultraviolet to the red spectrum of the light. Species-specific opsin gene repertoires correlate strongly with underwater light habitats, ecology, and color-based sexual selection. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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