Novel Molecular Resources to Facilitate Future Genetics Research on Freshwater Mussels (Bivalvia: Unionidae)

Molecular data have been an integral tool in the resolution of the evolutionary relationships and systematics of freshwater mussels, despite the limited number of nuclear markers available for Sanger sequencing. To facilitate future studies, we evaluated the phylogenetic informativeness of loci from the recently published anchored hybrid enrichment (AHE) probe set Unioverse and developed novel Sanger primer sets to amplify two protein-coding nuclear loci with high net phylogenetic informativeness scores: fem-1 homolog C (FEM1) and UbiA prenyltransferase domain-containing protein 1 (UbiA). We report the methods used for marker development, along with the primer sequences and optimized PCR and thermal cycling conditions. To demonstrate the utility of these markers, we provide haplotype networks, DNA alignments, and summary statistics regarding the sequence variation for the two protein-coding nuclear loci (FEM1 and UbiA). Additionally, we compare the DNA sequence variation of FEM1 and UbiA to three loci commonly used in freshwater mussel genetic studies: the mitochondrial genes cytochrome c oxidase subunit 1 (CO1) and NADH dehydrogenase subunit 1 (ND1), and the nuclear internal transcribed spacer 1 (ITS1). All five loci distinguish among the three focal species (Potamilus fragilis, Potamilus inflatus, and Potamilus purpuratus), and the sequence variation was highest for ND1, followed by CO1, ITS1, UbiA, and FEM1, respectively. The newly developed Sanger PCR primers and methodologies for extracting additional loci from AHE probe sets have great potential to facilitate molecular investigations targeting supraspecific relationships in freshwater mussels, but may be of limited utility at shallow taxonomic scales.

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A Comparative Phylogeographic Approach to Facilitate Recovery of an Imperiled Freshwater Mussel (Bivalvia: Unionida: Potamilus inflatus)

Diversity ◽

10.3390/d12070281 ◽

2020 ◽

Vol 12 (7) ◽

pp. 281 ◽

Cited By ~ 1

Author(s):

Chase H. Smith ◽

Nathan A. Johnson

Keyword(s):

Genetic Diversity ◽

Life Histories ◽

Sequence Data ◽

Freshwater Mussels ◽

Genetic Relationships ◽

Freshwater Mussel ◽

Molecular Data ◽

Brood Stock ◽

Surrogate Species ◽

Approximate Bayesian

North American freshwaters are among the world’s most threatened ecosystems, and freshwater mussels are among the most imperiled inhabiting these systems. A critical aspect of conservation biology is delineating patterns of genetic diversity, which can be difficult when a taxon has been extirpated from a significant portion of its historical range. In such cases, evaluating conservation and recovery options may benefit by using surrogate species as proxies when assessing overall patterns of genetic diversity. Here, we integrate the premise of surrogate species into a comparative phylogeographic framework to hypothesize genetic relationships between extant and extirpated populations of Potamilus inflatus by characterizing genetic structure in co-distributed congeners with similar life histories and dispersal capabilities. Our mitochondrial and nuclear sequence data exhibited variable patterns of genetic divergence between Potamilus spp. native to the Mobile and Pascagoula + Pearl + Pontchartrain (PPP) provinces. However, hierarchical Approximate Bayesian Computation indicated that the diversification between Mobile and PPP clades was synchronous and represents a genetic signature of a common history of vicariance. Recent fluctuations in sea-level appear to have caused Potamilus spp. in the PPP to form a single genetic cluster, providing justification for using individuals from the Amite River as a source of brood stock to re-establish extirpated populations of P. inflatus. Future studies utilizing eDNA and genome-wide molecular data are essential to better understand the distribution of P. inflatus and establish robust recovery plans. Given the imperilment status of freshwater mussels globally, our study represents a useful methodology for predicting relationships among extant and extirpated populations of imperiled species.

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Faculty Opinions recommendation of Evaluating phylogenetic informativeness and data-type usage for new protein-coding genes across Vertebrata.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13360106.14730258 ◽

2011 ◽

Author(s):

Rafael Zardoya ◽

Diego San Mauro

Keyword(s):

Data Type ◽

Protein Coding ◽

Protein Coding Genes ◽

Phylogenetic Informativeness ◽

New Protein

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Sequence Variation in Two Protein-Coding Genes Correlates with Mycelial Compatibility Groupings in Sclerotium rolfsii

Phytopathology ◽

10.1094/phyto-07-12-0151-r ◽

2013 ◽

Vol 103 (5) ◽

pp. 479-487 ◽

Cited By ~ 6

Author(s):

Efrén Remesal ◽

Blanca B. Landa ◽

María del Mar Jiménez-Gasco ◽

Juan A. Navas-Cortés

Keyword(s):

Rna Polymerase Ii ◽

Sequence Variation ◽

Geographic Origin ◽

Sclerotium Rolfsii ◽

Nuclear Ribosomal Dna ◽

Causal Organism ◽

Protein Coding ◽

Protein Coding Genes ◽

Wide Range ◽

Mycelial Compatibility

Populations of Sclerotium rolfsii, the causal organism of Sclerotium root-rot on a wide range of hosts, can be placed into mycelial compatibility groups (MCGs). In this study, we evaluated three different molecular approaches to unequivocally identify each of 12 previously identified MCGs. These included restriction fragment length polymorphism (RFLP) patterns of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (rDNA) and sequence analysis of two protein-coding genes: translation elongation factor 1α (EF1α) and RNA polymerase II subunit two (RPB2). A collection of 238 single-sclerotial isolates representing 12 MCGs of S. rolfsii were obtained from diseased sugar beet plants from Chile, Italy, Portugal, and Spain. ITS-RFLP analysis using four restriction enzymes (AluI, HpaII, RsaI, and MboI) displayed a low degree of variability among MCGs. Only three different restriction profiles were identified among S. rolfsii isolates, with no correlation to MCG or to geographic origin. Based on nucleotide polymorphisms, the RPB2 gene was more variable among MCGs compared with the EF1α gene. Thus, 10 of 12 MCGs could be characterized utilizing the RPB2 region only, while the EF1α region resolved 7 MCGs. However, the analysis of combined partial sequences of EF1α and RPB2 genes allowed discrimination among each of the 12 MCGs. All isolates belonging to the same MCG showed identical nucleotide sequences that differed by at least in one nucleotide from a different MCG. The consistency of our results to identify the MCG of a given S. rolfsii isolate using the combined sequences of EF1α and RPB2 genes was confirmed using blind trials. Our study demonstrates that sequence variation in the protein-coding genes EF1α and RPB2 may be exploited as a diagnostic tool for MCG typing in S. rolfsii as well as to identify previously undescribed MCGs.

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Taxonomic reassessment of the freshwater mussel genus Unio (Bivalvia: Unionidae) in Russia and Ukraine based on morphological and molecular data

Zootaxa ◽

10.11646/zootaxa.4286.1.4 ◽

2017 ◽

Vol 4286 (1) ◽

pp. 93 ◽

Cited By ~ 18

Author(s):

OLGA KLISHKO ◽

MANUEL LOPES-LIMA ◽

ELSA FROUFE ◽

ARTHUR BOGAN ◽

LYUDMILA VASILIEV ◽

...

Keyword(s):

Freshwater Mussel ◽

Integrated Approach ◽

Molecular Data ◽

Coi Gene ◽

Data Set ◽

Widespread Species ◽

Molecular Analyses ◽

Morphological Variations ◽

Mtdna Coi ◽

Morphological And Molecular Data

The taxonomy of species within the genus Unio (Bivalvia: Unionidae: Unioninae) in Russia and Ukraine has been contentious due to the lack of correspondence between three concurrent yet divergent classifications. In order to clarify which classification system best reflects the evolutionary relationships among these taxa, we performed detailed morphological analyses on 720 Ukrainian and Russian specimens, complemented with molecular data (COI) from a selected number of specimens. The morphological character data set shows the existence of only three widespread species with slight eco-morphological variations. Statistical analyses of shell morphometric parameters and molecular analyses based on mtDNA COI gene fragment sequences confirm the existence of the same three species within a single genus, Unio, in Russia and Ukraine, that is U. pictorum, U. tumidus and U. crassus. Results from molecular analyses suggest the existence of an additional subgroup within the U. crassus lineage, U. crassus cf. courtilieri that deserves further research. The present integrated approach confirms the validity of the classification by Zhadin (1952) and rejects the complex classifications of Starobogatov et al. (2004) and Bogatov & Kijashko (2016).

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Cryptic speciation in a biodiversity hotspot: multilocus molecular data reveal new velvet worm species from Western Australia (Onychophora : Peripatopsidae : Kumbadjena)

Invertebrate Systematics ◽

10.1071/is18024 ◽

2018 ◽

Vol 32 (6) ◽

pp. 1249 ◽

Cited By ~ 1

Author(s):

Shoyo Sato ◽

Rebecca S. Buckman-Young ◽

Mark S. Harvey ◽

Gonzalo Giribet

Keyword(s):

Western Australia ◽

18S Rrna ◽

Mitochondrial Protein ◽

Molecular Data ◽

12S Rrna ◽

Protein Coding ◽

Complex Morphology ◽

Velvet Worm ◽

Three New Species ◽

Western Australian

There is a yet uncovered multitude of species to be found among Western Australian Onychophora. Kumbadjena, one of the two genera that reside in this region, has been previously suggested to house an extensive species complex. Morphology alone has not been able to elucidate the diversity in this genus and has instead muddled species delineations. Topologies and species delimitation analyses resulting from the sequences of two mitochondrial ribosomal markers (12S rRNA and 16S rRNA), one nuclear ribosomal marker (18S rRNA), and one mitochondrial protein-coding gene (cytochrome c oxidase subunit I) are indicative of several undescribed species. Fixed diagnostic nucleotide changes in the highly conserved sequences of 18S rRNA warrant distinction of three new species of Kumbadjena: K. toolbrunupensis, sp. nov., K. karricola, sp. nov., and K. extrema, sp. nov. The geographic distributions of the proposed species suggest that Kumbadjena is another example of short-range endemism, a common occurrence in the flora and fauna of the region. The extensive biodiversity and endemism in the region necessitates conservation to preserve the species and processes that promote speciation harboured by Western Australia.

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Morphology and distribution of the freshwater mussel Diplodon granosus, a rare and poorly understood species

Acta Amazonica ◽

10.1590/1809-4392201903910 ◽

2020 ◽

Vol 50 (1) ◽

pp. 44-53 ◽

Cited By ~ 1

Author(s):

Igor Christo MIYAHIRA ◽

Maria Cristina Dreher MANSUR ◽

Daniel Mansur PIMPÃO ◽

Sheyla Regina Marques COUCEIRO ◽

Sonia Barbosa dos SANTOS

Keyword(s):

South America ◽

Freshwater Mussels ◽

Freshwater Mussel ◽

Wide Distribution ◽

Large Area ◽

The North ◽

Coastal Rivers ◽

The Status ◽

Long Time

ABSTRACT Diplodon granosus was one of the first freshwater mussels to be described for South America. However, the status of the species was confusing for a long time, receiving different taxonomic treatments. In this paper, we redescribe the shell, with new data on the soft parts and information on the distribution and conservation of D. granosus, a rarely recorded species. The shell is thin, not inflated; the macrosculpture is composed only by granules that cover the whole shell, not forming bars; the microsculpture comprises short spikes. In the soft parts we highlight the few, weak and irregularly distributed lamellar connections of the outer demibranch and some features of the stomach, such as the distally enlarged minor typhlosole. There are records of D. granosus over a large area of South America, from Guiana to Argentina. However, most of these records are related to other species and the distribution of D. granosus is restricted to the north of South America in the basins of the Amazonas and Orinoco rivers, and coastal rivers in between. Despite this wide distribution, the species occurs in specific habitats, mainly streams (igarapés), resulting in an extremely fragmented occurrence. Thus, any disturbance to these habitats can threat this freshwater mussel.

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Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽

10.7717/peerj.10364 ◽

2020 ◽

Vol 8 ◽

pp. e10364

Author(s):

Natalia I. Abramson ◽

Fedor N. Golenishchev ◽

Semen Yu. Bodrov ◽

Olga V. Bondareva ◽

Evgeny A. Genelt-Yanovskiy ◽

...

Keyword(s):

Mitochondrial Genome ◽

De Novo ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Morphological Characters ◽

Molecular Data ◽

Phylogenetic Position ◽

Skull Morphology ◽

Protein Coding ◽

Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

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An integrated approach for synonymization of Rotylenchus rhomboides with R. goodeyi (Nematoda: Hoplolaimidae) reveals high intraspecific mitogenomic variation

Phytopathology ◽

10.1094/phyto-08-21-0363-r ◽

2021 ◽

Author(s):

Phougeishangbam Rolish Singh ◽

Bart van de Vossenberg ◽

Katarzynar Rybarczyk-Mydłowska3 ◽

Magdalena Kowalewska-Groszkowska ◽

Wim Bert ◽

...

Keyword(s):

Dna Sequences ◽

Integrated Approach ◽

Morphological Characters ◽

Molecular Data ◽

Cox1 Gene ◽

Protein Coding ◽

Genome Shotgun Sequence ◽

Important Character ◽

Rna Genes ◽

Level Identification

Rotylenchus is a widely-distributed economically important plant-parasitic nematode group whose species-level identification relies largely on limited morphological characters including character-based tabular keys and molecular data of ribosomal and mitochondrial genes. In this study, a combined morphological and molecular analysis of three populations of R. goodeyi from Belgium, Poland and the Netherlands revealed important character variations of this species leading to synonymisation of R. rhomboides with R. goodeyi, and a high nucleotide variation within cox1 gene sequences in these populations. Additional Illumina sequencing of DNA from individuals of the Dutch population revealed two variants of mitogenomes each of approximately 23 Kb in size, differing by about 9% and containing eleven protein coding genes, two ribosomal RNA genes and up to 29 transfer RNA genes. In addition to the first representative whole genome shotgun sequence datasets of the genus Rotylenchus, this study also provides the full length mitogenome and the ribosomal DNA sequences of R. goodeyi.

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Rare sequence variation and DNA methylation : effects on alcohol and tobacco use phenotypes

10.32469/10355/70042 ◽

2019 ◽

Author(s):

◽

Jacqueline Marisa Otto

Keyword(s):

Dna Methylation ◽

Tobacco Use ◽

Sequence Variation ◽

Rare Variants ◽

Cpg Islands ◽

Protein Coding ◽

University Of Missouri ◽

Rare Variation ◽

The University ◽

Regulatory Dna

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Alcohol and tobacco use and dependence are known to be influenced by the effects of common variants enriched in non-coding gene regulatory regions, as well as rare protein-coding variation. In contrast, the role of rare non-coding regulatory variation is unknown. Epigenetic factors such as DNA methylation also influence gene expression, and some of these effects are under genomic control. The current study investigated the effects of rare coding and non-coding variation in regions susceptible to DNA methylation, and whether differential levels of methylation mediated their effects in association with alcohol and tobacco use and dependence. Data from whole-genome sequencing and DNA methylation microarrays for participants in the UCSF Family Alcoholism Study (N = 1,852) were used for set-based tests of rare variation, region-based differential methylation, and epigenetic mediation in relation to quantitative measures of alcohol and tobacco use and DSM-IV dependence diagnoses. Rare variants in exonic and intronic regions, as well as CpG islands, were weighted by a measure of deleteriousness and were significantly associated with alcohol and tobacco use phenotypes. Similarly, differential levels of DNA methylation exhibited significant association with lifetime and current measures of use and dependence. However, there was a relative lack of evidence for epigenetic mediation of rare variation, likely due to a lack of power. Findings from the current study suggest that rare regulatory DNA sequence variation and differential levels of DNA methylation influence risk for alcohol and tobacco use, but whether there exists epigenetic mediation of rare variation requires larger sample sizes in future studies.

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