Design of SNP Markers for Aldabra Giant Tortoises using ddRAD-seq

Abstract The Aldabra giant tortoise ( Aldabrachelys gigantea ) is one of only two remaining giant tortoise species worldwide. Captive-bred A. gigantea are being used in rewilding projects in the Western Indian Ocean to functionally replace the extinct endemic giant tortoise species and restore degraded island ecosystems. Furthermore, large-scale translocations may become necessary as rising sea levels threaten the only wild population on the low-lying Aldabra Atoll. Critical management decisions would be greatly facilitated by insights on the genetic structure of breeding populations. We used a double-digest restriction-associated DNA sequencing (ddRAD-seq) approach to identify single nucleotide polymorphisms (SNP) among the wild population and two additional captive populations of A. gigantea . A total of 149 unlinked, putatively neutral genome-wide SNPs were identified. The values of expected heterozygosity ranged from 0.32 to 0.5, whereas the minor allele frequency ranged from 0.20 to 0.5. These novel SNP markers will serve as useful tools for informing the conservation of A. gigantea .

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Design of SNP markers for Aldabra giant tortoises using low coverage ddRAD-seq

Conservation Genetics Resources ◽

10.1007/s12686-021-01225-4 ◽

2021 ◽

Author(s):

F. G. Çilingir ◽

D. Hansen ◽

A. Ozgul ◽

C. Grossen

Keyword(s):

Large Scale ◽

Wild Population ◽

Western Indian Ocean ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Sea Levels ◽

Breeding Populations ◽

Captive Populations ◽

Rising Sea Levels ◽

Low Coverage

AbstractThe Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two remaining giant tortoise species worldwide. Captive-bred A. gigantea are being used in rewilding projects in the Western Indian Ocean to functionally replace the extinct endemic giant tortoise species and restore degraded island ecosystems. Furthermore, large-scale translocations may become necessary as rising sea levels threaten the only wild population on the low-lying Aldabra Atoll. Critical management decisions would be greatly facilitated by insights on the genetic structure of breeding populations. We used a double-digest restriction-associated DNA sequencing (ddRAD-seq) approach to identify single nucleotide polymorphisms (SNP) among the wild population and two additional captive populations of A. gigantea. A total of 1674 unlinked, putatively neutral genome-wide SNPs were identified. The values of expected heterozygosity ranged from 0.33 to 0.5, whereas the minor allele frequency ranged from 0.20 to 0.5. These novel SNP markers will serve as useful tools for informing the conservation of A. gigantea.

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An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods

Scientific Reports ◽

10.1038/s41598-021-87244-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Juan Moles ◽

Shahan Derkarabetian ◽

Stefano Schiaparelli ◽

Michael Schrödl ◽

Jesús S. Troncoso ◽

...

Keyword(s):

Machine Learning ◽

Deep Sea ◽

Weddell Sea ◽

Nucleotide Polymorphisms ◽

Sea Levels ◽

Suitable Material ◽

Genetic Lineages ◽

Genome Wide ◽

Gastropod Mollusks ◽

Double Digestion

AbstractSampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for species in the family Antarctophilinidae. We also reevaluated the fossil record associated with this taxon to provide further insights into the origin of the group. Novel approaches to identify distinctive genetic lineages, including unsupervised machine learning variational autoencoder plots, were used to establish species hypothesis frameworks. In this sense, three undescribed species and a complex of cryptic species were identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further observed that the shallow waters around the Scotia Arc and on the continental shelf in the Weddell Sea present high endemism and diversity. In contrast, likely due to the glacial pressure during the Cenozoic, a deep-sea group with fewer species emerged expanding over great areas in the South-Atlantic Antarctic Ridge. Our study agrees on how diachronic paleoclimatic and current environmental factors shaped Antarctic communities both at the shallow and deep-sea levels, promoting Antarctica as the center of origin for numerous taxa such as gastropod mollusks.

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Secure large-scale genome-wide association studies using homomorphic encryption

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1918257117 ◽

2020 ◽

Vol 117 (21) ◽

pp. 11608-11613 ◽

Cited By ~ 1

Author(s):

Marcelo Blatt ◽

Alexander Gusev ◽

Yuriy Polyakov ◽

Shafi Goldwasser

Keyword(s):

Large Scale ◽

Homomorphic Encryption ◽

Association Studies ◽

Genome Wide Association ◽

Single Server ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

User Interactions ◽

Individual Level ◽

Genome Wide

Genome-wide association studies (GWASs) seek to identify genetic variants associated with a trait, and have been a powerful approach for understanding complex diseases. A critical challenge for GWASs has been the dependence on individual-level data that typically have strict privacy requirements, creating an urgent need for methods that preserve the individual-level privacy of participants. Here, we present a privacy-preserving framework based on several advances in homomorphic encryption and demonstrate that it can perform an accurate GWAS analysis for a real dataset of more than 25,000 individuals, keeping all individual data encrypted and requiring no user interactions. Our extrapolations show that it can evaluate GWASs of 100,000 individuals and 500,000 single-nucleotide polymorphisms (SNPs) in 5.6 h on a single server node (or in 11 min on 31 server nodes running in parallel). Our performance results are more than one order of magnitude faster than prior state-of-the-art results using secure multiparty computation, which requires continuous user interactions, with the accuracy of both solutions being similar. Our homomorphic encryption advances can also be applied to other domains where large-scale statistical analyses over encrypted data are needed.

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Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation

Nucleic Acids Research ◽

10.1093/nar/gkz854 ◽

2019 ◽

Vol 48 (D1) ◽

pp. D659-D667 ◽

Cited By ~ 2

Author(s):

Wenqian Yang ◽

Yanbo Yang ◽

Cecheng Zhao ◽

Kun Yang ◽

Dongyang Wang ◽

...

Keyword(s):

Large Scale ◽

Association Studies ◽

Genotype Imputation ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

High Quality ◽

Single Nucleotide ◽

Genome Wide ◽

Whole Genome Resequencing ◽

Missing Genotypes

Abstract Animal-ImputeDB (http://gong_lab.hzau.edu.cn/Animal_ImputeDB/) is a public database with genomic reference panels of 13 animal species for online genotype imputation, genetic variant search, and free download. Genotype imputation is a process of estimating missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs) and thus can be widely used in large-scale genome-wide association studies (GWASs) using relatively inexpensive and low-density SNP arrays. However, most animals except humans lack high-quality reference panels, which greatly limits the application of genotype imputation in animals. To overcome this limitation, we developed Animal-ImputeDB, which is dedicated to collecting genotype data and whole-genome resequencing data of nonhuman animals from various studies and databases. A computational pipeline was developed to process different types of raw data to construct reference panels. Finally, 13 high-quality reference panels including ∼400 million SNPs from 2265 samples were constructed. In Animal-ImputeDB, an easy-to-use online tool consisting of two popular imputation tools was designed for the purpose of genotype imputation. Collectively, Animal-ImputeDB serves as an important resource for animal genotype imputation and will greatly facilitate research on animal genomic selection and genetic improvement.

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Tropical Cyclone-Induced Hazards Caused by Storm Surges and Large Waves on the Coast of China

Geosciences ◽

10.3390/geosciences9030131 ◽

2019 ◽

Vol 9 (3) ◽

pp. 131 ◽

Cited By ~ 2

Author(s):

Zai-Jin You

Keyword(s):

Large Scale ◽

Storm Surges ◽

Chinese Economy ◽

Coastal Hazards ◽

Economic Losses ◽

Sea Levels ◽

The North ◽

Coastal Waves ◽

Storm Wave ◽

Rising Sea Levels

The mainland coast of China is about 18,000 km long and houses about 70% of China’s largest cities and 50% of its population. For the last few decades, the rapid growth of the Chinese economy has resulted in extensive development of the coastal infrastructure and property, large-scale expansion of coastal ports, excessive reclamation of coastal land, and a significant increase in the coastal population. Previous studies have indicated that tropical cyclones (TCs) have struck the coast of China at a higher frequency and intensity, and TC-induced coastal hazards have resulted in heavy human losses and huge losses to the Chinese coastal economy. In analyzing the long-term and most recent coastal hazard data collected on the coast of China, this study has found that TC-induced storm surges are responsible for 88% of the direct coastal economic losses, while TC-induced large coastal waves have caused heavy loss of human lives, and that the hazard-caused losses are shown to increase spatially from the north to south, peak in the southern coastal sector, and well correlate to storm wave energy flux. The frequency and intensity of coastal hazards on the coast of China are expected to increase in response to future changing TC conditions and rising sea levels. A simple two-parameter conceptual model is also presented for the assessment of coastal inundation and erosion hazards on the coast of China.

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De Novo Transcriptomic Resources in the Brain of Vespa velutina for Invasion Control

Insects ◽

10.3390/insects11020101 ◽

2020 ◽

Vol 11 (2) ◽

pp. 101

Author(s):

Miao Wang ◽

Hanyu Li ◽

Huoqing Zheng ◽

Liuwei Zhao ◽

Xiaofeng Xue ◽

...

Keyword(s):

Large Scale ◽

Target Genes ◽

De Novo ◽

Transcriptome Profiling ◽

Molecular Study ◽

Snp Markers ◽

Nucleotide Polymorphisms ◽

Illumina Hiseq ◽

Vespa Velutina ◽

Genes Encoding

The invasion of Vespa velutina presents a great threat to the agriculture economy, the ecological environment, and human health. An effective strategy for this hornet control is urgently required, but the limited genome information of Vespa velutina restricts the application of molecular-genomic tools for targeted hornet management. Therefore, we conducted large-scale transcriptome profiling of the hornet brain to obtain functional target genes and molecular markers. Using an Illumina HiSeq platform, more than 41 million clean reads were obtained and de novo assembled into 182,087 meaningful unigenes. A total of 56,400 unigenes were annotated against publicly available protein sequence databases and a set of reliable Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNP) markers were developed. The homologous genes encoding crucial behavior regulation factors, odorant binding proteins (OBPs), and vitellogenin, were also identified from highly expressed transcripts. This study provides abundant molecular targets and markers for invasive hornet control and further promotes the genetic and molecular study of Vespa velutina.

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Development and Characterization of PCR Markers in Cucumber

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.127.4.545 ◽

2002 ◽

Vol 127 (4) ◽

pp. 545-557 ◽

Cited By ~ 51

Author(s):

Gennaro Fazio ◽

Jack E. Staub ◽

Sang Min Chung

Keyword(s):

Large Scale ◽

Cost Effective ◽

Snp Markers ◽

Yield Component ◽

Nucleotide Polymorphisms ◽

Pcr Markers ◽

Dinucleotide Repeats ◽

Sequence Characterized Amplified Region ◽

Tetranucleotide Repeats ◽

Multiple Lateral Branching

Highly polymorphic microsatellites or simple sequence repeat (SSR), along with sequence characterized amplified region (SCAR) and single nucleotide polymorphisms (SNP), markers are reliable, cost-effective, and amenable for large scale analyses. Molecular polymorhisms are relatively rare in cucumber (Cucumis sativus L.) (3% to 8%). Therefore, experiments were designed to develop SSR, SCAR and SNP markers, and optimize reaction conditions for PCR. A set of 110 SSR markers was constructed using a unique, strategically applied methodology that included the GeneTrapper (Life Technologies, Gaithersburg, Md.) kit to select plasmids harboring microsatellites. Of these markers, 58 (52%) contained dinucleotide repeats (CT, CA, TA), 21 (19%) possessed trinucleotide repeats (CTT, ATT, ACC, GCA), 3 (2.7%) contained tetranucleotide repeats (TGCG, TTAA, TAAA), 4 (3.6%) enclosed pentanucleotide repeat (ATTTT, GTTTT, GGGTC, AGCCC), 3 (2.7%) contained hexanucleotide repeats (CCCAAA, TAAAAA, GCTGGC) and 21 possessed composite repeats. Four SCARs (L18-3 SCAR, AT1-2 SCAR, N6-A SCAR, and N6-B SCAR) and two PCR markers based on SNPs (L18-2H19 A and B) that are tightly linked to multiple lateral branching (i.e., a yield component) were also developed. The SNP markers were developed from otherwise monomorphic SCAR markers, producing genetically variable amplicons. The markers L18-3 SCAR and AT1-2 SCAR were codominant. A three-primer strategy was devised to develop a codominant SCAR from a sequence containing a transposable element, and a new codominant SCAR product was detected by annealing temperature gradient (ATG) PCR. The use of a marker among laboratories can be enhanced by methodological optimization of the PCR. The utility of the primers developed was optimized by ATG-PCR to increase reliability and facilitate technology transfer. This array of markers substantially increases the pool of genetic markers available for genetic investigation in Cucumis.

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Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome

Nucleic Acids Research ◽

10.1093/nar/gkaa1269 ◽

2021 ◽

Vol 49 (3) ◽

pp. 1497-1516

Author(s):

Wilfried M Guiblet ◽

Marzia A Cremona ◽

Robert S Harris ◽

Di Chen ◽

Kristin A Eckert ◽

...

Keyword(s):

Large Scale ◽

Nucleotide Substitution ◽

Genetic Diseases ◽

Nucleotide Polymorphisms ◽

Dna Structures ◽

Cellular Processes ◽

Genome Wide ◽

Dna Types ◽

Flanking Regions

Abstract Approximately 13% of the human genome can fold into non-canonical (non-B) DNA structures (e.g. G-quadruplexes, Z-DNA, etc.), which have been implicated in vital cellular processes. Non-B DNA also hinders replication, increasing errors and facilitating mutagenesis, yet its contribution to genome-wide variation in mutation rates remains unexplored. Here, we conducted a comprehensive analysis of nucleotide substitution frequencies at non-B DNA loci within noncoding, non-repetitive genome regions, their ±2 kb flanking regions, and 1-Megabase windows, using human-orangutan divergence and human single-nucleotide polymorphisms. Functional data analysis at single-base resolution demonstrated that substitution frequencies are usually elevated at non-B DNA, with patterns specific to each non-B DNA type. Mirror, direct and inverted repeats have higher substitution frequencies in spacers than in repeat arms, whereas G-quadruplexes, particularly stable ones, have higher substitution frequencies in loops than in stems. Several non-B DNA types also affect substitution frequencies in their flanking regions. Finally, non-B DNA explains more variation than any other predictor in multiple regression models for diversity or divergence at 1-Megabase scale. Thus, non-B DNA substantially contributes to variation in substitution frequencies at small and large scales. Our results highlight the role of non-B DNA in germline mutagenesis with implications to evolution and genetic diseases.

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Inhabiting the machine

10.26686/wgtn.17011988.v1 ◽

2021 ◽

Author(s):

◽

George Goodwin

Keyword(s):

Financial Management ◽

Urban Poor ◽

Tamil Nadu ◽

Architectural Design ◽

Large Scale ◽

Sea Levels ◽

Civil Society Organisations ◽

Slum Dwellers ◽

Basic Services ◽

Rising Sea Levels

<p>Like many cities across India, Chennai (capital of Tamil Nadu) has two tiers of slums — those with official government recognition and those without. Slums with official government recognition are then further categorised to either be objectionable or unobjectionable. Recognised slums receive government funding to provide new tenements and basic services on site. But recent studies have shown that 4.8 sq km of the Chennai metropolitan area are comprised of either unrecognised or objectionable slums. The current government strategy is to forcibly relocate families from unrecognised or objectionable slums to large-scale, high-rise settlement colonies on the distant outskirts of Chennai. Numerous civil society organisations, however, have documented that eviction and relocation results in extreme trauma for these families. The Transparent Chennai Project at the Institute for Financial Management and Research in Chennai argues that: “A far more reasonable strategy would be to once again implement the Tamil Nadu Slum Clearance Act in the spirit that it was written, and start to recognise slums and improve them in situ” (Raman and Narayan). This thesis proposes that architectural design can improve conditions for Chennai’s urban poor without resorting to forced relocation. It argues that a new framework for slum housing can be designed that is capable of: protecting slum dwellers from environmental disasters such as rising sea levels, storm surge, and tsunamis; mitigating environmental pollution to improve hygiene; and providing economic sources of fresh water and energy through sustainable means. It further argues that this framework can be achieved in a culturally sensitive manner by acknowledging traditional and historically significant regional architectural typologies.</p>

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COPHYLOGENETIC ANALYSES OF TRACHYMYRMEX ANT-FUNGAL SPECIFICITY: ‘ONE TO ONE WITH SOME EXCEPTIONS’

10.22541/au.162211773.35216786/v1 ◽

2021 ◽

Author(s):

Katherine Beigel ◽

Alix Matthews ◽

Katrin Kellner ◽

Christine Pawlik ◽

Matthew Greenwold ◽

...

Keyword(s):

Large Scale ◽

Phylogenetic Analyses ◽

Marker Genes ◽

Snp Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

Native Populations ◽

Symbiotic Fungi ◽

Fungal Specificity

Over the past few decades, large-scale phylogenetic analyses of fungus-gardening ants and their symbiotic fungi have depicted strong concordance among major clades of ants and their symbiotic fungi, yet within clades, fungus sharing is somewhat widespread among unrelated ant lineages. These symbioses are thought to be explained by a diffuse coevolution model within major clades. Understanding horizontal exchange within clades has been limited by conventional genetic markers that lack both interspecific and geographic variation. To examine whether reports of horizontal exchange was indeed symbiont sharing or an issue of employing relatively uninformative molecular markers, samples of Trachymyrmex arizonensis and Trachymyrmex pomonae and their fungi were collected from native populations in Arizona and genotyped using conventional marker genes and genome-wide single nucleotide polymorphisms (SNPs). Conventional markers of the fungal symbionts generally exhibited cophylogenetic patterns that were consistent with some symbiont sharing, but most fungal clades had low support. SNP analysis, in contrast, indicated that each ant species exhibited fidelity to its own fungal subclade with only one instance of a colony growing a fungus that was otherwise associated with a different ant species. This evidence supports a pattern of codivergence between Trachymyrmex species and their fungi, and thus a diffuse coevolutionary model may not accurately predict symbiont exchange. These results suggest that fungal sharing across host species in these symbioses may be less extensive than previously thought.

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