Tag: RAD-seq

Revolutionizing urban greening: multispectral | EurekAlert!

Ornamental plants, valued for their varied morphological characteristics, are increasingly used in urban greening initiatives such as rooftop greening. But this application presents challenges like limited soil depth and no irrigation, requiring plants such as the Phedimus species, known for their resilience to these conditions. Current research focuses on understanding the genetic…

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Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet’s whelk [PeerJ]

Introduction Rapidly advancing next generation sequencing technologies such as whole genome sequencing, genotyping-in-thousands by sequencing (GT-seq), and restriction-site-associated DNA sequencing (RAD-seq), are becoming more available and affordable for non-model organisms (Park & Kim, 2016; Ellegren, 2014; Van Wyngaarden et al., 2017; Bootsma et al., 2020). However, applying these technologies to…

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RAD-Seq analysis of wild Japanese garlic (Allium macrostemon Bunge) growing in Japan revealed that this neglected crop was previously actively utilized

Allium macrostemon Bunge, commonly referred to as “no-biru” in Japan, is a widespread wild onion species found across the country. Despite being deeply entwined in ancient Japanese culture, it remains an underutilized crop in Japan. Determining the origins of its domestic populations and understanding their genetic composition is crucial to…

Continue Reading RAD-Seq analysis of wild Japanese garlic (Allium macrostemon Bunge) growing in Japan revealed that this neglected crop was previously actively utilized

Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses.

Abstract Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups. Both nuclear and plastome…

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RADseq data analysis course

Dear all, there are still a few seats available for the upcoming RADseq data analysis course! Dates: online October 30th – November 3rd Website: www.physalia-courses.org/courses-workshops/course16/ Our course will introduce you to various approaches for obtaining reduced representation genome sequencing data, with a special focus on data analysis using Stacks. We’ll…

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Characterization and organelle genome sequencing of Pyropia species from Myanmar

Yang, L. E. et al. Redefining Pyropia (Bangiales, Rhodophyta): Four new genera, resurrection of Porphyrella and description of Calidia pseudolobata sp. Nov. from China. J. Phycol. 56, 862–879 (2020). Article  CAS  PubMed  Google Scholar  Mumford Jr, T. F. Porphyra as Food: Cultivation and Economics in Algae and Human Affairs (ed….

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Isolation and characterization of 32 SNP markers in Spinibarbus hollandi based on restriction site-associated DNA sequencing (RADseq)

Spinibarbus hollandi (Cyprinidae, Barbinae) is an economically important species and widely distributed in numbers of rivers throughout South China. However, wild S. hollandi resources have declined sharply in recent years as a result of over fishing, environmental pollution and other human disturbance. Therefore, it is extremely urgent to protect germplasm…

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The meaning of wild: Genetic and adaptive consequences from large-scale releases of domestic mallards

Grabenstein, K. C. & Taylor, S. A. Breaking barriers: causes, consequences, and experimental utility of human-mediated hybridization. Trends Ecol. Evol. 33, 198–212 (2018). Article  PubMed  Google Scholar  Crispo, E., Moore, J. S., Lee‐Yaw, J. A., Gray, S. M. & Haller, B. C. Broken barriers: human‐induced changes to gene flow and…

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RADseq data analysis with Stacks

News:Course – RADseq data analysis with Stacks 0 Dear all, We are excited to announce our upcoming course on “RAD-SEQ DATA ANALYSIS” that will take place online from 30th October to 3rd November 2023. Course website: www.physalia-courses.org/courses-workshops/course16/ This course is designed to introduce you to various approaches for obtaining reduced…

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Tracing the introduction of the invasive common myna using population genomics

Acclimatisation (6 January 1877) Southland Times. Page 2. paperspast.natlib.govt.nz/newspapers/ST18770105.2.7. Accessed 21 January 2022 Adamack AT, Gruber B (2014) PopGenReport: simplifying basic population genetic analyses in R. Methods Ecol Evol 5:384–387. doi.org/10.1111/2041-210x.12158 Article  Google Scholar  Andrews S (2010) FastQC. A quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc/ Andrews KR,…

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Virtual RAD-seq Analysis Workshop!

News:Virtual RAD-seq Analysis Workshop! 0 The Computational Biology Core at the University of Connecticut’s Institute for Systems Genomics is offering a virtual RAD-seq analysis workshop April 17-20 2023. The workshop will cover an introduction to linux and high performance computing before going through a complete analysis starting with raw reads…

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Investigating the genetic basis of vertebrate dispersal combining RNA-seq, RAD-seq and quantitative genetics

Although animal dispersal is known to play key roles in ecological and evolutionary processes such as colonization, population extinction and local adaptation, little is known about its genetic basis, particularly in vertebrates. Untapping the genetic basis of dispersal should deepen our understanding of how dispersal behaviour evolves, the molecular mechanisms…

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Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes

Luo, M. C. et al. Synteny analysis in rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials. BMC Genom. 16, 707 (2015). Article  Google Scholar  Martinez-Garcia, P. J. et al. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of…

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Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe

Charlesworth, B. & Charlesworth, D. Population genetics from 1966 to 2016. Heredity 118, 2–9 (2017). CAS  Google Scholar  Orsini, L., Vanoverbeke, J., Swillen, I., Mergeay, J. & Meester, L. Drivers of population genetic differentiation in the wild: Isolation by dispersal limitation, isolation by adaptation and isolation by colonization. Mol. Ecol….

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Best BLAST hit alone cannot be used as evidence of fraud

Blanco-Fernandez, C. et al. Fraud in highly appreciated fish detected from DNA in Europe may undermine the development goal of sustainable fishing in Africa. Sci. Rep. 11, 11423. doi.org/10.1038/s41598-021-91020-w (2021). Article  ADS  CAS  Google Scholar  Lewis, S. G. & Boyle, M. The expanding role of traceability in seafood: Tools and…

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Tiny crustacean reveals deepest parts of oceans like isolated islands

A tiny crustacean measuring just three centimetres in length is helping scientists unlock one of the most perplexing questions of the oceans’ hadal zone–how isolated are the animals that live in our deepest ocean trenches? A new paper Barriers to gene flow in the deepest ocean ecosystem: Evidence from global population…

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Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq

The cultivated peanut (Arachis hypogaea L.) is an important oil crop but has a narrow genetic diversity. Molecular markers can be used to probe the genetic diversity of various germplasm. In this study, the restriction site associated DNA (RAD) approach was utilized to sequence 31 accessions of Taiwanese peanut germplasm,…

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Genetic diversity of loquat (Eriobotrya japonica) revealed using RAD-Seq SNP markers & More Science News

Our research analyzed the genetic diversity of 95 cultivars and strains of loquat collected from everywhere in the world. On the premise of the evaluation of the inhabitants construction of 19 Chinese loquat cultivars and strains by RAD-Seq, Hubei Province in China has been recommended as the middle of origin…

Continue Reading Genetic diversity of loquat (Eriobotrya japonica) revealed using RAD-Seq SNP markers & More Science News

Read counts an order of magnitude higher on one chromosome

Read counts an order of magnitude higher on one chromosome 3 Hi, I am having an issue with a sequencing run that when demultiplexed, aligned, and filtered each individual has 1-2 million reads, but these reads are predominantly on one chromosome. For background these are oncorhynchus mykiss and o. clarki…

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Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data

Introduction Incipient species are critical for evolutionary biologists to study speciation, but they also challenge taxonomy due to gene flow or ancestral polymorphism. The former and contrasting population size lead to larger intraspecific than interspecific variations, a phenomenon called the species-definition anomaly zone (Jiao and Yang, 2021). The latter results…

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Detection of candidate gene LsACOS5 and development of InDel marker for male sterility by ddRAD-seq and resequencing analysis in lettuce

Ryder, E. J. Lettuce, Endive and Chicory (CABI Publishing, 1999). Google Scholar  Seki, K. et al. A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.). Hortic. Res. 7, 1–14 (2020). Article  Google Scholar  Odland,…

Continue Reading Detection of candidate gene LsACOS5 and development of InDel marker for male sterility by ddRAD-seq and resequencing analysis in lettuce

Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs

1. Thompson, J. N. & Pellmyr, O. Evolution of oviposition behavior and host preference in Lepidoptera. Annu. Rev. Entomol. 36, 65–89 (1991). Article  Google Scholar  2. Bowers, M. D. Iridoid glycosides and host-plant specificity in larvae of the buckeye butterfly, Junonia coenia (Nymphalidae). J. Chem. Ecol. 10, 1567–1577 (1984). CAS …

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