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Articles by Mark Blaxter
Chromosome-level genomes of scleractinian corals: gene prediction and functional annotation
Abstract Scleractinia (stony corals) are a diverse taxonomic order within the phylum Cnidaria, comprising more than 1,600 species described to date. Most of these corals play a key role as reef builders by secreting calcium carbonate, forming rigid skeletons that provide the structural foundation of tropical coral reef ecosystems.
Why the Earth BioGenome Project is a digital library of life
Professor, Julie Ann Wrigley Global Futures Laboratory, Arizona State University Programme Lead, Tree of Life Program, The Wellcome Trust Sanger Institute Biodiversity loss is accelerating with significant potential ramifications for food security, human health and economic stability across the world. Only about 1% of the DNA of all known animals, plants, fungi and protists has been sequenced, leading to a knowledge gap about how species adapt.
The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution - Nature
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Abstract Cell types are fundamental functional units that can be traced across the tree of life. Rapid advances in single-cell technologies, coupled with the phylogenetic expansion in genome sequencing, present opportunities for the molecular characterization of cells across a broad range of organisms. Despite these developments, our understanding of eukaryotic cell diversity remains limited and we are far from decoding this diversity from genome sequences.
By Arnau Sebé-Pedrós, Amos Tanay, Detlev Arendt, Stein Aerts, John Archibald Verified, Maria Arnone, Mark Blaxter, Phillip A. Cleves, Susana M. Coelho, Mafalda Dias, Casey Dunn, Anamaria Elek, Jonathan Frazer, Toni Gabaldón, Jesse Gillis, Roderic Guigó, Oliver Hobert, Allon M. Klein, Harris A. Lewin, Christopher Lowe, Jacob M. Musser, Lior Pachter, Irene Papatheodorou, Michael Passalacqua, Nikolaus Rajewsky, Seung Y. Rhee, Thomas Richards, Tatjana Sauka-Spengler, Lauren Saunders, Eve Seuntjens, Jordi Solana, Yuyao Song, Ulrich Technau, Bo Wang
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Nature
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Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly
Keywords genomics chromosome evolution sex chromosome genome assembly evolutionary biology Lepidoptera Introduction The rate of karyotypic evolution across the tree of life is remarkably low.
Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution
Abstract Myxozoans are obligate endoparasites that belong to the phylum Cnidaria. Compared to their closest free-living relatives, they have evolved highly simplified body plans and reduced genomes. Kudoa iwatai, for example, has lost upwards of two thirds of genes thought to have been present in its ancestors. However, little is known about myxozoan genome architecture because of a lack of sufficiently contiguous genome assemblies.
Oatk: a de novo assembly tool for complex plant organelle genomes
Abstract Plant organelle genomes, particularly the large mitochondrial genomes with intricate repetitive structures, present significant challenges for assembly. The advent of long-read sequencing technologies provides a transformative opportunity to generate complete genomes, but problems of resolving alternative structures remain. Here we introduce a novel tool for plant organelle genome assembly from high-accuracy long reads.
Diversity and specificity of molecular functions in cyanobacterial symbionts - Scientific Reports
Abstract Cyanobacteria are globally occurring photosynthetic bacteria notable for their contribution to primary production and production of toxins which have detrimental ecosystem impacts. Furthermore, cyanobacteria can form mutualistic symbiotic relationships with a diverse set of eukaryotes, including land plants, aquatic plankton and fungi.
High heteroplasmy is associated with low mitochondrial copy number and selection against non-synonymous mutations in the snail Cepaea nemoralis - BMC Genomics
We first assembled and annotated a reference C. nemoralis mitochondrial genome, using a snail from the matriline (C691, accession OP910114; Tables 1, 2; Figure S1). This genome has the expected full complement of 13 protein coding genes and 2 rRNA genes. It also has a full complement of annotated tRNA genes, unlike the original accession (U23045; [36, 37]), but with two copies of tRNA-Val (see next section).
Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution - Nature Communications
Abstract Theory predicts that compensatory genetic changes reduce negative indirect effects of selected variants during adaptive evolution, but evidence is scarce. Here, we test this in a wild population of Hawaiian crickets using temporal genomics and a high-quality chromosome-level cricket genome. In this population, a mutation, flatwing, silences males and rapidly spread due to an acoustically-orienting parasitoid.
Genome evolution in intracellular parasites: Microsporidia and Apicomplexa
INTRODUCTION In eukaryotic evolution, the transition to parasitism has occurred multiple times. In fact, this transition has occurred so many times, that Poulin (2011) suggested that the evolution of parasitism was inevitable, as all living organisms are concentrated fountains of the resources which are scarce in abiotic environments.
Specialization in Molecular Functions and Secondary Metabolite Production Potential in Cyanobacterial Symbionts
Abstract Cyanobacteria are globally occurring photosynthetic bacteria notable for their contribution to primary production and their production of toxins which have detrimental impacts on ecosystems. Beyond this, cyanobacteria can form mutualistic symbiotic relationships with a diverse set of eukaryotes, ranging from land plants to fungi.
Polyploidy is widespread in Microsporidia
Abstract Microsporidia are obligate intracellular eukaryotic parasites with an extremely broad host range. They have both economic and public health importance. Ploidy in microsporidia is variable, with a few species formally identified as diploid and one as polyploid. Given the increase in the number of studies sequencing microsporidian genomes, it is now possible to assess ploidy levels across all currently-explored microsporidian diversity.
Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map - Heredity
Abstract Molluscs are a highly speciose phylum that exhibits an astonishing array of colours and patterns, yet relatively little progress has been made in identifying the underlying genes that determine phenotypic variation. One prominent example is the land snail Cepaea nemoralis for which classical genetic studies have shown that around nine loci, several physically linked and inherited together as a ‘supergene’, control the shell colour and banding polymorphism.
plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets
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Phylogenomic analysis of Wolbachia genomes from the Darwin Tree of Life biodiversity genomics project
WO prophage insertions expand genome size Wolbachia can itself be infected by double-stranded DNA temperate bacteriophages, WO phage, which can integrate in the genome of its host as a prophage. Four modules are necessary for construction and function of phage particles during the lytic stage: head, baseplate, tail, and fibre, and inserted and pseudogenised WO phage can be identified and discriminated based on the presence and completeness of these components.
plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
New Tree of Life Gateway explores the evolution of life to aid conservation of biodiversity
Wellcome Open Research » Blog » New Tree of Life Gateway explores the evolution of life to aid conservation of biodiversity New Tree of Life Gateway explores the evolution of life to aid conservation of biodiversity Professor Mark Blaxter, Tree of Life Programme Lead at Wellcome Sanger Institute introduces the new Tree of life Gateway on Wellcome Open Research that launched today.
Building genomic infrastructure: Sequencing platinum‐standard reference‐quality genomes of all cetacean species
LETTER Phillip A. Morin Corresponding Author E-mail address: phillip.morin@noaa.gov https://orcid.org/0000-0002-3279-1519 Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, California Correspondence Phillip A Morin, Southwest Fisheries Science Center, 8901 La Jolla Shores Drive, La Jolla, CA 92037. Email: phillip.morin@noaa.gov Contribution: Conceptualization, Writing - original draft Search for more papers by this author Get access to the full version of this article.
Genome-wide methylation is modified by caloric restriction in Daphnia magna
BMC Genomics201920:197 https://doi.org/10.1186/s12864-019-5578-4 © The Author(s). 2019 Received: 28 June 2018 Accepted: 1 March 2019 Published: 8 March 2019 Abstract Background The degradation of epigenetic control with age is associated with progressive diseases of ageing, including cancers, immunodeficiency and diabetes.
Silent crickets reveal the genomic footprint of recent adaptive trait loss
Silent crickets reveal the genomic footprint of recent adaptive trait loss Sonia Pascoal, Judith E. Risse, Xiao Zhang, Mark Blaxter, Timothee Cezard, Richard J. Challis, Karim Gharbi, John Hunt, Sujai Kumar, Emma Langan, Xuan Liu, Jack G. Rayner, Michael G. Ritchie, Basten L. Snoek, Urmi Trivedi, Nathan Bailey bioRxiv 489526; doi: https://doi.org/10.1101/489526
Sex- and Gamete-Specific Patterns of X Chromosome Segregation in a Trioecious Nematode
Genetic Crosses Suggest Unorthodox Patterns of Meiotic X Chromosome Segregation that Are Both Sex and Gamete Specific During Hermaphrodite Oogenesis, Both X Chromosomes Appear to Segregate to the First Polar Body During Hermaphrodite Spermatogenesis, X Chromatids Appear to Separate Precociously in Meiosis I and Then Differentially Partition to the Functional Sperm Genotyping of X Chromosome SNP Markers Reveals Patterns of Chromosome Segregation in Female Oocyte Meiosis and Hermaphrodite...
Beyond DNA barcoding: the species description of the nematode Caenorhabditis monodelphis includes its whole genome sequence - BMC Series blog
DNA barcoding is now a standard part of the biodiversity toolkit. Nearly 20 years ago, the idea arose – simultaneously in several groups – that advances in DNA sequencing might make it possible to identify species cheaply and efficiently using small parts of their genomes. Despite early scepticisms, the DNA barcoding movement, driven by Paul Hebert and colleagues at the Biodiversity Institute of Ontario, has been a runaway success.
Reminder to deposit DNA sequences
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Eight things I learnt from #tardigate
Tardigrades, endearing eight legged minibeasts related to insects and spiders and also known as water bears or moss piglets, are among my favourite animals. In late November 2015, a colleague, Bob Goldstein, emailed me to say that he and his team were about to publish an analysis of the genome of the tardigrade Hypsibius dujardini.
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