[PDF] The axolotl genome and the evolution of key tissue formation regulators | Semantic Scholar (2024)

The high‐quality genome of the Asiatic toad will provide a solid foundation to understand the genetic basis of its many biological processes and reveal a dynamic evolution of olfactory and vomeronasal receptor gene families which was likely driven by the water‐to‐land transition.

A highly contiguous long-read based genome assembly for the most successful temperate invasive fish, the benthic round goby, is reported, and gene families that may promote its impressive ecological success are analyzed and a recurring theme across all analyzed gene families are gene expansions.

To better understand the immune response in axolotl, the immunoglobulin loci of A. mexicanum share the same general genome architecture as most studied tetrapods and local size restrictions indicate evolutionary constraints likely to be imposed by high transcriptional demand of certain Ig genes, as well as the V(D)J recombination over very long genomic distance ranges.

This study reveals skeletal muscle is barely required for the guidance of other cells, as well the patterning in complex tissue regeneration in axolotls, and provides refined views of the roles of muscle cell in vertebrate appendage regeneration.

The chromosome-scale assembly of the giant, 32 Gb axolotl genome is described and it is shown that gene regulation occurs over very large genomic distances and that mitotic chromosomes are packaged efficiently.

A broader sampling of species using next-generation sequencing approaches is needed to reveal shared and unique mechanisms of regeneration, and more generally, the evolutionary history of salamander limb regeneration.

The evolutionary context in which salamanders emerged is covered, and the varieties of mechanisms deployed during salamander regeneration are outlined, and how these mechanisms are currently being explored and how they have advanced the understanding of animal regeneration.

Functional enrichment analyses underline the presence of common pathways between regenerative and nonregenerative stages, cell proliferation and its regulation associated pathways, immune system related pathways and muscle tissue and ECM remodeling and degradation pathways were represented at different rate between both stages.

This study evaluates the encoding genetic sequences and provides the first transcriptome assembly of Yenyuan stream salamander based on mixed samples from the liver, spermary, muscle and spleen tissues, and constructed a robust phylogenetic tree based on 56 single-copy orthologues, which indicates that based on phylogenetic position, the Yenyua streamsalamander presents the closest relationship with the Chinese giant salamanders of the investigated vertebrates.

The establishment of the first colony of axolotls in Colombia to study tissue regeneration and the perspectives on the use A. mexicanum as a model organism in Colombia are discussed emphasizing its possible uses in regeneration and developmental biology.

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This report reports the first successful assembly of T. aestivum, using deep sequencing coverage from a combination of short Illumina reads and very long Pacific Biosciences reads, and represents by far the most complete and contiguous assembly of the wheat genome to date.

This assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.

The 22-gigabase genome of loblolly pine is sequenced using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences, which generated approximately 12-fold coverage in long reads using the MaSuRCA mega-reads assembly algorithm.

This year's highlights include newly designed home and gateway pages; a new ‘multi-region’ track display configuration for exon-only, gene-only and custom regions visualization; new genome browsers for three species; eight updated genome assemblies; extended support for new data types such as CRAM, RNA-seq expression data and long-range chromatin interaction pairs; and the unveiling of a new supported mirror site in Japan.

VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH and is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging.

MGEScan is presented, a user-friendly system that combines these two programs with a Galaxy workflow system accelerated with MPI and Python threading on compute clusters, and visualizes the custom annotation tracks for mobile genetic elements in public genome browsers.

Comparison of RNA-seq transcriptome profiling studies in three regenerative animal models reveals a common miRNA-regulated genetic network of blastema genes, which could serve as a foundation for future functional studies to examine the process of natural cellular reprogramming in an injury context.

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