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  • In the original article,Box 1 was not printed in its entirety, and two references were badly quoted in page 3 of the pdf and were missing in the reference list.

  • Genomics

    A deep dive into genome assemblies of non-vertebrate animals

    10.24072/pcjournal.128 - Peer Community Journal, Volume 2 (2022), article no. e29.

    Non-vertebrate species represent about 95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

  • Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity has been often reported in Fungi, which may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in detail for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de novo whole-genome assembly obtained from a new method of DNA extraction and long-reads sequencing Nanopore technology obtained from a Japanese isolate sampled in the native area of the species. The comparison with a recently published reference genome revealed stable gene and transposable elements (TEs) repertoires. We also showed that the C. parasitica genome is lowly compartmentalized, with a poor association between TEs and genes, such as those potentially involved in host interactions (i.e., genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high-quality assembled genomes, and questions the role of structural variations in the invasive success of this fungal pathogen species.

  • Geometric morphometrics revolutionized domestication studies through the precise quantification of the phenotype of ancient plant and animal remains. Geometric morphometrics allow for an increasingly detailed understanding of the past agrobiodiversity and our ability to characterize large scale ancient phenotypes has led to what can be named archaeophenomics : the large scale phenotyping of ancient remains. This review describes advances in the bioarchaeological study of domesticated species and their wild relatives where their phenomes are quantified through geometric morphometrics. The two main questions addressed by archaeophenomics are i) taxonomic identification, including domestication signature, and ii) the inference of the spatio-temporal agrobiodiversity dynamics. Archaeophenomics is a growing field in bioarchaeology of domestic species that will benefit in the near future from advances in artificial intelligence and from an increasing interest in multiproxy approaches combining morphometric data with e.g. isotopes or archaeogenomics.

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