Anchoring the CerEla1.0 Genome Assembly to Red Deer (Cervus elaphus) and Cattle (Bos taurus) Chromosomes and Specification of Evolutionary Chromosome Rearrangements in Cervidae

The family Cervidae groups a range of species with an increasing economic significance. Their karyotypes share 35 evolutionary conserved chromosomal segments with cattle (Bos taurus). Recent publication of the annotated red deer (Cervus elaphus) whole genome assembly (CerEla1.0) has provided a basis for advanced genetic studies. In this study, we compared the red deer CerEla1.0 and bovine ARS-UCD1.2 genome assembly and used fluorescence in situ hybridization with bovine BAC probes to verify the homology between bovine and deer chromosomes, determined the centromere-telomere orientation of the CerEla1.0 C-scaffolds and specified positions of the cervid evolutionary chromosome breakpoints. In addition, we revealed several incongruences between the current deer and bovine genome assemblies that were shown to be caused by errors in the CerEla1.0 assembly. Finally, we verified the centromere-to-centromere orientation of evolutionarily fused chromosomes in seven additional deer species, giving a support to previous studies on their chromosome evolution.

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Metagenomic analysis of the cow, sheep, reindeer and red deer rumen

Scientific Reports ◽

10.1038/s41598-021-81668-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Laura Glendinning ◽

Buğra Genç ◽

R. John Wallace ◽

Mick Watson

Keyword(s):

Cervus Elaphus ◽

Rangifer Tarandus ◽

Red Deer ◽

Bos Taurus ◽

Novel Species ◽

Ovis Aries ◽

Metagenomic Analysis ◽

Reference Dataset ◽

Microbial Genomes ◽

Ruminant Species

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A highly contiguous nuclear genome assembly of the mandarinfish Synchiropus splendidus (Syngnathiformes: Callionymidae)

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab306 ◽

2021 ◽

Author(s):

Martin Stervander ◽

William A Cresko

Keyword(s):

Genome Assembly ◽

Nuclear Genome ◽

Phylogenetic Position ◽

Blue Color ◽

Long Reads ◽

The Family ◽

Commercially Important ◽

Genomic Resource ◽

Genome Assemblies ◽

Important Fish

Abstract The fish order Syngnathiformes has been referred to as a collection of misfit fishes, comprising commercially important fish such as red mullets as well as the highly diverse seahorses, pipefishes, and seadragons—the well-known family Syngnathidae, with their unique adaptations including male pregnancy. Another ornate member of this order is the species mandarinfish. No less than two types of chromatophores have been discovered in the spectacularly colored mandarinfish: the cyanophore (producing blue color) and the dichromatic cyano-erythrophore (producing blue and red). The phylogenetic position of mandarinfish in Syngnathiformes, and their promise of additional genetic discoveries beyond the chromatophores, made mandarinfish an appealing target for whole genome sequencing. We used linked sequences to create synthetic long reads, producing a highly contiguous genome assembly for the mandarinfish. The genome assembly comprises 483 Mbp (longest scaffold 29 Mbp), has an N50 of 12 Mbp, and an L50 of 14 scaffolds. The assembly completeness is also high, with 92.6% complete, 4.4% fragmented, and 2.9% missing out of 4,584 BUSCO genes found in ray-finned fishes. Outside the family Syngnathidae, the mandarinfish represents one of the most contiguous syngnathiform genome assemblies to date. The mandarinfish genomic resource will likely serve as a high-quality outgroup to syngnathid fish, and furthermore for research on the genomic underpinnings of the evolution of novel pigmentation.

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The hormone neuroparsin seems essential in Lepidoptera but not in domesticated silkworms

10.1101/716746 ◽

2019 ◽

Author(s):

Jan A. Veenstra

Keyword(s):

Bombyx Mori ◽

Genome Assembly ◽

Galleria Mellonella ◽

Sequence Similarity ◽

Neuroendocrine Cells ◽

Primary Sequence ◽

Genome Assemblies ◽

Limited Sequence ◽

Wax Moth

AbstractThe primary sequence of the Arthropod neurohormone neuroparsin is so variable that so far no orthologs from moths and butterflies have been characterized, even though classical neurosecretory stains identify cells that are homologous to those producing this hormone in other insect species. Here Lepidopteran cDNAs showing limited sequence similarity to other insect neuroparsins are described. That these cDNAs do indeed code for authentic neuroparsins was confirmed by in situ hybridization in the wax moth, Galleria mellonella, which labeled the neuroparsin neuroendocrine cells. Although in virtually all genome assemblies from Lepidoptera a neuroparsin gene could be identified, the genome assembly from the silkworm, Bombyx mori, has a neuroparsin gene containing a 16 nucleotide deletion that renders this gene nonfunctional. Although only a small number of all silkworm strains carry this deletion, it suggests that the domestication of the silkworm has rendered the function of this neurohormone dispensable.

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Complete mitochondrial genome sequence of a Hungarian red deer (Cervus elaphus hippelaphus) from high-throughput sequencing data and its phylogenetic position within the family Cervidae

Acta Biologica Hungarica ◽

10.1556/018.67.2016.2.2 ◽

2016 ◽

Vol 67 (2) ◽

pp. 133-147 ◽

Cited By ~ 5

Author(s):

Krisztián Frank ◽

Endre Barta ◽

Nóra Á. Bana ◽

János Nagy ◽

Péter Horn ◽

...

Keyword(s):

Mitochondrial Genome ◽

High Throughput ◽

Cervus Elaphus ◽

Red Deer ◽

High Throughput Sequencing ◽

Complete Mitochondrial Genome ◽

Phylogenetic Position ◽

Sequencing Data ◽

High Throughput Sequencing Data ◽

The Family

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Metagenomic analysis of the cow, sheep, reindeer and red deer rumen

10.1101/2020.02.12.945139 ◽

2020 ◽

Author(s):

Laura Glendinning ◽

Buğra Genç ◽

R John Wallace ◽

Mick Watson

Keyword(s):

Cervus Elaphus ◽

Rangifer Tarandus ◽

Red Deer ◽

Bos Taurus ◽

Ovis Aries ◽

Metagenomic Analysis ◽

Link Type ◽

Ruminant Species ◽

European Nucleotide Archive ◽

Core Set

AbstractThe rumen microbiota comprises a community of microorganisms which specialise in the degradation of complex carbohydrates from plant-based feed. These microbes play a highly important role in ruminant nutrition and could also act as sources of industrially useful enzymes. In this study, we performed a metagenomic analysis of samples taken from the ruminal contents of cattle (Bos Taurus), sheep (Ovis aries), reindeer (Rangifer tarandus) and red deer (Cervus elaphus). We constructed 391 metagenome-assembled genomes originating from 16 microbial phyla. We compared our genomes to other publically available microbial genomes and found that they contained 279 novel species. We also found significant differences between the microbiota of different ruminant species in terms of the abundance of microbial taxonomies, carbohydrate-active enzyme genes and KEGG orthologs. However, we found that the vast majority of carbohydrate-active enzymes were present in all of our sample types, which may indicate that there is a core set of these enzymes which are present across ruminants and are independent of diet and environmental conditions. We present a dataset of rumen-derived genomes which in combination with other publicly-available rumen genomes can be used as a reference dataset in future metagenomic studies.Data SummaryThe paired-read fastq files supporting the conclusions of this article are available in the European Nucleotide Archive repository (https://www.ebi.ac.uk/ena/browser/view/PRJEB34458). The RUG fasta files supporting the conclusions of this article are available in the Edinburgh DataShare repository (https://doi.org/10.7488/ds/2640).

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