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

Miluse Vozdova,Svatava Kubickova,Halina Cernohorska,Jan Fröhlich,Jiri Rubes

doi:10.3390/ani11092614

Miluse Vozdova, Svatava Kubickova + Show 3 more

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https://doi.org/10.3390/ani11092614

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Abstract

Simple SummaryThe red deer (Cervus elaphus) de novo genome assembly (CerEla1.0) has provided a great resource for genetic studies in various deer species. In this study, we used gene order comparisons between C. elaphus CerEla1.0 and B. taurus ARS-UCD1.2 genome assemblies and fluorescence in situ hybridization (FISH) with bovine BAC probes to verify the red deer-bovine chromosome relationships and anchor the CerEla1.0 C-scaffolds to karyotypes of both species. We showed the homology between bovine and deer chromosomes and determined the centromere-telomere orientation of the CerEla1.0 C-scaffolds. Using a set of BAC probes, we were able to narrow the positions of evolutionary chromosome breakpoints defining the family Cervidae. In addition, we revealed several errors in the current CerEla1.0 genome assembly. Finally, we expanded our analysis to other Cervidae and confirmed the locations of the cervid evolutionary fissions and orientation of the fused chromosomes in eight cervid species. Our results can serve as a basis for necessary improvements of the red deer genome assembly and provide support to other genetic studies 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.

Highlights

The family Cervidae (Ruminantia) groups more than fifty extant deer species, including species with growing economic importance
Fissions of several ancestral pecoran chromosomes conserved in Bos taurus (BTA, 2n = 60) as BTA1, 2, 5, 6, 8, 9 and intrachromosomal rearrangements of the BTA1 orthologue and the X chromosome were detected in Cervidae using bovine BAC (Bacterial Artificial Chromosome) probes [13,14]
Samples of whole peripheral blood of cattle (Bos taurus) and eight deer species including the red deer (C. elaphus) were obtained from captive born animals held in the Prague zoological garden and/or in deer enclosures in Bila Lhota and Frycovice (Czech Republic)

Summary

Introduction

The family Cervidae (Ruminantia) groups more than fifty extant deer species, including species with growing economic importance. Deer species can be divided into three subfamilies: Cervinae, Capreolinae and Hydropotinae [1] and show a great karyotype diversity reflecting chromosome evolution of the taxon. The 2n = 70 karyotypes of Hydropotes inermis and Mazama gouzoubira, involving 68 acrocentric autosomes, an acrocentric X and a small submetacentric Y, most probably represent an ancestral cervid karyotype [4] which evolved from the hypothetical ancestral pecoran karyotype (2n = 58) by six chromosome fissions [5]. Comparative cytogenetic studies revealing interspecies chromosome homologies and tracking of evolutionary karyotype rearrangements have been still scarce in Cervidae, with the exception of Muntjacini. Fissions of several ancestral pecoran chromosomes conserved in Bos taurus (BTA, 2n = 60) as BTA1, 2, 5, 6, 8, 9 and intrachromosomal rearrangements of the BTA1 orthologue and the X chromosome were detected in Cervidae using bovine BAC (Bacterial Artificial Chromosome) probes [13,14]

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