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. 2023 Mar 23;24(1):142.
doi: 10.1186/s12864-023-09189-5.

Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights

William Poisson  1   2   3 , Julien Prunier  4 , Alexandra Carrier  1   2   3 , Isabelle Gilbert  1   2   3 , Gabriela Mastromonaco  5 , Vicky Albert  6 , Joëlle Taillon  6 , Vincent Bourret  6 , Arnaud Droit  7 , Steeve D Côté  8 , Claude Robert  9   10   11
Affiliations

Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights

William Poisson et al. BMC Genomics. .

Abstract

Background: Genome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes of Rangifer tarandus (caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since most populations are declining.

Results: We have designed specific probes based on Oligopaint FISH technology to upgrade the latest published reindeer and caribou chromosome-level genomes. Using this oligonucleotide-based method, we found six mis-assembled scaffolds and physically mapped 68 of the largest scaffolds representing 78% of the most recent R. tarandus genome assembly. Combining physical mapping and comparative genomics, it was possible to document chromosomal evolution among Cervidae and closely related bovids.

Conclusions: Our results provide validation for the current chromosome-level genome assembly as well as resources to use chromosome banding in studies of Rangifer tarandus.

Keywords: Chromosome; Fluorescence in situ hybridization; Genome assembly; Idiogram; Karyotype; Oligopaint; Rangifer tarandus; Scaffold.

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Conflict of interest statement

The authors declare that they have no interests or affiliations that influenced the design of this study or the interpretation of its results.

Figures

Fig. 1
Fig. 1
Oligonucleotide’s structure and scaffolds’ color pattern. a Oligo comprising a reverse primer sequence (yellow), genome homolog sequence (purple), forward primer sequence (orange) and adapter (green) complementary to the detection oligo (blue) linked to the fluorophore (red). Hybridization of the homolog with its specific genomic complementary sequence (black) is followed by hybridization of the fluorophore-bearing oligo. b The 68 scaffolds to be assembled on chromosomes are painted with one to five probes each labeled blue, yellow, or red, giving these three colours or green (blue + yellow), orange (yellow + red) or violet (red + blue). Two-probe patterns were repeated among two or three scaffolds because of limited color possibilities but were hybridized separately to ensure accurate chromosome attribution
Fig. 2
Fig. 2
Hybridization of probes for scaffold mapping. a Hybridization of a group of ten scaffold probe sets, the first step for scaffold anchoring. Scaffold probes were labeled with FAM (cyan), ATTO-550 (yellow), ATTO-647 (red) or with a pair to generate another color (green for FAM + ATTO-550, orange for ATTO-550 + ATTO-647, violet for FAM + ATTO-647). b Example of unclear or mis-assembled signal scaffolds confirmed by hybridization in a smaller group. c Whole karyotype covered by the 68 scaffold probe sets allowing identification of all chromosomes with a single hybridization. All scaffolds were assigned to one pair of chromosomes by identifying their color scheme. Scale bar = 5 μm
Fig. 3
Fig. 3
Validation of doubtful scaffolds integrity visualized on in situ chromosomes. White arrows in images a–d indicate mis-assembled scaffold splits on chromosome pairs: scaffold 1 on chromosome pairs 7 and 20, scaffold 2 on 16 and 18, scaffold 12 on 1 and 4, scaffold 20 on 2 and 34. Green arrows indicate well-assembled scaffold 7 on chromosome pair 27. Probes hybridized also with non-lysed cells (N). e Reorganized scaffold 21, the first part (including the first probe) is inverted and positioned after the second and third probes. f Mis-assembled scaffold 25 split on chromosome pairs 3 and 8. Scale bar, 5 μm
Fig. 4
Fig. 4
Centromere positioning revealed by hybridization on late metaphase chromosomes. More condensed chromosomes and clear separation of chromatids make centromere easier to distinguish. Inset: chromatid attachment point (centromere to the upper left side) visualized on R. tarandus chromosome 1. Scale bar = 5 μm
Fig. 5
Fig. 5
Idiographic and physical mapping of Rangifer tarandus scaffolds. All scaffolds were positioned on a chromosome. Centromeres are represented by black tips or bands. The first 33 chromosomes are acrocentric. The only submetacentric chromosome is #34. The X chromosome is the largest and is metacentric. All X chromosome scaffolds were placed on the short arm. The Y chromosome was not studied
Fig. 6
Fig. 6
Sankey diagram illustrating associations between Rangifer tarandus chromosomes (RtChr, left) and Bos taurus chromosomes (BtChr, right). Chromosomal rearrangements (fusion and fissions) are shown in colour. Except for the coloured chromosomes, chromosomal order is maintained overall, the biggest discrepancy being of four chromosomal positions (i.e., RtChr13)
Fig. 7
Fig. 7
Jupiter plot representing mapping of the corrected R. tarandus assembly on the B. taurus genome. The 111 largest scaffolds (on the right) show high synteny with the 29 autosomes plus X chromosomes from the cattle assembly (ARS-UCD1.2). Intersecting bands, which represent non-syntenic regions between the two species, are fewer in comparison with the previous mapping [20]
Fig. 8
Fig. 8
Suggested evolution of bovine chromosome 1 ancestral ortholog in Cervidae and Bovidae. Relative to bovine chromosome 1 and its caprine ortholog, three events appear to have been passed on to R. tarandus and O. hemionus. First, fission of the common ancestor’s bovine chromosome 1 ortholog gave rise to a short acrocentric chromosome (containing R. tarandus scaffold 7, green) and a longer one (containing scaffolds 13, 20 and 56, yellow, blue, red). A translocation then occurred within the distal portion of the longer one, near the centromere. The order of these two events has not been confirmed. Finally, a pericentric inversion of the proximal part of the longer chromosome occurred, leading to a submetacentric configuration in the genera Odocoileus and Rangifer
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