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

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.

Whole-genome sequencing of reindeer (Rangifer tarandus) populations reveals independent origins of dwarf ecotypes and potential molecular mechanisms underpinning cold adaptation

“…Recently, a high-quality chromosome-level assembly of the Canadian R. t. caribou has been published by Poisson et al [17] (2.58 Gb), with a very large scaffold N50 (54.36 Mb) (Supplementary Table 1). However, this assembly still has large gap regions (Supplementary Table 1).…”

“…To assess the quality of our reindeer assembly, we downloaded the following available deer genomes (together with one sequencing lane of raw reads in each case): Chinese reindeer genome [16] was downloaded from http://gigadb.org/dataset/100370, caribou genome [17] was downloaded from NCBI (GCA_019903745.2), white-tailed deer (Odocoileus virginianus) genome was downloaded from NCBI (GCF_002102435.1, Ovir.te v1.0), hog deer (Axis porcinus) genome [50] was downloaded from NCBI (GCA_003798545.1, ASM379854 v1) and red deer (Cervus elaphus) genome [51] was downloaded from NCBI (GCA_002197005.1, CerEla1.0). The quality of our Hardangervidda reindeer assembly was compared to these other deer assemblies by FRC analysis.…”

Use of the Phylobone database for the annotation of bone extracellular matrix proteins in reindeer (Rangifer tarandus)

“…The initial Phylobone database included the annotation of six members of the Cervidae family (including Cervus hanglu yarkandensis , Odocoileus virginianus texanus , Cervus canadensis , Cervus elaphus , Muntiacus muntjak and Muntiacus reevesi ), as they have been suggested as potential models for bone regeneration. 4 Although, the reindeer genome has been fully sequenced at a chromosome level, 5 – 7 it was not included in the first version of the database due to the lack of annotation of several proteins. Extracting proteins from the mineral-rich bone ECM is challenging, requiring decalcification and chemical treatments for analysis.…”

Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human

“…New approaches do not always provide a direct link to information on the evolution of the vertebrate genome obtained using cytogenetic approaches 11 . Proper organization of sequenced fragments, such as contigs and scaffolds, in relation to each other, as well as the positioning of superscaffolds into structured chromosomes, is often a challenging step in the construction of a reliable genome reference 26 , 27 . Sequencing and positioning of repeat-containing sequences and genomes with segmental duplications is a daunting task 28 , 29 .…”

“…In recent years, the need for close integration of the latest advances in cytogenetics, genome sequencing, epigenomics, and cell biology has been actively emphasized 12 , 30 . In addition to increasing the quality assurance of bioinformatic genome assembly, the need to validate assemblies with different approaches, all of which are mainly based on FISH, has been noted 11 , 27 , 31 – 34 . The integration may be much more successful in answering fundamental biological questions than genomic or cytogenetic approaches alone 12 .…”