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Gnu at the zoo

The blue wildebeest aka common wildebeest or brindled gnu (Connochaetes taurinus) is a large African antelope from the Bovidae (cow, goat and sheep) family. The blue wildebeest is currently widespread: the population is estimated to be around 1.5 million, and is stable. At least in part this population success is thought to be brought about by management-controlled translocations in private game farms, reserves and conservancies [1].

Today, we continue our survey into ruminant genomics by sharing a chromosome-length blue wildebeest genome assembly. This is once again based on the recent Science paper by Chen, Qiu, Juiang, Wang, Lin, Li et al. (See our previous posts for the Chinese muntjac and gerenuk based on the same work.) Thank you, SeaWorld, for the sample used to generate the Hi-C data and create the upgrade!

We take this opportunity to further our comparison of Bovidae genomes, below, through their alignment to the genome assembly of cattle, from (Zimin et al., Genome Biol. 2009). This is the first genome in our collection with a different chromosome count: the assembly suggests (independently but in agreement with published data) 2n=58 for the blue wildebeest and 2n=60 for the other 3 Bovidae assemblies shared by DNA Zoo (bison, sable antelope and gerenuk).

Whole-genome alignments of the four Bovidae genomes to the cow reference Bos_taurus_UMD_3.1.1. The species included are: bison (Bison_UMD1.0_HiC), sable antelope (Sable_antelope_masurca.scf_HiC), gerenuk (GRK_HiC) and the blue wildebeest (BWD_HiC). The orange circle highlights a change in the position of the bit corresponding to cow chromosome #25 in the blue wildebeest genome as compared to all other genomes in the family: both cow chromosome #25 and #2 align to the chromosome labeled #1 in the blue wildebeest, suggesting a fusion.

This chromosome count change is brought about by a fusion of a bit corresponding to chromosome #25 in the cow (highlighted in the image above) to the bit corresponding to cow chromosome #2. (The fused chromosome is labeled #1 in the new wildebeest genome assembly.) The fusion is obvious in the assembly data, along with a few other smaller rearrangements. It is worth noting that 2;25 fusion has been previously mapped using G-banded karyotyping, by Cynthia Steiner and colleagues at the San Diego Zoo Institute for Conservation Research. See image below from their paper (Steiner et al., Journal of Heredity 2014)!

Figure 1B from (Steiner et al., Journal of Heredity, 2014): G-banded karyotype of the blue wildebeest. Autosomal arms are numbered according to standard karyotype of cattle. (The highlight (by DNA Zoo) shows the fused chromosome.)

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