A hill-areas mouse

The canyon mouse (Peromyscus crinitus) is native to North America [1]. Its preferred habitat is arid, rocky desert making it a great model organism to study adaptation to desert. Gaining a deeper understanding of desert adaptation (e.g., osmoregulation and water metabolism) is important for conservation, climate change studies, and human health (for instance, understanding kidney disease).

In collaboration with the MacManes lab at the University of New Hampshire, today we share the chromosome-length genome assembly for the canyon mouse. The draft genome assembly was generated using 10X data by Matthew MacManes, Anna Tigano and Jocelyn Colella at the University of New Hampshire. The fibroblast culture for Hi-C library preparation came from the archive collected at the Texas Medical Center.

Check out below how the new genome assembly compares to a publicly available genome of a close relative, the prairie deer mouse (P. maniculatus, ~5MY divergence [2]). The genome assembly, HU_Pman_2.1, was shared by J.-M. Lassance and H.E. Hoekstra at Harvard University and Howard Hughes Medical Institute, here. We also include a comparison to the golden hamster chromosome-length genome assembly (Mesocricetus auratus, upgrade of genome assembly MesAur1.0), a rodent from the same family from the DNA Zoo collection (Cricetidae, ~20MY divergence [3]).

Whole-genome alignment plots between the chromosome-length canyon mouse genome assembly (pecr10X_v2_HiC) and the assemblies of the prairie deer mouse (HU_Pman_2.1) and the golden hamster (MesAur1.0_HiC).

It is worth noting that the sample used for Hi-C library preparation proved to have a polymorphic karyotype. The fasta shared today represents one of these karyotypes, the one most consistent with an individual animal used to create the draft genome assembly. We are now working to sequence more canyon mice to figure out if this polymorphism is a feature or a bug. So, stay tuned for more info on this, and for more Peromyscus genomes and data!

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.)

Ostrich-sized birds

The common ostrich Struthio camelus is the largest living bird: a male ostrich can reach a height of 9.2 feet (2.8 meters) and weigh over 344 pounds (156 kilos) [1]. Ostriches are flightless. In the 18th century, ostrich feathers were so popular in ladies’ fashion that they disappeared from all of North Africa. If not for ostrich farming, which began in 1838, then the world’s largest bird would probably be extinct [2]!

Today, we share a chromosome-length genome assembly for the common ostrich. This is an upgrade from a draft generated by the Avian Genome Consortium, see (Zhang, Li et al., Science, 2014) and accompanying papers for more details. We thank the Oklahoma City Zoo for providing us with a sample used for Hi-C library preparation!

Birds are divided into two clades, the paleognaths and the neognaths. The paleognaths are a much smaller clade, and with the exception of the tinamou, they are flightless. With today’s upgrade to ostrich, we’ve now released chromosome-length assemblies of most of the paleognath genera (the ostrich, the emu, the cassowary and greater rhea). To complete the collection, we’re still looking for samples of tinamou and kiwi - if you have a sample, even a pretty low-quality sample, it could make a big difference. Please consider sending it along!

Below is a whole-genome alignment plot comparing the ostrich chromosomes to those of the other paleognaths in our collection: the emu, the cassowary and greater rhea (all DNA Zoo upgrades from Sackton et al., Science, 2019). Also included is the alignment to the chicken chromosomes, from the International Chicken Genome Sequencing Consortium.

Whole-genome alignments between the new chromosome-length assembly for the common ostrich (ASM69896v1_HiC) and the genome assemblies of the emu, cassowary and greater rhea (droNov1_HiC, casCas1_HiC and rheAme1_HiC, respectively, all DNA Zoo upgrades of genomes from Sackton et al., Science, 2019), as well as chicken (GRCg6a, from the International Chicken Genome Sequencing Consortium).

Because the original draft and the Hi-C signal have been generated using samples from female birds, both Z and W chromosomes are represented in the DNA Zoo assembly. The structure of the ostrich Z was recently explored in (Yazdi and Ellegren, Genome Biol Evol, 2018). There, they generated a genetic map for the ostrich Z chromosome (chr# 6 in the new genome assembly), building on 2015 improvements using optical mapping data from (Zhang et al., GigaScience, 2015).

It is worth noting that while we have not used the optical and genetic mapping data for our assembly, our conclusions on the syntenic relationship between the ostrich Z and the chicken Z, shown above, broadly agree with those suggested by the published genetic map (see figure below). These suggest a large ~30Mb collinear region near the p-end of the sex chromosome. The highly rearranged portion towards the q-end (~50Mb) corresponds to the pseudoautosomal region (where recombination is possible between the Z and the W chromosomes).

Fig. S2 from Yazdi and Ellegren, Genome Biol Evol, 2018: The grouping of genes into synteny blocks between the ostrich and chicken Z chromosome. Grey: genes with conserved gene orientation between the two species. Red: inverted genes in one species compared to the other.