Sterling Archer’s greatest fear: the American alligator

This week, we’re continuing our investigation of crocodilian genomics by assembling the chromosomes of the American alligator Alligator mississippiensis, the largest reptile in North America.

The new genome assembly is based on the draft data published in (St John et al., Genome Biology, 2012) and improved in (Rice et al., Genome Research, 2017). The sample used for Hi-C library preparation was donated by an alligator named Bo living at the Texas State Aquarium. That’s him on the blog post cover image (© Texas State Aquarium)!

Comparative gatoromics reveals nearly identical karyotypes. A different highly quantitative comparison is due to Sterling Archer.

Whole genome alignment of the 16 chromosomes of the new American alligator genome assembly ASM28112v4_HiC to the Chinese alligator chromosomes from ASM45574v1_HiC (see DNA Zoo blog post https://www.dnazoo.org/blog/alligator-bytes).

Alligator bytes

The Chinese alligator Alligator sinensis is widely considered to be the most endangered species in the crocodilian family, with less than 120 alligators left in the wild [1]. To help with the conservation efforts, we are releasing the chromosome-length genome assembly for the Chinese alligator.

The new genome assembly is based on the ASM45574v1 draft from (Wan, Pan, Hu et al., Cell Research, 2013). We thank Moody Gardens for the sample used for Hi-C library preparation!

Check out the whole genome alignments between the 16 chromosomes of the Chinese alligator and chicken chromosomes, from the International Chicken Genome Sequencing Consortium, below. Previously, we have highlighted results that suggest species in Sauria tend to have a highly conservative chromosome structure [2, 3]. Interestingly, the data from the Chinese alligator breaks this trend, showing a highly divergent karyotype!

Whole genome alignment of the chromosome-length genome assembly for the Alligator sinensis to the chromosomes of the chicken (left). Many chromosomal rearrangements are mapped between the two species. Compare this to the whole genome alignment from one of our previous posts, between the chicken and Chelonia mydas, a member of the turtle family and a more distant relative to the chicken than the Chinese alligator (right).

Press paws for the African wild dog

Today we are releasing the chromosome-length genome assembly for the African wild dog Lycaon pictus. African wild dogs are considered one of Africa’s most effective predators, boasting an 80% success rate with hunts; far higher than the 30% rate of lions [1]. They are classified as endangered by IUCN due to loss of habitat and susceptibility to disease spread by domestic animals [2].

This assembly was done in collaboration with Ellie Armstrong, Dmitri Petrov, Ryan Taylor, John Stuelpnagel, Peter Blinston and others from the Lycaon pictus whole genome shotgun sequencing project [3]. The genomic material for DNA-Seq was provided by Painted Dog Conservation, and the sample for Hi-C library preparation was donated by the Houston Zoo.

It must be noted that there is some disagreement in the literature about the karyotype for this species [4, 5]. We are grateful to Marlys Houck and Ann Misuraca from the San Diego Zoo Institute for Conservation Research for confirming our prediction for the 39 haploid chromosome count.

We also share an earlier version of this genome assembly, based on the version of the draft from (Armstrong et al., Gigascience, 2019), here. Check out the whole-genome alignments of the two assemblies to the dog genome canFam3.1 (Lindblad-toh et al., Nature, 2005), below!

Whole genome alignment of the chromosome-length genome assembly for the Lycaon pictus to the chromosomes of domestic dog, from (Lindblad-toh et al., Nature, 2005).