Turnip for this!

Brassica rapa is a plant that has many widely cultivated subspecies (cultivars). To name a few, the list includes turnip, napa cabbage, bomdong, bok choy and field mustard. Napa cabbage is a main ingredient in kimchi!

Today, we are sharing an update to the Brassica rapa reference Brapa_1.0 (GCA_000309985.1) from (Brassica rapa Genome Sequencing Project Consortium, Nat. Genet., 2011). See how the new reference aligns to Brassica oleracea, another commonly cultivated plant from the Brassica family, below. The genome assembly for B. oleracea used for whole genome alignment is Brassica_oleracea_HDEM.

Whole-genome alignment plot between B. rapa and B. oleracea genome assemblies.

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).