A cormorant in the spotlight

The double-crested cormorant (Phalacrocorax auritus) is a member of the cormorant family of seabirds. Once threatened by the use of DDT, the numbers of this bird have increased markedly in recent years [1]. Currently, the double-crested cormorants are protected under the Migratory Bird Treaty Act [2].

Today, we share a chromosome-length upgrade to the draft genome assembly for the double-crested cormorant published in (Burga et al., Science, 2017). We are grateful to SeaWorld for the sample used for Hi-C library preparation!

Check out our usual whole-genome alignment analysis below to compare how the chromosomes of the new genome assembly for the double-crested cormorant compare to those of the chicken, from the International Chicken Genome Sequencing Consortium. Once again we see the conservative bird karyotype, for the first time in core waterbirds!

Whole-genome alignment plots between the chromosome-length double-crested cormorant genome assembly (ASM217345v1_HiC) and the chicken (GRCg6a) genome assembly.

Condors, the long and the short of it

The California condor Gymnogyps californianus is one of the largest flying birds. Its 9.8 ft (3.0 m) wingspan is the widest of any North American bird. It can reach flying speeds of up to 55 miles per hour (88 kilometers per hour), and can fly to altitudes of 15,000 feet (4,600 meters) [1]!

The California condor population was almost wiped out by the destruction of habitat, poaching, and lead poisoning. In 1982, only 22 birds remained in the wild. A conservation plan was put in place by the United States government, and numbers rose through captive breeding. But the species is still listed as critically endangered by the IUCN [2].

To help with the California condor conservation efforts we collaborated with Cynthia Steiner (San Diego Zoo), Oliver Ryder (San Diego Zoo), David Mindell (UC Berkeley), Rauri Bowie (UC Berkeley) and Jeff Wall (UCSF) to create chromosome-length genome assemblies for the California condor. We thank The Peregrine Fund, Chris Parish and Rick Watson for their help in providing the blood sample used for Hi-C.

We were fortunate in this case to have both short read (Illumina) and long read (PacBio) DNA-Seq data. This gave us the opportunity to compare the results of assembling an unknown genome using both short and long reads. (A similar comparison for human is presented in (Dudchenko et al., bioRxiv, 2018).)

The short read assembly (Illumina DNA-Seq [contigged using w2rap] + Hi-C [scaffolded via 3D-DNA + JBAT]) is shared here. The long read assembly (PacBio DNA-Seq [FALCON] + Hi-C [3D-DNA+JBAT]) is shared here. Note that while the assemblies are otherwise independent of each other, they use the same Hi-C data for scaffolding.

The results are roughly what one might expect. The contig N50 is much larger for the long read assembly (17Mb vs 63kb). It also has more bases in the chromosome-length scaffolds (~1.19Gb vs. ~1.07Gb; there’s some ambiguity because of the difficulty in distinguishing between long unanchored scaffolds and bird microchromosomes.) The scaffolds are in excellent agreement, as shown below. The overall results are comparable to what we reported in human.

Comparison of the short-read-based genome assembly (gc_Illumina_HiC) and the assembly based on long-read DNA-Seq data (gc_PacBio_HiC).

Check the whole-genome alignments below to compare the chromosome-length scaffolds from the new California condor genome assemblies and those of chicken (from the International Chicken Genome Sequencing Consortium) and the golden eagle (from an earlier DNA Zoo release). Despite the fact that the condor and the golden eagle are much closer relatives than the condor and chicken, the condor does not display a karyotype similar to that of the golden eagle. Rather, we once again see the relatively conservative avian karyotype that we have seen throughout many of our bird blog posts (3, 4, 5), and all the way to the turtle genome assembly.

Whole-genome alignment plots between the chromosome-length California condor genome assembly (PacBio version gc_PacBio_HiC) and the golden eagle (Aquila_chrysaetos-1.0.2_HiC) and the chicken (GRCg6a) genome assemblies.

Kiss me not

Chagas disease or American trypanosomiasis is a potentially deadly disease caused by the parasite Trypanosoma cruzi. This parasite is spread to people and animals by the feces of insects from the Triatominae subfamily, also known as kissing bugs. Chagas disease affects about 10 million people worldwide, and approximately 10,000 people die from it annually. See this recently published Chagas disease overview from the Texas Chagas Task Force for more information!

Today, we upgrade the genome of Rhodnius prolixus, a major vector of Chagas disease. This work was based on the draft published by (Mesquita, Vionette-Amaral et al., PNAS, 2015), and relied on a sample from BEI Resources to generate the necessary Hi-C data. The chromosome-length assembly is shared here.

Very little is currently known about R. prolixus chromosomes, but what there is in the literature is in agreement with the new chromosome-length genome assembly. For example, prior research suggests that R. prolixus has a 2n=22 karyotype (see contact map below for the immediate validation of the chromosome number in a haploid assembly) and an XY sex determination system [1, 2, 3].

Note that in organisms with an XY sex determination system (and those in which X and Y are sufficiently diverged) one expects the X chromosome to have half the coverage of autosomes in male samples (for example, this is true of mammalian samples). Indeed, this is what we see when visualizing the Hi-C contact map from a male sample, below!

Screenshot of the chromosome-length genome assembly map in Juicebox assembly tools. The blue half-squares outline the boundaries of 11 chromosomes. A coverage track is included to help outline the sex chromosome (#10, highlighted with arrow).