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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).

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Congratulations to Olga of the DNA Zoo team who was named one of Technology Review’s 35 Innovators under 35 today!

It is a great accomplishment and a reflection of all the wonderful work she and the whole team at DNA Zoo as well as DNA Zoo collaborators have done to dramatically accelerate the process of genome assembly!

More information about past and present Technology Review winners and judges is available here:

Read more on the announcement and Olga’s work here:

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Mandrills (Mandrillus sphinx) are primates from equatorial Africa. They are exceptionally colorful, perhaps more so than any other mammal. The bright blue colors on the male mandrill's face are produced from light refraction in collagen fibers, an example of structural coloration. Mandrills are also the largest of all monkeys! The mandrill is classified as vulnerable by IUCN.

This week, we revisited the draft genome assembly from (Yin, Yan et al., bioRxiv, 2018), from a team led by Karsten Kristiansen at the University of Copenhagen. We've now upgraded the genome to include chromosome-length scaffolds. We thank Houston Zoo for providing us with a sample used for Hi-C library preparation!

See below our usual analysis to compare how the 21 chromosomes in the new mandrill genome assembly relate to those of the mandrill’s close relative, the human.

Whole genome alignment between the current best human genome reference, GRCh38 (hg38), and GBI_mandrill_1.0_HiC, the upgraded mandrill genome assembly.

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