All our base are belong to you

We are happy to announce the public release of the raw sequencing data for our first 64 species.

The data is shared on NCBI Sequence Read Archive under BioProject accession PRJNA512907 and includes raw Hi-C data for 64 species and raw WGS data for 8 species. In total, the data spans 131 experiments and 7,294,602,040,208 bases!

We are grateful to Illumina, Macrogen, Novogene, the Broad Institute, BCM-HGSC and BCM GARP core for help in data production.

Our data policy is the usual.

Stay tuned for more!

No drama piranha

The red-bellied piranha, also known as the red piranha (Pygocentrus nattereri), is a species of piranha native to South America and a popular aquarium fish. Through media influence, the red-bellied piranha has developed a reputation as a ferocious predator, but scientists believe that the animals’ fearsome reputation has been exaggerated [1].

This week we are releasing the chromosome-length assembly for the red-bellied piranha, based on the work by W.C. Warren and M. Schartl [2]. We are grateful to Moody Gardens for the sample used for Hi-C library preparation!

Check out the alignments of the new assembly to the two most closely related fish genome assemblies out there: the Mexican tetra Astyanax mexicanus, from (McGaugh et al. Nat Commun., 2014), and the channel catfish Ictalurus punctatus, from (Liu et al. Nat Commun., 2016). Looks like the content of the chromosomes is largely preserved.

Whole genome alignments of the red-bellied piranha genome assembly to the assemblies of the Mexican tetra (left) and channel catfish (right).

Turning the leaf for the silkworm caterpillar

Today we are releasing the chromosome-length genome assembly for the silkmoth Bombyx mori. The caterpillar stage of the silkmoth, the silkworm, is a valuable source of silk. A single silkworm produces a single continuous silk thread up to 1,300 meters (4,250 feet) in length, and it takes 1700 to 2000 silkworm cocoons to make one silk dress [1]!

The new genome assembly, shared here, is based on the work from the International Silkworm Genome Consortium (International Silkworm Genome Consortium, Insect Biochemistry and Molecular Biology, 2008). The Hi-C data for the upgrade was generated using insects from the Carolina Biological Supply Company.

To validate the assembly, we compare the positions of 1,451 SNP markers from the Silkworm Genome Research Program website predicted from linkage mapping with their coordinates on the new assembly, below. The datasets are in excellent agreement!

Comparison of SNP marker positions according to the linkage data and predicted by the new assembly.