Reef-building corals play an important role in marine ecosystems, and analyzing their proteomes from a structural perspective can assist in the future exploration of their biology. Here we have integrated mass spectrometry with the newly published ColabFold to obtain digital structural proteomes of dominant reef-building corals.
We identified 8,382 proteins co-expressed in A. muricata, M. foliosa and P. verrucosa, and 8,166 of these had predicted structures after around 4,060 GPU hours of computation. The resulting dataset covers 83.6% of residues with a confident prediction, while 25.9% have very high confidence.
Our work provides insight-worthy predictions for coral research, confirms the reliability of ColabFold in practice, and is expected to be a reference case in the impending high-throughput era of structural proteomics.

Ginkgo biloba is one of the worlds most ancient plants, a living fossil that has remained essentially unchanged in terms of gross morphology for more than 200 million years. Representing one of the four extant gymnosperm lineages and having no living relatives, it possesses a suite of fascinating characteristics including including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses, and dioecious reproduction, making it an ideal model species for biological studies.
Here we present an updated chromosome-level genome assembly using HiC technology as a major improvement of the ginkgo draft assembly. A chromosome-level reference represents a valuable resource to facilitate of studies of biologic diversity, evolutionary history, and population genetics. With technological advances, we constructed to update the existing draft assembly to the chromosome-level using Hi-C, which has been proven to be a fast, inexpensive, and accurate technology that can be applied to many species. The fresh plant leaves of two-years seedling (TM301S) were crosslinked with 1% formaldehyde. To destroy the cell wall, formaldehyde fixed powder was added to Buffer solution. The restriction endonuclease MboI was used to digest DNA, followed by biotinylated residue labeling. The Hi-C library was then sequenced on BGISEQ-500 platform with 50 bp pair-end sequencing. HiC-Pro pipeline (v2.11.1) was implemented in quality control. Of all 653,202,535 raw pair-end reads, there are 32% (207,324,555) paired Hi-C reads are valid and suitable for following analysis. Basing on these valid Hi-C reads, we used Juicer (v1.6.2) and Aiden labs Hi-C assembly pipeline (v180922) to assemble the genome with the main parameter "-m haploid -s 4 -c 12", generating 12 chromosomes spanning 9.03 Gb (~94% of the whole genome).

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