Authors: Kevin Wong and Hollie Putnam
Abstract:
Coral reefs are threatened both locally and globally by anthropogenic impacts, which to date have contributed to substantial declines in coral cover world-wide. However, some corals are more resilient to these environmental changes and therefore have increased relative abundance on local scales and may represent prominent members shaping future reef communities. Here, we provide the first draft reference genome for one such reef-building coral, the mustard hill coral, Porites astreoides. This reference genome was generated from a sample collected in Bermuda, with DNA sequenced via Pacific Biosciences HiFi long-read technology to provide an initial draft reference genome assembly. Assembly of the PacBio reads with FALCON UnZip resulted in a 667 Gbp assembly with 3,051 contigs with a N50 of 412,256. The genome BUSCO completeness analysis resulted in 90.9% of the metazoan gene set. An ab initio transcriptome was also produced with 64,636 gene models with a transcriptome BUSCO completeness analysis of 77.5% when compared to the metazoan gene set. The function annotation was obtained through a hierarchical approach of SwissProt, TrEMBL, and NCBI nr database of which 86.6 % of proteins were annotated. Through our ab initio gene prediction for structural annotation and generation of a functional annotation for the P. astreoides draft genome assembly, we provide valuable resources for improving biological knowledge, which can facilitate comparative genomic analyses for corals, and enhance our capacity to test for the molecular underpinings of adaptation and acclimatization to support evidence-based restoration and human assisted evolution of corals
One adult Porites astreoides colony was collected from Bailey’s Bay Reef Flats in Bermuda on June 12, 2017 and cored into genetic replicates. The replicates were held under ambient conditions for 14 days (28°C with 12:12hr light cycle at ~115 umol photons) and then exposed to heated conditions (31°C with 12:12hr light cycle at ~115 umol photons) for 59 days. Samples were immediately snap frozen and stored at -80°C on August 28, 2017.
Corals were collected under permit 17060807 from the Government of Bermuda Department of Environment and Natural Resources.
https://meschedl.github.io/MESPutnam_Open_Lab_Notebook/HMW-Porites-Ex/ https://meschedl.github.io/MESPutnam_Open_Lab_Notebook/2nd-Por-Ex/
4 RNASeq datasets
https://meschedl.github.io/MESPutnam_Open_Lab_Notebook/porites-ex/ https://meschedl.github.io/MESPutnam_Open_Lab_Notebook/Zymoseq-RNA-Lib-Test/
PacBio 4 smrtcells at Genewiz Seqeuncing and Assembly Report
https://github.com/hputnam/Past_Genome/blob/master/genome_annotation_pipeline.md
- University of Rhode Island’s Committee for Research and Creative Activities Research Proposal Development Grant grant 2017-2018
- Heising-Simons Foundation to BIOS and URI subaward
- NSERC PGSD3 award #545967-2020