Whole genome assembly and annotation of the endangered Caribbean coral Acropora cervicornis.

Coral species in the genus Acropora are key ecological components of coral reefs worldwide and represent the most diverse genus of scleractinian corals. While key species of Indo-Pacific Acropora have annotated genomes, no annotated genome has been published for either of the two species of Caribbean Acropora. Here we present the first fully annotated genome of the endangered Caribbean staghorn coral, Acropora cervicornis. We assembled and annotated this genome using high-fidelity nanopore long-read sequencing with gene annotations validated with mRNA sequencing. The assembled genome size is 318 Mb, with 28,059 validated genes. Comparative genomic analyses with other Acropora revealed unique features in A. cervicornis, including contractions in immune pathways and expansions in signaling pathways. Phylogenetic analysis confirms previous findings showing that A. cervicornis diverged from Indo-Pacific relatives around 41 million years ago, with the closure of the western Tethys Sea, prior to the primary radiation of Indo-Pacific Acropora. This new A. cervicornis genome enriches our understanding of the speciose Acropora and addresses evolutionary inquiries concerning speciation and hybridization in this diverse clade.

The complete mitochondrial genome of Montiporavietnamensis (Scleractinia, Acroporidae).

Montiporavietnamensis Veron, 2000 (Cnidaria, Anthozoa, Scleractinia, Acroporidae) is an uncommon, but distinctive species of stony coral. The complete mitochondrial genome of M.vietnamensis was sequenced in this study for the first time, based on 32 pairs of primers newly designed according to seven species in the family Acroporidae. The mitogenome of M.vietnamensis has a circular form and is 17,885 bp long, including 13 protein-coding genes (PCGs), 2 tRNA (tRNAMet, tRNATrp), 2 rRNA genes and a putative control-region. The base composition of the complete mitogenome was 24.8% A, 14.2% C, 24.2% G and 36.8% T, with a higher AT content (61.6%) than GC content (38.4%). Based on 13 protein-coding genes, a Maximum Likelihood phylogenetic analysis showed that M.vietnamensis is clustered in the genus Montipora which belongs to the family Acroporidae. More stony coral species should be sequenced for basic molecular information and to help confirm the taxonomic status and evolutionary relationships of Scleractinia in the future.

Expansion and Diversification of Fluorescent Protein Genes in Fifteen Acropora Species during the Evolution of Acroporid Corals.

In addition to a purple, non-fluorescent chromoprotein (ChrP), fluorescent proteins (FPs) account for the vivid colors of corals, which occur in green (GFP), cyan (CFP), and red (RFP) FPs. To understand the evolution of the coral FP gene family, we examined the genomes of 15 Acropora species and three confamilial taxa. This genome-wide survey identified 219 FP genes. Molecular phylogeny revealed that the 15 Acropora species each have 9-18 FP genes, whereas the other acroporids examined have only two, suggesting a pronounced expansion of the FP genes in the genus Acropora. The data estimates of FP gene duplication suggest that the last common ancestor of the Acropora species that survived in the period of high sea surface temperature (Paleogene period) has already gained 16 FP genes. Different evolutionary histories of lineage-specific duplication and loss were discovered among GFP/CFPs, RFPs, and ChrPs. Synteny analysis revealed core GFP/CFP, RFP, and ChrP gene clusters, in which a tandem duplication of the FP genes was evident. The expansion and diversification of Acropora FPs may have contributed to the present-day richness of this genus.

The complete mitochondrial genome of Montipora efflorescens (Scleractinia: Acroporidae).

The complete mitogenome of the Sclreractinia, Montipora efflorescens Bernard, 1897 was sequenced for the first time. It had 17,887 bp, with 13 protein-coding genes, and two rRNA and two tRNA genes. Composition of M. efflorescens mitogenome was identical to that of typical Scleractinians. In conclusion, the complete mitogenome may provide detailed information on coral phylogeny.

Identification Acroporidae and Favidae by a newly approach called Reef Identification Knowhow Application-Reconstructed by 3D Imagery (RIKA-R3DI) Method.

With an increase on coral reefs vulnerability worldwide, an efficient and an integrated monitoring technique are required. Photographic and video methods are now becoming more attractive rather than conventional technique to optimize diver time. In this research, the level of effectiveness of RIKA-R3DI method was evaluated using Agisoft Photoscan. The method was based on the reconstructed images in three dimensional image assisted by a computer with Agisoft Photoscan to facilitate data processing. This research aims to identify Acroporidae and Favidae as the models of coral reef-building species. The samples were collected from the waters of Beralas Pasir Island, Bintan Regency. Visual engineering was conducted in the form of 3D viewing with attention to the corallite shape and size, as well as the color of the corals. The result was successful in identifying 4 species, i.e. Acropora microphthalma, A. sarmentosa, Favia maritima, F. vietnamensis. The keys benefit of this methodologies are: •The RIKA-R3DI method allows to reduce diving time during direct visual observation.•The method has high accuracy and is non-invasive, since it does not touch directly to the coral.•The application of RIKA-R3DI can be used to identified the coral species and evaluate the coral health status base on the percent coverage.

The complete mitochondrial genome of Alveopora japonica (Scleractinia: Acroporidae).

Here, for the first time, we sequenced the complete mitogenome of Alveopora japonica Eguchi, 1968 (Scleractinia: Acroporidae). Genome size was 17,886 bp with 13 protein-coding, two rRNA, and two tRNA genes. This gene composition was identical to the typical scleractinian pattern. Our results strongly support the recent transfer of this coral species to the family Acroporidae.

The complete mitochondrial genome of Montipora aequituberculata (Scleractinia, Acroporidae).

The complete mitogenome of the hexacorallia, Montipora aequituberculata has been amplified and sequenced. The mitogenome consists of 17,886 bp, with 13 protein-coding genes, 2 ribosomal RNA genes, 2 transfer RNA genes and a control region. It has been observed that ND5 gene is split into two parts by a large fragment of genes, which commonly presented in scleractinian coral. The overall base composition of the H-strand was A, 24.91%; G, 24.1%; C, 14.2%; and T, 36.8%, with a slight AT bias of 61.7%. The control region was 627 bp in length and located between 12S rRNA and COIII gene. Based on the neighbour-joining (NJ) tree, M. aequituberculata was grouped with M. cactus, Anacropora matthai and Acropora tenuis, and formed a clade of Acroporidae. In conclusion, the complete mitogenome of M. aequituberculata data may provide more informative for phylogenetic approach for corals phylogeny.