Biology subjects

Amaral, D. L. A. S.

Publications and source records attributed to Amaral, D. L. A. S..

4 recordsLinked to original sources

bioRxiv2025

The globally dispersed sun-coral species is _Tubastraea coccinea_ (Cnidaria: Anthozoa)

Species of the genus Tubastraea (sun corals) have dispersed globally over recent decades, but morphological trait identification has led to taxonomic confusion, with multiple authors proposing conflicting species identifications due to high morphological plasticity and overlapping diagnostic traits. We combined global-scale molecular phylogenetics with chromosome-level genome assemblies to resolve this taxonomic issue. Using mitochondrial and nuclear markers from 287 specimens across five ocean regions, including type localities in Bora Bora (T. coccinea) and Galapagos (T. tagusensis), we reconstructed phylogenetic relationships and inferred demographic history through approximate Bayesian computation. We also generated high-quality, chromosome-level genome assemblies for three morphologically distinct morphotypes from the Brazilian coastline. Phylogenetic and species delimitation analyses revealed two well-supported clades: a small, geographically restricted T. tagusensis clade confined to the Galapagos Islands, and a large cosmopolitan clade containing all worldwide samples, including T. coccinea from its type locality. Chromosome-level genomic analyses confirmed that the three morpho-types represent a single species, sharing a triploid karyotype of 14 chromosomes with extensive synteny and gene-tree discordance consistent with incomplete lineage sorting. Dispersed-route analyses identified the Centralwestern Pacific as the ancestral source, with at least three independent, humanmediated colonization events establishing populations in the Southwestern Atlantic, Gulf of Mexico, and Western Pacific. However, preliminary analysis suggests a Galapagos (Southeastern Pacific) origin rather than Centralwestern Pacific for the T. tagusensis and T. coccinea cluster. Our results definitively establish Tubastraea coccinea as the cosmopolitan species responsible for global dissemination, while T. tagusensis is endemic to the Galapagos and not involved in the worldwide dis-persion.

genetics↗

bioRxiv2022

A high quality chromosome-level genome assembly for the golden mussel (Limnoperna fortunei)

The golden mussel (Limnoperna fortunei) is a highly adaptive species that causes environmental and socioeconomic losses in invaded areas. Reference genomes have proven to be a valuable resource for studying the biology of invasive species. While the current golden mussel genome has been useful for identifying new genes, its high fragmentation hinders some applications. In this Data Note, we provide the first chromosome-level reference genome for the golden mussel. The genome was built using Hi-C, PacBio HiFi and 10X sequencing data. The final assembly contains 99.4% of its total length assembled to the 15 chromosomes of the species and a scaffold N50 of 97.05 Mb. Approximately 47% of the genome was annotated as repetitive sequences. A total of 34 862 protein-coding genes were predicted, of which 84.7% were functionally annotated. This new high quality genome is expected to support both basic and applied research on this invasive species. Species taxonomyEukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Spiralia; Lophotrochozoa; Mollusca; Bivalvia; Autobranchia; Pteriomorphia; Mytilida; Mytiloidea; Mytilidae; Arcuatulinae; Limnoperna; Limnoperna fortunei (Dunker, 1857) (NCBI Taxonomy ID: 356393)

genomics↗

bioRxiv2021

Environmental DNA from a small sample of reservoir water can tell volumes about its biodiversity.

We evaluated the potential of metabarcoding in assessing the environmental DNA (eDNA) biodiversity profile in the water column of an hydroelectric power plant reservoir in southeast Brazil. Samples were obtained in three technical replicates at 1 km from the dam at 1, 13 and 25 m depths. For each minibarcodes -- COI, 12S and 16S -- 1.5 million paired-reads (150 base pairs) were sequenced. A total of 44 unique taxa were found. COI identified most of the taxa (34 taxa; 77.2 %) followed by 16S (14; 31.8 %) and 12S (10; 22.7 %). All minibarcodes identified fishes (13 taxa), however, COI detected other aquatic macro-invertebrates (18), algae (3) and amoebas (2). Richness was the same across the three depths (35 taxa), although, beta diversity suggested slightly divergent profiles. In just one location we identified 15 taxa never reported previously, 50% of the fish species identified in the last year of fishery monitoring and 13% of the species in biodiversity surveys performed from 2012 to 2021. Clustering into Amplicon Sequence Variants (ASV) showed that 12S and 16S are able to detect predominant haplotypes of fishes, suggesting they are suitable to study population genetics of this group. In this study we reviewed the species occurring within the Tres Irmaos reservoir according to previous conventional surveys and demonstrated that eDNA metabarcoding can be applied to monitor its biodiversity.

molecular biology↗

bioRxiv2019

The draft genome of the invasive coral Tubastraea sp.

Corals have been attracting huge attention due to the impact of climate change and ocean acidification on reef formation and resilience. Nevertheless, some coral species have been spreading very fast, replacing native species and affecting local biodiversity. Despite some focal efforts to understand the biology of these organisms, they remain understudied at the molecular level. This knowledge gap hinders the development of cost-effective strategies for management of invasive species. Here, we present the first Tubastraea sp. genome in one of the most comprehensive biological studies of a coral, that includes morphology, flow cytometry, karyotyping, transcriptomics, genomics, and phylogeny. The Tubastraea sp. genome is organized in 23 chromosome pairs and has 1.4 Gb making it the largest coral and Cnidaria genome sequenced to date. The hybrid assembly using short and long-reads has a N50 of 180,044 pb, 12,320 contigs and high completeness estimated as 91.6% of BUSCO complete genes. We inferred that almost half of the genome consists of repetitive elements, mostly interspersed repeats. Gene content was estimated as about 94,000, a high number that warrants deeper scrutiny. The Tubastraea sp. genome is a fundamental study which promises to provide insights not only about the genetic basis for the extreme invasiveness of this particular coral species, but to understand the adaptation flaws of some reef corals in the face of anthropic-induced environmental disturbances. We expect the data generated in this study will foster the development of efficient technologies for the management of corals species, whether invasive or threatened.

genomics↗