Biology subjects

Rebelo, M. d. F.

Publications and source records attributed to Rebelo, M. d. F..

5 recordsLinked to original sources

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↗

bioRxiv2019

Identification of suitable reference genes for qPCR expression analysis on the gonads of the invasive mussel Limnoperna fortunei

Limnoperna fortunei -- popularly known as the Golden mussel -- is an aggressive invasive species that has been causing environmental damage and adversely affecting economic sectors dependent on freshwater ecosystems in South America. As a non-model species, knowledge about its biology is very limited, especially molecular mechanisms that contribute to its invasiveness, such as its high reproduction rate. Quantitative PCR (qPCR) is considered the gold standard technique to determine gene expression levels and its accuracy relies on the use of stably expressed reference genes for data normalization and to minimize technical variability. Our goal was to identify reliable reference genes to perform gene expression analysis on the gonads of L. fortunei. The stability of five candidate genes (RPS3, EF1a, HS6ST3B, NAPA and UBE2F) in the gonads of male and female mussels was evaluated by using two algorithms, Bestkeeper and Genorm. Results show that NAPA, UBE2F and RPS3 genes are stable enough to compose a reliable normalization factor for gene expression analyses comparing both sexes. HS6ST3B and NAPA were found to be more stable in female gonads; thus, their application as a normalization factor is preferable for studies limited to female processes only.

molecular biology↗

bioRxiv2019

Gonad transcriptome of golden mussel Limnoperna fortunei reveals potential sex differentiation genes

The golden mussel Limnoperna fortunei is an Asian invasive bivalve that threats aquatic biodiversity and causes economic damage, especially to the hydroelectric sector in South America. Traditional control methods have been inefficient to stop the advance of the invasive mollusk, which currently is found in 40% of Brazilian hydroelectric power plants. In order to develop an effective strategy to stop golden mussel infestations, we need to better understand its reproductive and sexual mechanisms. In this study, we sequenced total RNA samples from male and female golden mussel gonads in the spawning stage. A transcriptome was assembled resulting in 200,185 contigs with 2,250 bp N50 and 99.3% completeness. Differential expression analysis identified 3,906 differentially expressed transcripts between the sexes. We searched for genes related to the sex determination/differentiation pathways in bivalves and model species and investigated their expression profiles in the transcriptome of the golden mussel gonads. From a total of 187 genes identified in the literature, 131 potential homologs were found in the L. fortunei transcriptome, of which 15 were overexpressed in males and four in females. To this group belong gene families relevant to sexual development in various organisms, from mammals to invertebrates, such as Dmrt (doublesex and mab3-related-transcription factor), Sox (SRY-related HMG-box) and Fox (forkhead box).

bioinformatics↗

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↗

bioRxiv2018

First Draft Genome of a Brazilian Atlantic Rainforest Burseraceae reveals commercially-promising genes involved in terpenic oleoresins synthesis

BackgroundProtium species produce abundant aromatic oleoresins composed mainly of different types of terpenes, which are highly sought after by the flavor and fragrance industry.\n\nResultsHere we present (i) the first draft genome of an endemic tree of the Brazils Atlantic Rainforest (Mata Atlantica), Protium kleinii Cuatrec., (ii) a first characterization of its genes involved in the terpene pathways, and (iii) the composition of the resins volatile fraction. The de novo draft genome was assembled using Illumina paired-end-only data, totalizing 407 Mb in size present in 229,912 scaffolds. The N50 is 2.60 Kb and the longest scaffold is 52.26 Kb. Despite its fragmentation, we were able to infer 53,538 gene models of which 5,434 were complete. The draft genome of P. kleinii presents 76.67 % (62.01 % complete and 14.66 % partial) of plant-core BUSCO genes. InterProScan was able to assign at least one Gene Ontology annotation and one Pfam domain for 13,629 and 26,469 sequences, respectively. We were able to identify 116 enzymes involved in terpene biosynthesis, such as monoterpenes -terpineol, 1,8-cineole, geraniol, (+)-neomenthol and (+)-(R)-limonene. Through the phylogenetic analysis of the Terpene Synthases gene family, three candidates of limonene synthase were identified. Chemical analysis of the resins volatile fraction identified four monoterpenes: terpinolene, limonene, -pinene and -phellandrene.\n\nConclusionThese results provide resources for further studies to identify the molecular bases of the main aroma compounds and new biotechnological approaches to their production.

genomics↗