Hashimoto, D. T. | bioRxiv Science

bioRxiv2024

De novo assembly and characterization of a highly degenerated ZW sex chromosome in the fish Megaleporinus macrocephalus

BackgroundMegaleporinus macrocephalus (piaucu) is a Neotropical fish within Characoidei that presents a well-established heteromorphic ZZ/ZW sex-determination system and thus, constitutes a good model for studying W and Z chromosomes in fishes. We used PacBio reads and Hi-C to assemble a chromosome-level reference genome for M. macrocephalus. We generated family segregation information to construct a genetic map, pool-seq of males and females to characterize its sex system, and RNA-seq to highlight candidate genes of M. macrocephalus sex determination. ResultsM. macrocephalus reference genome is 1,282,030,339 bp in length and has a contig and scaffold N50 of 5.0 Mb and 45.03 Mb, respectively. Based on patterns of recombination suppression, coverage, Fst, and sex-specific SNPs, three major regions were distinguished in the sex chromosome: W-specific (highly differentiated), Z-specific (in degeneration), and PAR. The sex chromosome gene repertoire was composed of genes from the TGF-{beta} family (amhr2, bmp7) and Wnt/{beta}-catenin pathway (wnt4, wnt7a), and some of them were differentially expressed. ConclusionsThe chromosome-level genome of piaucu exhibits high quality, establishing a valuable resource for advancing research within the group. Our discoveries offer insights into the evolutionary dynamics of Z and W sex chromosomes in fish, emphasizing ongoing degenerative processes and indicating complex interactions between Z and W sequences in specific genomic regions. Notably, amhr2 and bmp7 are potential candidate genes for sex determination in M. macrocephalus.

genomics↗

bioRxiv2022

Genetic diversity, virulence, antimicrobial resistance genes, and antimicrobial susceptibility of group B Streptococcus (GBS) linked to mass mortalities of cultured Nile tilapia in Brazil

Streptococcus agalactiae, group B Streptococcus (GBS), is the main bacterial pathogen of cultured Nile tilapia in many countries and causes extensive deaths in all stages of the farming cycle throughout the year. This study investigated the genetic diversity, virulence, presence of antibiotic resistance genes and antimicrobial susceptibility of 72 GBS linked to mass mortalities of cultured Nile tilapia in Brazil. Isolate identity was confirmed by morphological, biochemical and molecular analyses. Capsular serotype, multi-locus sequence typing (MLST) allelic profiles and putative pathogenic factors were identified by polymerase chain reaction (PCR), gel electrophoresis, sequencing and molecular analyses of different genes. The presence of antimicrobial resistance genes and antimicrobial susceptibility to florfenicol (FFC), oxytetracycline (OTC), thiamphenicol (TAP) and their combination were evaluated by PCR, followed by gel electrophoresis, and broth microdilution antimicrobial susceptibility testing, respectively. All clinical isolates studied were confirmed to be GBS, one from serotype III (IA2022) and 71 from serotype Ib, suggesting that serotype Ib was the most prevalent strain between 2011 and 2016 in the south and southern and southeastern regions of Brazil. Eight different allelic profiles were identified for the first time, being adhP- 52, pheS-2, atr-31, glnA-4, sdhA-2, tkt-19 the most predominant. Between one (glcK) and three (adhP and glnA) alleles were present at each locus. All strains, except IA2022, showed a partial gene deletion event on the glcK gene. The surface protein Rib and hypervirulent GBS adhesin BibA were detected in all strains, except for 18P, which was negative for rib. On the other hand, and {beta} antigens of the C protein were only detected in IA2022. All antimicrobials showed high minimum inhibitory concentration (MIC [≥] 16 {micro}g/mL) values against several strains with negative results for resistance genes. Despite indifference and antagonism being the most predominant activities in all combinations evaluated, the record of synergism, including in a strain with a resistance gene and phenotypic resistance, suggests that combination therapy can have therapeutic efficacy when well planned. The combination involving OTC and TAP or FFC is a likely candidate for improving the treatment of streptococcosis using combination therapy, even for strains showing phenotypic and genotypic resistance to OTC. This study provides pertinent data on pathogenic GBS genetic diversity, virulence, the presence of antibiotic resistance genes and antimicrobial susceptibility, which may be useful in the development of effective vaccines and therapeutic strategies for the prevention and control of streptococcosis in aquaculture farms.

microbiology↗