scholarly journals A Chromosome-Level Genome Assembly of Mozambique Tilapia (Oreochromis mossambicus) Reveals the Structure of Sex Determining Regions

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenjing Tao ◽  
Jianmeng Cao ◽  
Hesheng Xiao ◽  
Xi Zhu ◽  
Junjian Dong ◽  
...  
Keyword(s):  
Sex Determination ◽  
Genome Assembly ◽  
Oreochromis Mossambicus ◽  
Missense Mutations ◽  
Sequencing Data ◽  
High Coverage ◽  
Mozambique Tilapia ◽  
High Quality Genome ◽  
Chromosome Level

The Mozambique tilapia (Oreochromis mossambicus) is a fascinating taxon for evolutionary and ecological research. It is an important food fish and one of the most widely distributed tilapias. Because males grow faster than females, genetically male tilapia are preferred in aquaculture. However, studies of sex determination and sex control in O. mossambicus have been hindered by the limited characterization of the genome. To address this gap, we assembled a high-quality genome of O. mossambicus, using a combination of high coverage of Illumina and Nanopore reads, coupled with Hi-C and RNA-Seq data. Our genome assembly spans 1,007 Mb with a scaffold N50 of 11.38 Mb. We successfully anchored and oriented 98.6% of the genome on 22 linkage groups (LGs). Based on re-sequencing data for male and female fishes from three families, O. mossambicus segregates both an XY system on LG14 and a ZW system on LG3. The sex-patterned SNPs shared by two XY families narrowed the sex determining regions to ∼3 Mb on LG14. The shared sex-patterned SNPs included two deleterious missense mutations in ahnak and rhbdd1, indicating the possible roles of these two genes in sex determination. This annotated chromosome-level genome assembly and identification of sex determining regions represents a valuable resource to help understand the evolution of genetic sex determination in tilapias.

scholarly journals Chromosome-Level Assembly of the Common Lizard (Zootoca vivipara) Genome

2020 ◽  
Vol 12 (11) ◽  
pp. 1953-1960
Author(s):  
Andrey A Yurchenko ◽  
Hans Recknagel ◽  
Kathryn R Elmer
Keyword(s):  
Linkage Map ◽  
Single Copy ◽  
Phenotypic Traits ◽  
Sequencing Data ◽  
High Coverage ◽  
Squamate Reptiles ◽  
Common Lizard ◽  
Zootoca Vivipara ◽  
The Common ◽  
Chromosome Level

Abstract Squamate reptiles exhibit high variation in their phenotypic traits and geographical distributions and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46-Gb genome assembly has a scaffold N50 of 11.52 Mb with N50 contig size of 220.4 kb and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total, 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles.

scholarly journals Whole Genome Sequencing of the Mutamouse Model Reveals Strain- and Colony-Level Variation, and Genomic Features of the Transgene Integration Site

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Matthew J. Meier ◽  
Marc A. Beal ◽  
Andrew Schoenrock ◽  
Carole L. Yauk ◽  
Francesco Marchetti
Keyword(s):  
Integration Site ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Missense Mutations ◽  
Sequencing Data ◽  
Single Nucleotide Variants ◽  
High Coverage ◽  
Deletion Event ◽  
Transgene Integration

Abstract The MutaMouse transgenic rodent model is widely used for assessing in vivo mutagenicity. Here, we report the characterization of MutaMouse’s whole genome sequence and its genetic variants compared to the C57BL/6 reference genome. High coverage (>50X) next-generation sequencing (NGS) of whole genomes from multiple MutaMouse animals from the Health Canada (HC) colony showed ~5 million SNVs per genome, ~20% of which are putatively novel. Sequencing of two animals from a geographically separated colony at Covance indicated that, over the course of 23 years, each colony accumulated 47,847 (HC) and 17,677 (Covance) non-parental homozygous single nucleotide variants. We found no novel nonsense or missense mutations that impair the MutaMouse response to genotoxic agents. Pairing sequencing data with array comparative genomic hybridization (aCGH) improved the accuracy and resolution of copy number variants (CNVs) calls and identified 300 genomic regions with CNVs. We also used long-read sequence technology (PacBio) to show that the transgene integration site involved a large deletion event with multiple inversions and rearrangements near a retrotransposon. The MutaMouse genome gives important genetic context to studies using this model, offers insight on the mechanisms of structural variant formation, and contributes a framework to analyze aCGH results alongside NGS data.

scholarly journals ESCA pipeline: Easy-to-use SARS-CoV-2 genome Assembler

2021 ◽  
Author(s):  
Martina Rueca ◽  
Emanuela Giombini ◽  
Francesco Messina ◽  
Barbara Bartolini ◽  
Antonino Di Caro ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genome Assembly ◽  
Global Level ◽  
Sequencing Data ◽  
High Quality ◽  
Rapid Succession ◽  
Novel Variants ◽  
Low Coverage ◽  
High Quality Genome ◽  
Genome Assembler

Early sequencing and quick analysis of SARS-CoV-2 genome are contributing to un-derstand the dynamics of COVID19 epidemics and to countermeasures design at global level. Amplicon-based NGS methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession, harboring multiple deletions and amino acid changing mutations. To facilitate the analysis of NGS sequencing data obtained from amplicon-based sequencing methods, here we propose an easy-to-use SARS-CoV-2 genome Assembler: the ESCA pipeline. Results showed that ESCA can perform high quality genome assembly from IonTor-rent and Illumina raw data, and help the user in easily correct low-coverage regions. Moreover, ESCA includes the possibility to compare assembled genomes of multi sample runs through an easy table format.

scholarly journals A chromosome-level genome assembly and annotation of the humpback grouper Cromileptes altivelas

2020 ◽  
Author(s):  
Yun Sun ◽  
Dongdong Zhang ◽  
Jianzhi Shi ◽  
Guisen Chen ◽  
Ying Wu ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Chromosome Conformation ◽  
Protein Coding ◽  
Market Values ◽  
Final Assembly ◽  
Long Reads ◽  
High Gene ◽  
Food Fish ◽  
High Quality Genome ◽  
Chromosome Level

AbstractCromileptes altivelas that belongs to Serranidae in the order Perciformes, is widely distributed throughout the tropical waters of the Indo-West Pacific regions. Due to their excellent food quality and abundant nutrients, it has become a popular marine food fish with high market values. Here, we reported a chromosome-level genome assembly and annotation of the humpback grouper genome using more than 103X PacBio long-reads and high-throughput chromosome conformation capture (Hi-C) technologies. The N50 contig length of the assembly is as large as 4.14 Mbp, the final assembly is 1.07 Gb with N50 of scaffold 44.78 Mb, and 99.24% of the scaffold sequences were anchored into 24 chromosomes. The high-quality genome assembly also showed high gene completeness with 27,067 protein coding genes and 3,710 ncRNAs. This high accurate genome assembly and annotation will not only provide an essential genome resource for C. altivelas breeding and restocking, but will also serve as a key resource for studying fish genomics and genetics.

scholarly journals A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

2020 ◽  
Author(s):  
Tanaporn Uengwetwanit ◽  
Wirulda Pootakham ◽  
Intawat Nookaew ◽  
Chutima Sonthirod ◽  
Pacharaporn Angthong ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Penaeus Monodon ◽  
High Quality ◽  
High Molecular Weight Dna ◽  
Breeding Programs ◽  
Crustacean Species ◽  
Black Tiger Shrimp ◽  
Tiger Shrimp ◽  
High Quality Genome ◽  
Chromosome Level

AbstractThe black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.

scholarly journals The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Andrew Catanach ◽  
Mike Ruigrok ◽  
Deepa Bowatte ◽  
Marcus Davy ◽  
Roy Storey ◽  
...  
Keyword(s):  
New Zealand ◽  
Sex Determination ◽  
Genome Assembly ◽  
De Novo ◽  
Chromosome 21 ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Male Specimen ◽  
Sex Marker

Abstract Background The genetic control of sex determination in teleost species is poorly understood. This is partly because of the diversity of mechanisms that determine sex in this large group of vertebrates, including constitutive genes linked to sex chromosomes, polygenic constitutive mechanisms, environmental factors, hermaphroditism, and unisexuality. Here we use a de novo genome assembly of New Zealand silver trevally (Pseudocaranx georgianus) together with sex-specific whole genome sequencing data to detect sexually divergent genomic regions, identify candidate genes and develop molecular makers. Results The de novo assembly of an unsexed trevally (Trevally_v1) resulted in a final assembly of 579.4 Mb in length, with a N50 of 25.2 Mb. Of the assembled scaffolds, 24 were of chromosome scale, ranging from 11 to 31 Mb in length. A total of 28,416 genes were annotated after 12.8 % of the assembly was masked with repetitive elements. Whole genome re-sequencing of 13 wild sexed trevally (seven males and six females) identified two sexually divergent regions located on two scaffolds, including a 6 kb region at the proximal end of chromosome 21. Blast analyses revealed similarity between one region and the aromatase genes cyp19 (a1a/b) (E-value < 1.00E-25, identity > 78.8 %). Males contained higher numbers of heterozygous variants in both regions, while females showed regions of very low read-depth, indicative of male-specificity of this genomic region. Molecular markers were developed and subsequently tested on 96 histologically-sexed fish (42 males and 54 females). Three markers amplified in absolute correspondence with sex (positive in males, negative in females). Conclusions The higher number of heterozygous variants in males combined with the absence of these regions in females support a XY sex-determination model, indicating that the trevally_v1 genome assembly was developed from a male specimen. This sex system contrasts with the ZW sex-determination model documented in closely related carangid species. Our results indicate a sex-determining function of a cyp19a1a-like gene, suggesting the molecular pathway of sex determination is somewhat conserved in this family. The genomic resources developed here will facilitate future comparative work, and enable improved insights into the varied sex determination pathways in teleosts. The sex marker developed in this study will be a valuable resource for aquaculture selective breeding programmes, and for determining sex ratios in wild populations.

Molecular characterization of sdf1 and cxcr4 in the Mozambique tilapia, Oreochromis mossambicus

2017 ◽  
Vol 176 ◽  
pp. 51-63 ◽  
Author(s):  
Jorge Amat-Fernandez ◽  
Michael J. Hammond ◽  
Di Liang ◽  
Tianfang Wang ◽  
Tomer Ventura ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Oreochromis Mossambicus ◽  
Mozambique Tilapia
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