scholarly journals Inference of a genome-wide protein-coding gene set of the inshore hagfish Eptatretus burgeri

2020 ◽  
Author(s):  
Kazuaki Yamaguchi ◽  
Yuichiro Hara ◽  
Kaori Tatsumi ◽  
Osamu Nishimura ◽  
Jeramiah J. Smith ◽  
...  
Keyword(s):  
Single Copy ◽  
Sequence Information ◽  
High Coverage ◽  
Protein Coding ◽  
Sequencing Platform ◽  
Genome Wide ◽  
Mate Pair ◽  
A Genome ◽  
Gene Models ◽  
High Utility

AbstractThe group of hagfishes (Myxiniformes) arose from agnathan (jawless vertebrate) lineages and is one of the only two extant cyclostome taxa, together with lampreys (Petromyzontiformes). Even though whole genome sequencing has been achieved for diverse vertebrate taxa, genome-wide sequence information has been highly limited for cyclostomes. Here we sequenced the genome of the inshore hagfish Eptatretus burgeri using DNA extracted from the testis, with a short-read sequencing platform, aiming at reconstructing a high-coverage coding gene catalogue. The obtained genome assembly, scaffolded with mate-pair reads and paired RNA-seq reads, exhibited an N50 scaffold length of 293 Kbp, which allowed the genome-wide prediction of coding genes. This computation resulted in the gene models whose completeness was estimated at the complete coverage of more than 83 % and the partial coverage of more than 93 % by referring to evolutionarily conserved single-copy orthologs. The high contiguity of the assembly and completeness of resulting gene models promises a high utility in various comparative analyses including phylogenomics and phylome exploration.

scholarly journals A Nonsense Variant in Hephaestin Like 1 (HEPHL1) Is Responsible for Congenital Hypotrichosis in Belted Galloway Cattle

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 643
Author(s):  
Thibaud Kuca ◽  
Brandy M. Marron ◽  
Joana G. P. Jacinto ◽  
Julia M. Paris ◽  
Christian Gerspach ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Homozygosity Mapping ◽  
Mendelian Inheritance ◽  
Large Animal Model ◽  
Large Animal ◽  
Loss Of Function ◽  
Protein Coding ◽  
Positional Candidate ◽  
Genome Wide ◽  
A Genome

Genodermatosis such as hair disorders mostly follow a monogenic mode of inheritance. Congenital hypotrichosis (HY) belong to this group of disorders and is characterized by abnormally reduced hair since birth. The purpose of this study was to characterize the clinical phenotype of a breed-specific non-syndromic form of HY in Belted Galloway cattle and to identify the causative genetic variant for this recessive disorder. An affected calf born in Switzerland presented with multiple small to large areas of alopecia on the limbs and on the dorsal part of the head, neck, and back. A genome-wide association study using Swiss and US Belted Galloway cattle encompassing 12 cases and 61 controls revealed an association signal on chromosome 29. Homozygosity mapping in a subset of cases refined the HY locus to a 1.5 Mb critical interval and subsequent Sanger sequencing of protein-coding exons of positional candidate genes revealed a stop gain variant in the HEPHL1 gene that encodes a multi-copper ferroxidase protein so-called hephaestin like 1 (c.1684A>T; p.Lys562*). A perfect concordance between the homozygous presence of this most likely pathogenic loss-of-function variant and the HY phenotype was found. Genotyping of more than 700 purebred Swiss and US Belted Galloway cattle showed the global spread of the mutation. This study provides a molecular test that will permit the avoidance of risk matings by systematic genotyping of relevant breeding animals. This rare recessive HEPHL1-related form of hypotrichosis provides a novel large animal model for similar human conditions. The results have been incorporated in the Online Mendelian Inheritance in Animals (OMIA) database (OMIA 002230-9913).

A porcine brain-wide RNA editing landscape

2020 ◽  
Author(s):  
Jinrong Huang ◽  
Lin Lin ◽  
Zhanying Dong ◽  
Ling Yang ◽  
Tianyu Zheng ◽  
...  
Keyword(s):  
Rna Editing ◽  
Repetitive Sequences ◽  
Brain Regions ◽  
Mammalian Brain ◽  
Protein Coding ◽  
Porcine Brain ◽  
Coding Regions ◽  
Pig Brain ◽  
Genome Wide ◽  
A Genome

Abstract Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is an essential post-transcriptional modification. Although hundreds of thousands of RNA editing sites have been reported in mammals, brain-wide analysis of the RNA editing in the mammalian brain remains rare. Here, a genome-wide RNA editing investigation is performed in 119 samples, representing 30 anatomically defined subregions in the pig brain. We identify a total of 682,037 A-to-I RNA editing sites of which 97% are not identified before. Within the pig brain, cerebellum and olfactory bulb are regions with most edited transcripts. The editing level of sites residing in protein-coding regions are similar across brain regions, whereas region-distinct editing is observed in repetitive sequences. Highly edited conserved recoding events in pig and human brain are found in neurotransmitter receptors, demonstrating the evolutionary importance of RNA editing in neurotransmission functions. The porcine brain-wide RNA landscape provides a rich resource to better understand the evolutionally importance of post-transcriptional RNA editing.

scholarly journals Repertoire-wide gene structure analyses: a case study comparing automatically predicted and manually annotated gene models

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jeanne Wilbrandt ◽  
Bernhard Misof ◽  
Kristen A. Panfilio ◽  
Oliver Niehuis
Keyword(s):  
Structural Properties ◽  
Gene Structure ◽  
Comparative Studies ◽  
Gene Repertoire ◽  
Manual Annotation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Gene Sets ◽  
A Genome ◽  
Gene Models

Abstract Background The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies on gene structure, gene repertoires, and genome evolution. However, automatic annotation algorithms do not yet correctly identify all genes within a genome, and manual annotation is often necessary to obtain accurate gene models and gene sets. As manual annotation is time-consuming, only a fraction of the gene models in a genome is typically manually annotated, and this fraction often differs between species. To assess the impact of manual annotation efforts on genome-wide analyses of gene structural properties, we compared the structural properties of protein-coding genes in seven diverse insect species sequenced by the i5k initiative. Results Our results show that the subset of genes chosen for manual annotation by a research community (3.5–7% of gene models) may have structural properties (e.g., lengths and exon counts) that are not necessarily representative for a species’ gene set as a whole. Nonetheless, the structural properties of automatically generated gene models are only altered marginally (if at all) through manual annotation. Major correlative trends, for example a negative correlation between genome size and exonic proportion, can be inferred from either the automatically predicted or manually annotated gene models alike. Vice versa, some previously reported trends did not appear in either the automatic or manually annotated gene sets, pointing towards insect-specific gene structural peculiarities. Conclusions In our analysis of gene structural properties, automatically predicted gene models proved to be sufficiently reliable to recover the same gene-repertoire-wide correlative trends that we found when focusing on manually annotated gene models only. We acknowledge that analyses on the individual gene level clearly benefit from manual curation. However, as genome sequencing and annotation projects often differ in the extent of their manual annotation and curation efforts, our results indicate that comparative studies analyzing gene structural properties in these genomes can nonetheless be justifiable and informative.

scholarly journals Progress in plant genome sequencing: research directions

2019 ◽  
Vol 23 (1) ◽  
pp. 38-48 ◽  
Author(s):  
M. K. Bragina ◽  
D. A. Afonnikov ◽  
E. A. Salina
Keyword(s):  
Genome Sequencing ◽  
Plant Traits ◽  
Plant Genome ◽  
Targeted Sequencing ◽  
Genome Sequences ◽  
Crop Species ◽  
High Coverage ◽  
Protein Coding ◽  
Sequencing Technologies ◽  
A Genome

Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.

scholarly journals Host cell factors important for BHV-1 cell entry revealed by genome-wide CRISPR knockout screen

2020 ◽  
Author(s):  
Wenfang Spring Tan ◽  
Enguang Rong ◽  
Inga Dry ◽  
Simon Lillico ◽  
Andy Law ◽  
...  
Keyword(s):  
Host Cell ◽  
Viral Entry ◽  
Surface Proteins ◽  
Chain Elongation ◽  
Related Factors ◽  
Protein Coding ◽  
Cog Complex ◽  
Genome Wide ◽  
A Genome ◽  
Mdbk Cells

AbstractIn order to identify host factors that impact Bovine Herpes Virus Type 1 (BHV-1) infection we previously applied a genome wide CRISPR knockout screen with a library covering all bovine protein coding genes. We compiled a list of both pro-viral and anti-viral proteins involved in BHV-1 replication; here we provide further analysis of those that are potentially involved in viral entry into the host cell. These entry related factors include the cell surface proteins PVR and PVRL2, a group of enzymes directly or indirectly associated with the biosynthesis of Heparan Sulfate Proteoglycans (HSPG), and proteins that reside in the Golgi apparatus engaging in intra-Golgi trafficking. For the first time, we provide evidence that PVRL2 serves a receptor for BHV-1, mediating more efficient entry than the previously identified PVR. By knocking out two enzymes that catalyze HSPG chain elongation, HST2ST1 and GLCE, we demonstrated the significance of HSPG in BHV-1 entry. Another intriguing cluster of genes, COG1, COG2 and COG4-7 encodes for six subunits of the conserved oligomeric Golgi (COG) complex. MDBK cells lacking COG6 were less infectable by BHV-1 but release newly produced virions more efficiently as evidenced by fewer but bigger plaques compared to control cells, suggesting impaired HSPG biosynthesis. To facilitate candidate validation, we devised a one-step multiplex CRISPR interference (CRISPRi) system named CRISPR3i that enables quick and simultaneous deployment of three CRISPRs for efficient gene inactivation. Using CRISPR3i, we verified an additional 23 candidates, with many implicated in cellular entry.

scholarly journals Genome-wide sexually antagonistic variants reveal longstanding constraints on sexual dimorphism in the fruitfly

2017 ◽  
Author(s):  
Filip Ruzicka ◽  
Mark S. Hill ◽  
Tanya M. Pennell ◽  
Ilona Flis ◽  
Fiona C. Ingleby ◽  
...  
Keyword(s):  
Sexual Dimorphism ◽  
Evolutionary Dynamics ◽  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Sexual Antagonism ◽  
Protein Coding ◽  
Genome Wide ◽  
Genomic Location ◽  
Classic Theory ◽  
A Genome

The evolution of sexual dimorphism is constrained by a shared genome, leading to ‘sexual antagonism’ where different alleles at given loci are favoured by selection in males and females. Despite its wide taxonomic incidence, we know little about the identity, genomic location and evolutionary dynamics of antagonistic genetic variants. To address these deficits, we use sex-specific fitness data from 202 fully sequenced hemiclonal D. melanogaster fly lines to perform a genome-wide association study of sexual antagonism. We identify ~230 chromosomal clusters of candidate antagonistic SNPs. In contradiction to classic theory, we find no clear evidence that the X chromosome is a hotspot for sexually antagonistic variation. Characterising antagonistic SNPs functionally, we find a large excess of missense variants but little enrichment in terms of gene function. We also assess the evolutionary persistence of antagonistic variants by examining extant polymorphism in wild D. melanogaster populations. Remarkably, antagonistic variants are associated with multiple signatures of balancing selection across the D. melanogaster distribution range, indicating widespread and evolutionarily persistent (>10,000 years) genomic constraints. Based on our results, we propose that antagonistic variation accumulates due to constraints on the resolution of sexual conflict over protein coding sequences, thus contributing to the long-term maintenance of heritable fitness variation.

scholarly journals Cell-specific cis-natural antisense transcripts (cis-NATs) in the sperm and the pollen vegetative cells of Arabidopsis thaliana

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 93
Author(s):  
Peng Qin ◽  
Ann E. Loraine ◽  
Sheila McCormick
Keyword(s):  
Gene Expression ◽  
Vegetative Cell ◽  
Cell Types ◽  
Antisense Transcripts ◽  
Vegetative Cells ◽  
Natural Antisense Transcripts ◽  
Protein Coding ◽  
Regulate Gene Expression ◽  
Genome Wide ◽  
Gene Models

Background: cis-NATs (cis-natural antisense transcripts) are transcribed from opposite strands of adjacent genes and have been shown to regulate gene expression by generating small RNAs from the overlapping region. cis-NATs are important for plant development and resistance to pathogens and stress. Several genome-wide investigations identified a number of cis-NAT pairs, but these investigations predicted cis-NATS using expression data from bulk samples that included lots of cell types. Some cis-NAT pairs identified from those investigations might not be functional, because both transcripts of cis-NAT pairs need to be co-expressed in the same cell. Pollen only contains two cell types, two sperm and one vegetative cell, which makes cell-specific investigation of cis-NATs possible. Methods: We investigated potential protein-coding cis-NATs in pollen and sperm using pollen RNA-seq data and TAIR10 gene models using the Integrated Genome Browser.  We then used sperm microarray data and sRNAs in sperm and pollen to determine possibly functional cis-NATs in the sperm or vegetative cell, respectively. Results: We identified 1471 potential protein-coding cis-NAT pairs, including 131 novel pairs that were not present in TAIR10 gene models. In pollen, 872 possibly functional pairs were identified. 72 and 56 pairs were potentially functional in sperm and vegetative cells, respectively. sRNAs were detected at 794 genes, belonging to 739 pairs. Conclusion: These potential candidates in sperm and the vegetative cell are tools for understanding gene expression mechanisms in pollen.

scholarly journals Genome Assembly of the Dogface Butterfly Zerene cesonia

2019 ◽  
Vol 12 (1) ◽  
pp. 3580-3585 ◽  
Author(s):  
Luis Rodriguez-Caro ◽  
Jennifer Fenner ◽  
Caleb Benson ◽  
Steven M Van Belleghem ◽  
Brian A Counterman
Keyword(s):  
Genome Assembly ◽  
Developmental Plasticity ◽  
Hybrid Approach ◽  
Single Copy ◽  
Z Chromosome ◽  
High Quality ◽  
Protein Coding ◽  
Genomic Change ◽  
A Genome ◽  
Genomic Studies

Abstract Comparisons of high-quality, reference butterfly, and moth genomes have been instrumental to advancing our understanding of how hybridization, and natural selection drive genomic change during the origin of new species and novel traits. Here, we present a genome assembly of the Southern Dogface butterfly, Zerene cesonia (Pieridae) whose brilliant wing colorations have been implicated in developmental plasticity, hybridization, sexual selection, and speciation. We assembled 266,407,278 bp of the Z. cesonia genome, which accounts for 98.3% of the estimated 271 Mb genome size. Using a hybrid approach involving Chicago libraries with Hi-Rise assembly and a diploid Meraculous assembly, the final haploid genome was assembled. In the final assembly, nearly all autosomes and the Z chromosome were assembled into single scaffolds. The largest 29 scaffolds accounted for 91.4% of the genome assembly, with the remaining ∼8% distributed among another 247 scaffolds and overall N50 of 9.2 Mb. Tissue-specific RNA-seq informed annotations identified 16,442 protein-coding genes, which included 93.2% of the arthropod Benchmarking Universal Single-Copy Orthologs (BUSCO). The Z. cesonia genome assembly had ∼9% identified as repetitive elements, with a transposable element landscape rich in helitrons. Similar to other Lepidoptera genomes, Z. cesonia showed a high conservation of chromosomal synteny. The Z. cesonia assembly provides a high-quality reference for studies of chromosomal arrangements in the Pierid family, as well as for population, phylo, and functional genomic studies of adaptation and speciation.

scholarly journals Whole Genome Sequencing of the Blue Tilapia (Oreochromis aureus) Provides a Valuable Genetic Resource for Biomedical Research on Tilapias

Marine Drugs ◽  
2019 ◽  
Vol 17 (7) ◽  
pp. 386 ◽  
Author(s):  
Chao Bian ◽  
Jia Li ◽  
Xueqiang Lin ◽  
Xiyang Chen ◽  
Yunhai Yi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Genetic Resource ◽  
Draft Genome ◽  
Close Relative ◽  
Protein Coding ◽  
Oreochromis Aureus ◽  
Genome Wide ◽  
A Genome ◽  
Blue Tilapia ◽  
First Time

Blue tilapia (Oreochromis aureus) has been an economically important fish in Asian countries. It can grow and reproduce in both freshwater and brackish water conditions, whereas it is also considered as a significant invasive species around the world. This species has been widely used as the hybridization parent(s) for tilapia breeding with a major aim to produce novel strains. However, available genomic resources are still limited for this important tilapia species. Here, we for the first time sequenced and assembled a draft genome for a seawater cultured blue tilapia (0.92 Gb), with 97.8% completeness and a scaffold N50 of 1.1 Mb, which suggests a relatively high quality of this genome assembly. We also predicted 23,117 protein-coding genes in the blue tilapia genome. Comparisons of predicted antimicrobial peptides between the blue tilapia and its close relative Nile tilapia proved that these immunological genes are highly similar with a genome-wide scattering distribution. As a valuable genetic resource, our blue tilapia genome assembly will benefit for biomedical researches and practical molecular breeding for high resistance to various diseases, which have been a critical problem in the aquaculture of tilapias.

scholarly journals A porcine brain-wide RNA editing landscape

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jinrong Huang ◽  
Lin Lin ◽  
Zhanying Dong ◽  
Ling Yang ◽  
Tianyu Zheng ◽  
...  
Keyword(s):  
Rna Editing ◽  
Repetitive Sequences ◽  
Brain Regions ◽  
Mammalian Brain ◽  
Protein Coding ◽  
Coding Regions ◽  
Pig Brain ◽  
Genome Wide ◽  
A Genome ◽  
Editing Level

AbstractAdenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is an essential post-transcriptional modification. Although hundreds of thousands of RNA editing sites have been reported in mammals, brain-wide analysis of the RNA editing in the mammalian brain remains rare. Here, a genome-wide RNA-editing investigation is performed in 119 samples, representing 30 anatomically defined subregions in the pig brain. We identify a total of 682,037 A-to-I RNA editing sites of which 97% are not identified before. Within the pig brain, cerebellum and olfactory bulb are regions with most edited transcripts. The editing level of sites residing in protein-coding regions are similar across brain regions, whereas region-distinct editing is observed in repetitive sequences. Highly edited conserved recoding events in pig and human brain are found in neurotransmitter receptors, demonstrating the evolutionary importance of RNA editing in neurotransmission functions. Although potential data biases caused by age, sex or health status are not considered, this study provides a rich resource to better understand the evolutionary importance of post-transcriptional RNA editing.

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