scholarly journals Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity

2020 ◽  
Vol 10 (3) ◽  
pp. 907-915 ◽  
Author(s):  
Yusuke Takehana ◽  
Margot Zahm ◽  
Cédric Cabau ◽  
Christophe Klopp ◽  
Céline Roques ◽  
...  
Keyword(s):  
Draft Genome ◽  
Mangrove Ecosystem ◽  
Model Organisms ◽  
Comparative Genomic ◽  
Draft Genome Assembly ◽  
Functional Studies ◽  
Fish Model ◽  
Oryzias Javanicus ◽  
Wide Range ◽  
Adaptation To Salinity

The genus Oryzias consists of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behavior, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies. Complementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6,3 Mbp and a L50 of 37 scaffolds. We identified 21454 predicted transcripts for a total transcriptome size of 57, 146, 583 bps. We provide here a high-quality chromosome scale draft genome assembly of the euryhaline Javafish medaka (321 scaffolds anchored on 24 chromosomes (representing 97.7% of the total bases)), and give emphasis on the evolutionary adaptation to salinity.

scholarly journals Genome sequence of the euryhaline Javafish medaka, Oryzias javanicus: a small aquarium fish model for studies on adaptation to salinity

2019 ◽  
Author(s):  
Yusuke Takehana ◽  
Margot Zahm ◽  
Cédric Cabau ◽  
Christophe Klopp ◽  
Céline Roques ◽  
...  
Keyword(s):  
Draft Genome ◽  
Mangrove Ecosystem ◽  
Model Organisms ◽  
Comparative Genomic ◽  
Draft Genome Assembly ◽  
Functional Studies ◽  
Fish Model ◽  
Oryzias Javanicus ◽  
Wide Range ◽  
Adaptation To Salinity

ABSTRACTBackgroundThe genus Oryzias is constituted of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behaviour, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies.FindingsComplementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6.3 Mbp and a L50 of 37 scaffolds. We identified 21454 expressed transcripts for a total transcriptome size of 57, 146, 583 bps.ConclusionsWe provide here a high-quality draft genome assembly of the euryhaline Javafish medaka, and give emphasis on the evolutionary adaptation to salinity.

scholarly journals Draft Genome of Cochliopodium minus (Amoebozoa): Insights into Its Complex Sexual Behavior, Across Domain Gene Acquisitions and Metazoan Type Signaling

2022 ◽  
Author(s):  
Yonas I. Tekle ◽  
Fang Wang ◽  
Hanh Tran ◽  
T. Danielle Hayes ◽  
Joseph F. Ryan
Keyword(s):  
Sexual Behavior ◽  
Tyrosine Kinases ◽  
Draft Genome ◽  
Model Organisms ◽  
Transcriptome Data ◽  
Ideal Model ◽  
Transcriptomic Data ◽  
Draft Genome Assembly ◽  
Genomic Analyses ◽  
Key Genes

Abstract To date, genomic analyses in amoebozoans have been mostly limited to model organisms or medically important lineages. Consequently, the vast diversity of Amoebozoa genomes remain unexplored. A draft genome of Cochliopodium minus, an amoeba characterized by extensive cellular and nuclear fusions, is presented. C. minus has been a subject of recent investigation for its unusual sexual behavior. Cochliopodium’s sexual activity occurs during vegetative stage making it an ideal model for studying sexual development, which is sorely lacking in the group. Here we generate a C. minus draft genome assembly. From this genome, we detect a substantial number of lateral gene transfer (LGT) instances from bacteria (15%), archaea (0.9%) and viruses (0.7%) the majority of which are detected in our transcriptome data. We identify the complete meiosis toolkit genes in the C. minus genome, as well as the absence of several key genes involved in plasmogamy and karyogamy. Comparative genomics of amoebozoans reveals variation in sexual mechanism exist in the group. Similar to complex eukaryotes, C. minus (some amoebae) possesses Tyrosine kinases and duplicate copies of SPO11. We report a first example of alternative splicing in a key meiosis gene and draw important insights on molecular mechanism of sex in C. minus using genomic and transcriptomic data.

scholarly journals Draft Genome Assembly of the Entomopathogenic Bacterium Photorhabdus luminescens subsp. sonorensis Caborca

2019 ◽  
Vol 8 (36) ◽  
Author(s):  
Duy An Duong ◽  
Patricia Espinosa-Artiles ◽  
Rousel A. Orozco ◽  
István Molnár ◽  
S. Patricia Stock
Keyword(s):  
Secondary Metabolism ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gene Clusters ◽  
Insect Species ◽  
Photorhabdus Luminescens ◽  
Putative Gene ◽  
Content Type ◽  
Draft Genome Assembly ◽  
Wide Range

Photorhabdus luminescens subsp. sonorensis strain Caborca is an entomopathogenic bacterium with a dual lifestyle, namely, as a mutualist of the Heterorhabditis sonorensis nematode and a pathogen to a wide range of insect species. The genome assembly, in 231 contigs, is 5.2 Mbp long and includes 25 putative gene clusters for secondary metabolism.

scholarly journals Draft Genome of Cochliopodium minus (Amoebozoa): Insights into Its Complex Sexual Behavior, Across Domain Gene Acquisitions and Metazoan Type Signaling

2021 ◽  
Author(s):  
Yonas Isaak Tekle ◽  
Fang Wang ◽  
Hanh Tran ◽  
T. Danielle Hayes ◽  
Joseph F Ryan
Keyword(s):  
Sexual Behavior ◽  
Tyrosine Kinases ◽  
Draft Genome ◽  
Model Organisms ◽  
Transcriptome Data ◽  
Ideal Model ◽  
Transcriptomic Data ◽  
Draft Genome Assembly ◽  
Genomic Analyses ◽  
Key Genes

To date, genomic analyses in amoebozoans have been mostly limited to model organisms or medically important lineages. Consequently, the vast diversity of Amoebozoa genomes remain unexplored. A draft genome of Cochliopodium minus, an amoeba characterized by extensive cellular and nuclear fusions, is presented. C. minus has been a subject of recent investigation for its unusual sexual behavior. Cochliopodium's sexual activity occurs during vegetative stage making it an ideal model for studying sexual development, which is sorely lacking in the group. Here we generate a C. minus draft genome assembly. From this genome, we detect a substantial number of lateral gene transfer (LGT) instances from bacteria (15%), archaea (0.9%) and viruses (0.7%) the majority of which are detected in our transcriptome data. We identify the complete meiosis toolkit genes in the C. minus genome, as well as the absence of several key genes involved in plasmogamy and karyogamy. Comparative genomics of amoebozoans reveals variation in sexual mechanism exist in the group. Similar to complex eukaryotes, C. minus (some amoebae) possesses Tyrosine kinases and duplicate copies of SPO11. We report a first example of alternative splicing in a key meiosis gene and draw important insights on molecular mechanism of sex in C. minus using genomic and transcriptomic data.

scholarly journals ONT-based draft genome assembly and annotation of Alternaria atra

2021 ◽  
Author(s):  
Bhawna Bonthala ◽  
Corinn Sophia Small ◽  
Maximilian Anton Lutz ◽  
Alexander Graf ◽  
Stefan Krebs ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Plant Pathogens ◽  
Biocontrol Agent ◽  
Reference Genome ◽  
Gene Prediction ◽  
Draft Genome ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Reference Genome Assembly ◽  
Wide Range

Species of Alternaria (phylum Ascomycota, family Pleosporaceae) are known as serious plant pathogens, causing major losses on a wide range of crops. Alternaria atra (Preuss) Woudenb. & Crous (previously known as Ulocladium atrum) can grow as a saprophyte on many hosts and causes Ulocladium blight on potato. It has been reported that it can also be used as a biocontrol agent against a.o. Botrytis cinerea Here we present a scaffold-level reference genome assembly for A. atra. The assembly contains 43 scaffolds with a total length of 39.62 Mbp, with scaffold N50 of 3,893,166 bp , L50 of 4 and the longest 10 scaffolds containing 89.9% of the assembled data. RNA Seq-guided, gene prediction using BRAKER resulted in 12,173 protein-coding genes with their functional annotation. This first high-quality reference genome assembly and annotation for A. Atra can be used as a resource for studying evolution in the highly complicated Alternaria genus and might help understand the mechanisms defining its role as pathogen or biocontrol agent.

scholarly journals Diversity of Eukaryotic Translational Initiation Factor eIF4E in Protists

2012 ◽  
Vol 2012 ◽  
pp. 1-21 ◽  
Author(s):  
Rosemary Jagus ◽  
Tsvetan R. Bachvaroff ◽  
Bhavesh Joshi ◽  
Allen R. Place
Keyword(s):  
Regulation Of Gene Expression ◽  
Babesia Bovis ◽  
Initiation Factor ◽  
Model Organisms ◽  
Text Book ◽  
Translational Initiation ◽  
Functional Studies ◽  
Wide Range ◽  
Genome Features ◽  
Multicellular Organisms

The greatest diversity of eukaryotic species is within the microbial eukaryotes, the protists, with plants and fungi/metazoa representing just two of the estimated seventy five lineages of eukaryotes. Protists are a diverse group characterized by unusual genome features and a wide range of genome sizes from 8.2 Mb in the apicomplexan parasiteBabesia bovisto 112,000-220,050 Mb in the dinoflagellateProrocentrum micans. Protists possess numerous cellular, molecular and biochemical traits not observed in “text-book” model organisms. These features challenge some of the concepts and assumptions about the regulation of gene expression in eukaryotes. Like multicellular eukaryotes, many protists encode multiple eIF4Es, but few functional studies have been undertaken except in parasitic species. An earlier phylogenetic analysis of protist eIF4Es indicated that they cannot be grouped within the three classes that describe eIF4E family members from multicellular organisms. Many more protist sequences are now available from which three clades can be recognized that are distinct from the plant/fungi/metazoan classes. Understanding of the protist eIF4Es will be facilitated as more sequences become available particularly for the under-represented opisthokonts and amoebozoa. Similarly, a better understanding of eIF4Es within each clade will develop as more functional studies of protist eIF4Es are completed.

scholarly journals Prometheus: omics portals for interkingdom comparative genomic analyses

2017 ◽  
Author(s):  
Gunhwan Ko ◽  
Insu Jang ◽  
Namjin Koo ◽  
Seong-Jin Park ◽  
Sangho Oh ◽  
...  
Keyword(s):  
Domain Architecture ◽  
Industrial Applications ◽  
Model Organisms ◽  
Comparative Genomic ◽  
Identification System ◽  
New Paradigm ◽  
Comparative Analyses ◽  
Functional Studies ◽  
Gene Search ◽  
Functional Analyses

AbstractFunctional analyses of genes are crucial for unveiling biological responses, for genetic engineering, and for developing new medicines. However, functional analyses have largely been restricted to model organisms, representing a major hurdle for functional studies and industrial applications. To resolve this, comparative genome analyses can be used to provide clues to gene functions as well as their evolutionary history. To this end, we present Prometheus (http://prometheus.kobic.re.kr),web-based omics portal that contains more than 17,215 sequences from prokaryotic and eukaryotic genomes. This portal supports interkingdom comparative analyses via a domain architecture-based gene identification system, Gene Search, and users can easily and rapidly identify single or entire gene sets in specific pathways. Bioinformatics tools for further analyses are provided in Prometheus or through BioExpress, a cloud-based bioinformatics analysis platform. Prometheus suggests a new paradigm for comparative analyses with large amounts of genomic information.

scholarly journals Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader ‘Candidatus Leucobacter sulfamidivorax’ strain GP

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ana C. Reis ◽  
Boris A. Kolvenbach ◽  
Mohamed Chami ◽  
Luís Gales ◽  
Conceição Egas ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Culture Conditions ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Functional Studies ◽  
Conserved Genes ◽  
Gene Similarity

Abstract Background Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified. Results Previous studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements. Conclusions Comparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.

scholarly journals Complete Genome Sequence and Annotation of the Staphylococcus aureus Strain HG001

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
Isabelle Caldelari ◽  
Béatrice Chane-Woon-Ming ◽  
Céline Noirot ◽  
Karen Moreau ◽  
Pascale Romby ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Genome Assembly ◽  
Complete Genome Sequence ◽  
Draft Genome ◽  
Aureus Strain ◽  
Content Type ◽  
Draft Genome Assembly ◽  
Wide Range ◽  
Life Threatening ◽  
Current Annotation

ABSTRACT Staphylococcus aureus is an opportunistic Gram-positive pathogen responsible for a wide range of infections from minor skin abscesses to life-threatening diseases. Here, we report the draft genome assembly and current annotation of the HG001 strain, a derivative of the RN1 (NCT8325) strain with restored rbsU (a positive activator of SigB).

scholarly journals Draft genome of the Brazilian railroad worm Phrixothrix hirtus E.Olivier (Phengodidae: Coleoptera)

2021 ◽  
Author(s):  
Danilo Trabuco Amaral ◽  
Yasuo Mitani ◽  
Isabel Aparecida Silva Bonatelli ◽  
Ricardo Cerri ◽  
Yoshihiro Ohmiya ◽  
...  
Keyword(s):  
Gene Family ◽  
Genome Assembly ◽  
Red Light ◽  
Draft Genome ◽  
Gc Content ◽  
Gene Families ◽  
Neotropical Region ◽  
Comparative Genomic ◽  
List Type ◽  
Draft Genome Assembly

AbstractThe Neotropical region is the richest in bioluminescent Coleoptera species, however, its bioluminescence megadiversity is still underexplored in terms of genomic organization and evolution, mainly within the Phengodidae family. The railroad worm Phrixothrix hirtus is an important biological model and symbolic species due to its bicolor bioluminescence, being the only organism that produces true red light among bioluminescent terrestrial species. Here, we performed the partial genome assembly of P. hirtus, combining short and long reads generated with Illumina sequencing, providing an important source of genomic information and a framework for comparative genomic analyses for the evaluation of the bioluminescent system in Elateroidea. The estimated genome size has ∼3.4Gb, 32% of GC content, and 67% of repetitive elements, being the largest genome described in the Elateroidea superfamily. Several events of gene family expansions associated with anatomical development and morphogenesis, as well as distinct odorant-binding receptors and retrotransposable elements were found in this genome. Similar molecular functions and biological processes are shared with other studied species of Elateriformia. Common genes putatively associated with bioluminescence production and control, including two luciferase genes that displayed 7 exons and 6 introns, and genes that could be involved in luciferin biosynthesis were found, indicating that there are no clear differences about the presence or absence of gene families associated with bioluminescence in Elateroidea. In P. hirtus the conversion of L- to D-luciferin seems to involve additional steps using a Palmitoyl-CoA thioesterase instead of an Acyl-CoA synthetase, which was found in Lampyridae species.HighlightsFirst draft genome assembly of Phengodidae, the largest one described in Coleoptera;Gene family expansions associated with anatomical development and morphogenesis;Bioluminescent control and luciferin biosynthesis genes are common within Elateroidea;Despite similar bioluminescent system, metabolic routes may have evolved independently;

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