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

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.

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

10.1101/2021.12.21.473654 ◽

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.

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Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors

Scientific Data ◽

10.1038/sdata.2016.30 ◽

2016 ◽

Vol 3 (1) ◽

Cited By ~ 58

Author(s):

Luisa Orsini ◽

Donald Gilbert ◽

Ram Podicheti ◽

Mieke Jansen ◽

James B. Brown ◽

...

Keyword(s):

Daphnia Magna ◽

Draft Genome ◽

Model Organisms ◽

Transcriptome Data ◽

Rna Seq ◽

Data Set ◽

Environmental Genomics ◽

Environmental Perturbations ◽

Gene Environment ◽

Genomic Tools

Abstract The full exploration of gene-environment interactions requires model organisms with well-characterized ecological interactions in their natural environment, manipulability in the laboratory and genomic tools. The waterflea Daphnia magna is an established ecological and toxicological model species, central to the food webs of freshwater lentic habitats and sentinel for water quality. Its tractability and cyclic parthenogenetic life-cycle are ideal to investigate links between genes and the environment. Capitalizing on this unique model system, the STRESSFLEA consortium generated a comprehensive RNA-Seq data set by exposing two inbred genotypes of D. magna and a recombinant cross of these genotypes to a range of environmental perturbations. Gene models were constructed from the transcriptome data and mapped onto the draft genome of D. magna using EvidentialGene. The transcriptome data generated here, together with the available draft genome sequence of D. magna and a high-density genetic map will be a key asset for future investigations in environmental genomics.

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

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400725 ◽

2020 ◽

Vol 10 (3) ◽

pp. 907-915 ◽

Cited By ~ 4

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.

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

10.1101/593673 ◽

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.

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Draft Genome Sequence of a Clinically Isolated Extensively Drug-Resistant Pseudomonas aeruginosa Strain

Genome Announcements ◽

10.1128/genomea.00162-16 ◽

2016 ◽

Vol 4 (2) ◽

Author(s):

Bhavani Manivannan ◽

Niranjana Mahalingam ◽

Sudhir Jadhao ◽

Amrita Mishra ◽

Pravin Nilawe ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Antibiotic Resistance ◽

Genome Assembly ◽

Biofilm Formation ◽

Draft Genome ◽

Drug Resistant ◽

Draft Genome Assembly ◽

Extensively Drug Resistant ◽

History Of ◽

Urinary Tuberculosis

We present the draft genome assembly of an extensively drug-resistant (XDR) Pseudomonas aeruginosa strain isolated from a patient with a history of genito urinary tuberculosis. The draft genome is 7,022,546 bp with a G+C content of 65.48%. It carries 7 phage genomes, genes for quorum sensing, biofilm formation, virulence, and antibiotic resistance.

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Draft Genome Sequence of Dermatophagoides pteronyssinus, the European House Dust Mite

Genome Announcements ◽

10.1128/genomea.00789-17 ◽

2017 ◽

Vol 5 (32) ◽

Cited By ~ 8

Author(s):

Rose Waldron ◽

Jamie McGowan ◽

Natasha Gordon ◽

Charley McCarthy ◽

E. Bruce Mitchell ◽

...

Keyword(s):

Genome Sequence ◽

Gene Prediction ◽

Draft Genome ◽

Dermatophagoides Pteronyssinus ◽

Mite Species ◽

Draft Genome Sequence ◽

Comparative Genomic ◽

Genomic Analyses ◽

Dust Mite ◽

Functional Analyses

ABSTRACT Dermatophagoides pteronyssinus is the European dust mite and a major source of human allergens. Here, we present the first draft genome sequence of the mite, as well as the ab initio gene prediction and functional analyses that will facilitate comparative genomic analyses with other mite species.

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Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly

The Plant Journal ◽

10.1111/j.1365-313x.2012.05017.x ◽

2012 ◽

Vol 71 (6) ◽

pp. 895-906 ◽

Cited By ~ 99

Author(s):

Luming Yang ◽

Dal-Hoe Koo ◽

Yuhong Li ◽

Xuejiao Zhang ◽

Feishi Luan ◽

...

Keyword(s):

Genetic Mapping ◽

Genome Assembly ◽

Draft Genome ◽

High Density ◽

Chromosome Rearrangements ◽

Draft Genome Assembly

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The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations

10.1101/585695 ◽

2019 ◽

Cited By ~ 1

Author(s):

Mosè Manni ◽

Felipe A. Simao ◽

Hugh M. Robertson ◽

Marco A. Gabaglio ◽

Robert M. Waterhouse ◽

...

Keyword(s):

Draft Genome ◽

Gene Families ◽

Sister Group ◽

Sensu Stricto ◽

Comparative Genomic ◽

Gene Repertoire ◽

Animal Group ◽

Origin And Evolution ◽

Genomic Analyses ◽

Metabolism Gene

AbstractThe dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gbp draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion which might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behaviour, and duplicated apoptotic genes might underlie its high regenerative potential.The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

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First draft genome of loach (Orenectus shuilongensis; Cypriniformes: Nemacheilidae) provide insights into the evolution of cavefish

10.21203/rs.3.rs-192229/v1 ◽

2021 ◽

Author(s):

Zhijin Liu ◽

Xuekun Qian ◽

Ziming Wang ◽

Huamei Wen ◽

Ling Han ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Eye Development ◽

Draft Genome ◽

Evolutionary Process ◽

Integrated Approach ◽

Sequencing Data ◽

Retina Development ◽

Draft Genome Assembly ◽

Surface Dwelling

Abstract BcakgroundLoaches of the superfamily Cobitoidea (Cypriniformes, Nemacheilidae) are small elongated bottom-dwelling freshwater fishes with several barbels near the mouth. The genus Oreonectes with 18 currently recognized species contains representatives for all three key stages of the evolutionary process (a surface-dwelling lifestyle, facultative cave persistence, and permanent cave dwelling). Some Oreonectes species show typical cave dwelling-related traits, such as partial or complete leucism and regression of the eyes, rendering them as suitable study objects of micro-evolution. Genome information of Oreonectes species is therefore an indispensable resource for research into the evolution of cavefishes.ResultsHere we assembled the genome sequence of O. shuilongensis, a surface-dwelling species, using an integrated approach that combined PacBio single-molecule real-time sequencing and Illumina X-ten paired-end sequencing. Based on in total 50.9 Gb of sequencing data, our genome assembly from Canu and Pilon spans approximately 515.64 Mb (estimated coverage of 100 ×), containing 803 contigs with N50 values of 5.58 Mb. 25,247 protein-coding genes were predicted, of which 95.65% have been functionally annotated. We also performed genome re-sequencing of three additional cave-dwelling Oreonectes fishes. Twenty-nine pseudogenes annotated using DAVID showed significant enrichment for the GO terms of “eye development” and “retina development in camera-type eye”. It is presumed that these pseudogenes might lead to eye degeneration of semi/complete cave-dwelling Oreonectes species. Furthermore, Mc1r (melanocortin-1 receptor) is a pseudogenization by a deletion in O. daqikongensis, likely blocking biosynthesis of melanin and leading to the albino phenotype.ConclusionsWe here report the first draft genome assembly of Oreonectes fishes, which is also the first genome reference for Cobitidea fishes. Pseudogenization of genes related to body color and eye development may be responsible for loss of pigmentation and vision deterioration in cave-dwelling species. This genome assembly will contribute to the study of the evolution and adaptation of fishes within Oreonectes and beyond (Cobitidea).

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The genome and transcriptome of the Phalaenopsis yield insights into floral organ development and flowering regulation

10.7287/peerj.preprints.1707v1 ◽

2016 ◽

Cited By ~ 1

Author(s):

Jian-Zhi Huang ◽

Chih-Peng Lin ◽

Ting-Chi Cheng ◽

Ya-Wen Huang ◽

Yi-Jung Tsai ◽

...

Keyword(s):

Economic Value ◽

Draft Genome ◽

Floral Organ ◽

Cool Temperature ◽

Organ Development ◽

Nucleotide Polymorphisms ◽

Protein Coding ◽

Draft Genome Assembly ◽

Genome Data ◽

Expression Of Genes

Phalaenopsis orchid is an important potted flower with high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802’, a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal the key role of PhAGL6b in the regulation of flower organ development involves alternative splicing. We also show gibberellin pathways that regulate the expression of genes control flowering time during the stage in reproductive phase change induced by cool temperature. Our work should contribute a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

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