scholarly journals A Chromosome-Level Genome Assembly of the Dark Sleeper Odontobutis potamophila

2021 ◽  
Vol 13 (2) ◽  
Author(s):  
Yongyi Jia ◽  
Jianbo Zheng ◽  
Shili Liu ◽  
Fei Li ◽  
Meili Chi ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Single Copy ◽  
Chromatin Interaction ◽  
Protein Coding ◽  
Functional Studies ◽  
Sex Control ◽  
Odontobutis Potamophila ◽  
High Quality Genome ◽  
Insight Into ◽  
Gaining Insight

Abstract The dark sleeper, Odontobutis potamophila, is a commercially valuable fish that widely distributed in China and Southeast Asia countries. The phenomenon of sexual dimorphism in growth is conspicuous, which the males grow substantially larger and faster than the females. However, the high-quality genome resources for gaining insight into sex-determining mechanisms to develop sex-control breeding are still lacking. Here, a chromosomal-level genome assembly of O. potamophila was generated from a combination of Illumina reads, 10× Genomics sequencing, and Hi-C chromatin interaction sequencing. The assembled genome was 1,134.62 Mb with a contig N50 of 22.25 Mb and a scaffold N50 of 24.85 Mb, representing 94.4% completeness (Benchmarking Universal Single-Copy Orthologs). Using Hi-C data, 96.49% of the total contig bases were anchored to the 22 chromosomes, with a contig N50 of 22.25 Mb and a scaffold N50 of 47.68 Mb. Approximately 54.18% of the genome were identified as repetitive elements, and 23,923 protein-coding genes were annotated in the genome. The assembled genome can be used as a valuable resource for molecular breeding and functional studies of O. potamophila in the future.

scholarly journals Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes

Toxins ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 488 ◽  
Author(s):  
Shiyong Zhang ◽  
Jia Li ◽  
Qin Qin ◽  
Wei Liu ◽  
Chao Bian ◽  
...  
Keyword(s):  
High Throughput ◽  
Genome Assembly ◽  
Raw Materials ◽  
Pelteobagrus Fulvidraco ◽  
Yellow Catfish ◽  
High Quality ◽  
Protein Coding ◽  
Toxin Genes ◽  
Sequencing Platforms ◽  
High Quality Genome

Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species.

scholarly journals Genome Assembly and Sex-Determining Region of Male and Female Populus × sibirica

2021 ◽  
Vol 12 ◽  
Author(s):  
Nataliya V. Melnikova ◽  
Elena N. Pushkova ◽  
Ekaterina M. Dvorianinova ◽  
Artemy D. Beniaminov ◽  
Roman O. Novakovskiy ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Single Copy ◽  
Dioecious Species ◽  
Male And Female ◽  
Male Genome ◽  
Oxford Nanopore ◽  
Genome Assemblies ◽  
First Time ◽  
High Quality Genome ◽  
Y Haplotype

The genus Populus is presented by dioecious species, and it became a promising object to study the genetics of sex in plants. In this work, genomes of male and female Populus × sibirica individuals were sequenced for the first time. To achieve high-quality genome assemblies, we used Oxford Nanopore Technologies and Illumina platforms. A protocol for the isolation of long and pure DNA from young poplar leaves was developed, which enabled us to obtain 31 Gb (N50 = 21 kb) for the male poplar and 23 Gb (N50 = 24 kb) for the female one using the MinION sequencer. Genome assembly was performed with different tools, and Canu provided the most complete and accurate assemblies with a length of 818 Mb (N50 = 1.5 Mb) for the male poplar and 816 Mb (N50 = 0.5 Mb) for the female one. After polishing with Racon and Medaka (Nanopore reads) and then with POLCA (Illumina reads), assembly completeness was 98.45% (87.48% duplicated) for the male and 98.20% (76.77% duplicated) for the female according to BUSCO (benchmarking universal single-copy orthologs). A high proportion of duplicated BUSCO and the increased genome size (about 300 Mb above the expected) pointed at the separation of haplotypes in a large part of male and female genomes of P. × sibirica. Due to this, we were able to identify two haplotypes of the sex-determining region (SDR) in both assemblies; and one of these four SDR haplotypes, in the male genome, contained partial repeats of the ARR17 gene (Y haplotype), while the rest three did not (X haplotypes). The analysis of the male P. × sibirica SDR suggested that the Y haplotype originated from P. nigra, while the X haplotype is close to P. trichocarpa and P. balsamifera species. Moreover, we revealed a Populus-specific repeat that could be involved in translocation of the ARR17 gene or its part to the SDR of P. × sibirica and other Populus species. The obtained results expand our knowledge on SDR features in the genus Populus and poplar phylogeny.

scholarly journals The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding

2021 ◽  
Author(s):  
Priyanka Sharma ◽  
Valentine Murigneux ◽  
Jasmine Haimovitz ◽  
Catherine J. Nock ◽  
Wei Tian ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Morphological Characteristics ◽  
Single Copy ◽  
Protein Coding ◽  
Core Eudicots ◽  
Wide Range ◽  
Genes Encoding ◽  
Long Read ◽  
In The Wild

SummaryMacadamia, a recently domesticated expanding nut crop in the tropical and subtropical regions of the world, is one of the most economically important genera in the diverse and widely adapted Proteaceae family. All four species of Macadamia are rare in the wild with the most recently discovered, M. jansenii, being endangered. The M. jansenii genome has been used as a model for testing sequencing methods using a wide range of long read sequencing techniques. Here we report a chromosome level genome assembly, generated using a combination of Pacific Biosciences sequencing and Hi-C, comprising 14 pseudo-molecules, with a N50 of 58 Mb and a total 758 Mb genome assembly size of which 56% is repetitive. Completeness assessment revealed that the assembly covered 96.9% of the conserved single copy genes. Annotation predicted 31,591 protein coding genes and allowed the characterization of genes encoding biosynthesis of cyanogenic glycosides, fatty acid metabolism and anti-microbial proteins. Re-sequencing of seven other genotypes confirmed low diversity and low heterozygosity within this endangered species. Important morphological characteristics of this species such as small tree size and high kernel recovery suggest that M. jansenii is an important source of these commercial traits for breeding. As a member of a small group of families that are sister to the core eudicots, this high-quality genome also provides a key resource for evolutionary and comparative genomics studies.

scholarly journals High-Quality Genome Assembly and Annotation of the California Harvester Ant Pogonomyrmex californicus (Buckley, 1867)

2020 ◽  
Author(s):  
Jonas Bohn ◽  
Reza Halabian ◽  
Lukas Schrader ◽  
Victoria Shabardina ◽  
Raphael Steffen ◽  
...  
Keyword(s):  
Genome Assembly ◽  
High Quality ◽  
Protein Coding ◽  
Primary Polygyny ◽  
Pogonomyrmex Californicus ◽  
The North ◽  
Harvester Ant ◽  
Mating Flights ◽  
North And South America ◽  
High Quality Genome

ABSTRACTThe harvester ant genus Pogonomyrmex is endemic to arid and semiarid habitats and deserts of North and South America and California harvester ant Pogonomyrmex californicus is the most widely distributed Pogonomyrmex species in the North America. P. californicus colonies are usually monogynous, i.e. a colony has one queen. However, in a few populations in California, primary polygyny evolved, i.e. several queens cooperate in colony founding after their mating flights and continue to coexist in mature colonies. Here, we present high quality genome assembly and annotation of P. californicus. The size of the assembly is 241 Mb, which is in good agreement with previously estimated genome size and we were able to annotate 17,889 genes in total, including 15,688 protein-coding ones with BUSCO completeness at the 95% level. This high quality genome will pave the way for investigations of the genomic underpinnings of social polymorphism in queen number, regulation of aggression, and the evolution of adaptations to dry habitats in P. californicus.

scholarly journals Chromosome-level genome assembly of the horned-gall aphid, Schlechtendalia chinensis (Hemiptera: Aphididae: Erisomatinae)

2021 ◽  
Author(s):  
Hong-Yuan Wei ◽  
Yu-Xian Ye ◽  
Hai-Jian Huang ◽  
Ming-Shun Chen ◽  
Zi-Xiang Yang ◽  
...  
Keyword(s):  
Host Plant ◽  
Genome Assembly ◽  
Single Copy ◽  
Phylogenomic Analysis ◽  
Gall Formation ◽  
Eriosoma Lanigerum ◽  
High Quality ◽  
Protein Coding ◽  
Host Alternation ◽  
Single Clade

AbstractThe horned gall aphid Schlechtendalia chinensis, is an economically important insect that induces galls valuable for medicinal and chemical industries. S. chinensis manipulates its host plant to form well-organized horned galls during feeding. So far, more than twenty aphid genomes have been reported; however, all of those are derived from free-living aphids. Here we generated a high-quality genome assembly of S. chinensis, representing the first genome sequence of a galling aphid. The final genome assembly was 280.43 Mb, with 97% of the assembled sequences anchored into thirteen chromosomes. S. chinensis presents the smallest aphid genome size among available aphid genomes to date. The contig and scaffold N50 values were 3.39 Mb and 20.58 Mb, respectively. The assembly included 96.4% of conserved arthropod and 97.8% of conserved Hemiptera single-copy orthologous genes based on BUSCO analysis. A total of 13,437 protein-coding genes were predicted. Phylogenomic analysis showed that S. chinensis formed a single clade between the Eriosoma lanigerum clade and the Aphidini+Macrosiphini aphid clades. In addition, salivary proteins were found to be differentially expressed when S. chinensis underwent host alternation, indicating their potential roles in gall formation and plant defense suppression. A total of 36 cytochrome P450 genes were identified in S. chinensis, considerably fewer compared to other aphids, probably due to its small host plant range. The high-quality S. chinensis genome assembly and annotation provide an essential genetic background for future studies to reveal the mechanism of gall formation and to explore the interaction between aphids and their host plants.

scholarly journals High-quality genome assembly and high-density genetic map of asparagus bean

2019 ◽  
Author(s):  
Qiuju Xia ◽  
Ru Zhang ◽  
Xuemei Ni ◽  
Lei Pan ◽  
Yangzi Wang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Agronomic Traits ◽  
High Density ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Economically Valuable Traits ◽  
Sequencing Strategy ◽  
Asparagus Bean ◽  
High Quality Genome

AbstractAsparagus bean (Vigna. unguiculata ssp. sesquipedialis), known for its very long and tender green pods, is an important vegetable crop broadly grown in the developing countries. Despite its agricultural and economic values, asparagus bean does not have a high-quality genome assembly for breeding novel agronomic traits. In this study, we reported a high-quality 632.8 Mb assembly of asparagus bean based on the whole genome shotgun sequencing strategy. We also generated a high-density linkage map for asparagus bean, which helped anchor 94.42% of the scaffolds into 11 pseudo-chromosomes. A total of 42,609 protein-coding genes and 3,579 non-protein-coding genes were predicted from the assembly. Taken together, these genomic resources of asparagus bean will facilitate the investigation of economically valuable traits in a variety of legume species, so that the cultivation of these plants would help combat the protein and energy malnutrition in the developing world.

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 First annotated genome of a mandibulate moth, Neomicropteryx cornuta, generated using PacBio HiFi sequencing

2021 ◽  
Author(s):  
Xuankun Li ◽  
Emily Ellis ◽  
David Plotkin ◽  
Yume Imada ◽  
Masaya Yago ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Genome Annotation ◽  
Single Copy ◽  
Early Evolution ◽  
High Recovery ◽  
High Quality ◽  
Evolutionary Transitions ◽  
A Genome ◽  
High Quality Genome ◽  
Papilio Polytes

Abstract We provide a new, annotated genome assembly of Neomicropteryx cornuta, a species of the so-called “mandibulate archaic moths” (Lepidoptera: Micropterigidae). These moths belong to a lineage that is thought to have split from all other Lepidoptera more than 300 million years ago and are consequently vital to understanding the early evolution of superorder Amphiesmenoptera, which contains the order Lepidoptera (butterflies and moths) and its sister order Trichoptera (caddisflies). Using PacBio HiFi sequencing reads, we assembled a highly-contiguous genome with a contig N50 of nearly 17 Mbp. The assembled genome length of 541,115,538 bp is about half the length of the largest published Amphiesmenoptera genome (Limnephilus lunatus, Trichoptera) and double the length of the smallest (Papilio polytes, Lepidoptera). We find high recovery of universal single copy orthologs with 98.1% of BUSCO genes present and provide a genome annotation of 15,643 genes aided by resolved isoforms from PacBio IsoSeq data. This high-quality genome assembly provides an important resource for studying ecological and evolutionary transitions in the early evolution of Amphiesmenoptera.

scholarly journals Hybrid genome assembly and gene repertoire of the root endophyte Clitopilus hobsonii QYL-10 (Entolomataceae, Agaricales, Basidiomycetes)

2021 ◽  
Author(s):  
LONG PENG ◽  
Xiaoliang Shan ◽  
Yuchen Wang ◽  
Francis Martin ◽  
Rytas Vilgalys ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Gc Content ◽  
Gene Clusters ◽  
Gene Repertoire ◽  
Root Tips ◽  
Protein Coding ◽  
Root Endophyte ◽  
Functional Studies ◽  
Hybrid Genome ◽  
Genes Encoding

Clitopilus hobsonii (Entolomataceae, Agaricales, Basidiomycetes) is a common soil saprotroph. There is also evidence that C. hobsonii can act as a root endophyte benefiting tree growth. Here, we report the genome assembly of C. hobsonii QYL-10 isolated from ectomycorrhizal root tips of Quercus lyrata. The genome size is 36.93 Mb, consisting of 13 contigs (N50=3.3 Mb) with 49.2% GC-content. Of them, 10 contigs approached the length of intact chromosomes, and 3 had telomeres at one end only. BUSCO analysis reported a completeness score of 98.4% using the Basidiomycota_odb10. Combining ab-initio, RNA-seq data, and homology-based predictions, we identified 12,710 protein-coding genes. Approximately, 1.43 Mb of Transposable elements (TEs) (3.88% of the assembly), 36 secondary metabolite biosynthetic gene clusters and 361 genes encoding putative CAZymes were identified. This genomic resource will allow functional studies aimed to characterize the symbiotic interactions between C. hobsonii and its host trees, but will also provide a valuable foundation for further research on comparative genomics of the Entolomataceae.

Sign in / Sign up

Export Citation Format

Share Document