A high‐quality chromosome‐level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation

Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today. Here we report the generation of an improved chromosome-level assembly for the Siamese fighting fish (Betta splendens) that was carried out during a practical university master’s course. The Siamese fighting fish is a popular aquarium fish and an emerging model species for research on aggressive behavior. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published Hi-C data. The use of ∼35x nanopore-based long-read data sequenced on a MinION platform (Oxford Nanopore Technologies) allowed us to generate a baseline assembly of only 1,276 contigs with a contig N50 of 2.1 Mbp, and a total length of 441 Mbp. Scaffolding using the Hi-C data resulted in 109 scaffolds with a scaffold N50 of 20.7 Mbp. More than 99% of the assembly is comprised in 21 scaffolds. The assembly showed the presence of 96.1% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly. We present an improved full chromosome-level assembly of the Siamese fighting fish generated during a university master’s course. The use of ∼35× long-read nanopore data drastically improved the baseline assembly in terms of continuity. We show that relatively in-expensive high-throughput sequencing technologies such as the long-read MinION sequencing platform can be used in educational settings allowing the students to gain practical skills in modern genomics and generate high quality results that benefit downstream research projects.

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Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)

GigaScience ◽

10.1093/gigascience/giaa092 ◽

2020 ◽

Vol 9 (8) ◽

Cited By ~ 1

Author(s):

Feng Shao ◽

Arne Ludwig ◽

Yang Mao ◽

Ni Liu ◽

Zuogang Peng

Keyword(s):

Dna Sequences ◽

Genome Assembly ◽

Gambusia Affinis ◽

Comparative Genomic ◽

Suitable Model ◽

High Quality ◽

Western Mosquitofish ◽

Poeciliid Fish ◽

Oxford Nanopore ◽

Chromosome Level

Abstract Background The western mosquitofish (Gambusia affinis) is a sexually dimorphic poeciliid fish known for its worldwide biological invasion and therefore an important research model for studying invasion biology. This organism may also be used as a suitable model to explore sex chromosome evolution and reproductive development in terms of differentiation of ZW sex chromosomes, ovoviviparity, and specialization of reproductive organs. However, there is a lack of high-quality genomic data for the female G. affinis; hence, this study aimed to generate a chromosome-level genome assembly for it. Results The chromosome-level genome assembly was constructed using Oxford nanopore sequencing, BioNano, and Hi-C technology. G. affinis genomic DNA sequences containing 217 contigs with an N50 length of 12.9 Mb and 125 scaffolds with an N50 length of 26.5 Mb were obtained by Oxford nanopore and BioNano, respectively, and the 113 scaffolds (90.4% of scaffolds containing 97.9% nucleotide bases) were assembled into 24 chromosomes (pseudo-chromosomes) by Hi-C. The Z and W chromosomes of G. affinis were identified by comparative genomic analysis of female and male G. affinis, and the mechanism of differentiation of the Z and W chromosomes was explored. Combined with transcriptome data from 6 tissues, a total of 23,997 protein-coding genes were predicted and 23,737 (98.9%) genes were functionally annotated. Conclusions The high-quality female G. affinis reference genome provides a valuable omics resource for future studies of comparative genomics and functional genomics to explore the evolution of Z and W chromosomes and the reproductive developmental biology of G. affinis.

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Chromosome-level genome assembly of Scapharca kagoshimensis reveals the expanded molecular basis of heme biosynthesis in ark shell

10.22541/au.162155566.67560449/v1 ◽

2021 ◽

Author(s):

Teng Weiming ◽

Xie Xi ◽

Hongtao Nie ◽

Yamin Sun ◽

Liu Xiangfeng ◽

...

Keyword(s):

Genome Assembly ◽

Molecular Basis ◽

Molecular Mechanisms ◽

Heme Biosynthesis ◽

High Quality ◽

Protein Coding ◽

Conserved Genes ◽

Long Time ◽

Muddy Sediments ◽

Chromosome Level

Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we reported a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells. Nineteen scaffolds corresponding to 19 chromosomes were constructed from 938 contigs (contig N50=2.01 Mb) to produce a final high-quality assembly with a total length of 1.11 Gb and scaffold N50 around 60.64 Mb. The genome assembly represents 93.4% completeness via matching 303 eukaryota core conserved genes. A total of 24,908 protein-coding genes were predicted and 24,551 genes (98.56%) of which were functionally annotated. The enrichment analyses suggested that genes in heme biosynthesis pathways were expanded and positive selection of the hemoglobin genes was also found in the genome of S. kagoshimensis, which gives important insights into the molecular mechanisms and evolution of the heme biosynthesis in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid foundation for investigating the molecular mechanisms that underlie the diverse biological functions and evolutionary adaptations of S. kagoshimensis.

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Chromosome-level assembly of the common lizard (Zootoca vivipara) genome

10.1101/520528 ◽

2019 ◽

Cited By ~ 1

Author(s):

Andrey A. Yurchenko ◽

Hans Recknagel ◽

Kathryn R. Elmer

Keyword(s):

Sequence Data ◽

Multiple Paternity ◽

Single Copy ◽

High Quality ◽

High Coverage ◽

Squamate Reptiles ◽

Common Lizard ◽

Zootoca Vivipara ◽

The Common ◽

Chromosome Level

ABSTRACTSquamate reptiles exhibit high variation in their traits and geographical distribution and are therefore fascinating taxa for evolutionary and ecological research. However, high-quality genomic recourses are very limited for this group of species, which inhibits some 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 sequence data, with RNAseq data and genetic linkage maps. The 1.46 Gbp genome assembly has scaffold N50 of 11.52 Mbp with N50 contig size of 220.4 Kbp 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 in the genome using a combination of three 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.

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LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology

Genome Biology ◽

10.1186/s13059-021-02475-z ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Patrick Driguez ◽

Salim Bougouffa ◽

Karen Carty ◽

Alexander Putra ◽

Kamel Jabbari ◽

...

Keyword(s):

De Novo ◽

Plant Genome ◽

Time Cost ◽

Sequencing Technology ◽

High Quality ◽

Plant Genomes ◽

Long Read ◽

Generate Plant ◽

Sequencing Platforms ◽

Chromosome Level

AbstractCurrently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology. LeafGo is optimized with ten different plant species, three of which are used to generate high-quality chromosome-level assemblies without any scaffolding technologies. Finally, we report the diploid genomes of Eucalyptus rudis and E. camaldulensis and the allotetraploid genome of Arachis hypogaea.

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Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra

Gigabyte ◽

10.46471/gigabyte.6 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Sven Winter ◽

Stefan Prost ◽

Jordi de Raad ◽

Raphael T. F. Coimbra ◽

Magnus Wolf ◽

...

Keyword(s):

Genome Assembly ◽

Morphological Differentiation ◽

Chromosome Length ◽

Morphological Transformation ◽

High Quality ◽

The North ◽

Repeat Content ◽

The Common ◽

Species Specific ◽

Chromosome Level

Background The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea. All three species show strong sexual dimorphism. The males show strong morphological differentiation, e.g., species-specific colouration and size relations, while the females of different species have few distinguishing characters. Callionymus belongs to the ‘benthic associated clade’ of the order Syngnathiformes. The ‘benthic associated clade’ so far is not represented by genome data and serves as an important outgroup to understand the morphological transformation in ‘long-snouted’ syngnatiformes such as seahorses and pipefishes. Findings Here, we present the chromosome-level genome assembly of C. lyra. We applied Oxford Nanopore Technologies’ long-read sequencing, short-read DNBseq, and proximity-ligation-based scaffolding to generate a high-quality genome assembly. The resulting assembly has a contig N50 of 2.2 Mbp and a scaffold N50 of 26.7 Mbp. The total assembly length is 568.7 Mbp, of which over 538 Mbp were scaffolded into 19 chromosome-length scaffolds. The identification of 94.5% complete BUSCO genes indicates high assembly completeness. Additionally, we sequenced and assembled a multi-tissue transcriptome with a total length of 255.5 Mbp that was used to aid the annotation of the genome assembly. The annotation resulted in 19,849 annotated transcripts and identified a repeat content of 27.7%. Conclusions The chromosome-level assembly of C. lyra provides a high-quality reference genome for future population genomic, phylogenomic, and phylogeographic analyses.

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Chromosome-Level Genome Assembly Reveals Significant Gene Expansion in the Toll and IMD Signaling Pathways of Dendrolimus kikuchii

Frontiers in Genetics ◽

10.3389/fgene.2021.728418 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jielong Zhou ◽

Peifu Wu ◽

Zhongping Xiong ◽

Naiyong Liu ◽

Ning Zhao ◽

...

Keyword(s):

Genome Assembly ◽

Phylogenetic Analyses ◽

Repetitive Sequences ◽

Gene Families ◽

Thaumetopoea Pityocampa ◽

High Quality ◽

Protein Coding ◽

Peptidoglycan Recognition Protein ◽

Recognition Protein ◽

Chromosome Level

A high-quality genome is of significant value when seeking to control forest pests such as Dendrolimus kikuchii, a destructive member of the order Lepidoptera that is widespread in China. Herein, a high quality, chromosome-level reference genome for D. kikuchii based on Nanopore, Pacbio HiFi sequencing and the Hi-C capture system is presented. Overall, a final genome assembly of 705.51 Mb with contig and scaffold N50 values of 20.89 and 24.73 Mb, respectively, was obtained. Of these contigs, 95.89% had unique locations on 29 chromosomes. In silico analysis revealed that the genome contained 15,323 protein-coding genes and 63.44% repetitive sequences. Phylogenetic analyses indicated that D. kikuchii may diverged from the common ancestor of Thaumetopoea. Pityocampa, Thaumetopoea ni, Heliothis virescens, Hyphantria armigera, Spodoptera frugiperda, and Spodoptera litura approximately 122.05 million years ago. Many gene families were expanded in the D. kikuchii genome, particularly those of the Toll and IMD signaling pathway, which included 10 genes in peptidoglycan recognition protein, 19 genes in MODSP, and 11 genes in Toll. The findings from this study will help to elucidate the mechanisms involved in protection of D. kikuchii against foreign substances and pathogens, and may highlight a potential channel to control this pest.

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Chromosomal-level reference genome of Chinese peacock butterfly (Papilio bianor) based on third-generation DNA sequencing and Hi-C analysis

GigaScience ◽

10.1093/gigascience/giz128 ◽

2019 ◽

Vol 8 (11) ◽

Cited By ~ 4

Author(s):

Sihan Lu ◽

Jie Yang ◽

Xuelei Dai ◽

Feiang Xie ◽

Jinwu He ◽

...

Keyword(s):

Reference Genome ◽

De Novo ◽

Demographic History ◽

Repetitive Sequences ◽

Population Expansion ◽

Chromatin Interaction ◽

Interglacial Period ◽

Last Interglacial ◽

High Quality ◽

Chromosome Level

AbstractBackgroundPapilio bianor Cramer, 1777 (commonly known as the Chinese peacock butterfly) (Insecta, Lepidoptera, Papilionidae) is a widely distributed swallowtail butterfly with a wide number of geographic populations ranging from the southeast of Russia to China, Japan, India, Vietnam, Myanmar, and Thailand. Its wing color consists of both pigmentary colored scales (black, reddish) and structural colored scales (iridescent blue or green dust). A high-quality reference genome of P. bianor is an important foundation for investigating iridescent color evolution, phylogeography, and the evolution of swallowtail butterflies.FindingsWe obtained a chromosome-level de novo genome assembly of the highly heterozygous P. bianor using long Pacific Biosciences sequencing reads and high-throughput chromosome conformation capture technology. The final assembly is 421.52 Mb on 30 chromosomes (29 autosomes and 1 Z sex chromosome) with 13.12 Mb scaffold N50. In total, 15,375 protein-coding genes and 233.09 Mb of repetitive sequences were identified. Phylogenetic analyses indicated that P. bianor separated from a common ancestor of swallowtails ∼23.69–36.04 million years ago. Demographic history suggested that the population expansion of this species from the last interglacial period to the last glacial maximum possibly resulted from its decreased natural enemies and its adaptation to climate change during the glacial period.ConclusionsWe present a high-quality chromosome-level reference genome of P. bianor using long-read single-molecule sequencing and Hi-C–based chromatin interaction maps. Our results lay the foundation for exploring the genetic basis of special biological features of P. bianor and also provide a useful data source for comparative genomics and phylogenomics among butterflies and moths.

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Chromosome-Level Genome Assembly and Annotation of a Sciaenid Fish, Argyrosomus japonicus

Genome Biology and Evolution ◽

10.1093/gbe/evaa246 ◽

2021 ◽

Vol 13 (2) ◽

Author(s):

Linlin Zhao ◽

Shengyong Xu ◽

Zhiqiang Han ◽

Qi Liu ◽

Wensi Ke ◽

...

Keyword(s):

Genome Assembly ◽

Wide Distribution ◽

High Quality ◽

Protein Coding ◽

Repeat Elements ◽

Long Reads ◽

The Family ◽

Solid Foundation ◽

Genomic Resource ◽

Chromosome Level

Abstract Argyrosomus japonicus is an economically and ecologically important fish species in the family Sciaenidae with a wide distribution in the world’s oceans. Here, we report a high-quality, chromosome-level genome assembly of A. japonicus based on PacBio and Hi-C sequencing technology. A 673.7-Mb genome containing 282 contigs with an N50 length of 18.4 Mb was obtained based on PacBio long reads. These contigs were further ordered and clustered into 24 chromosome groups based on Hi-C data. In addition, a total of 217.2 Mb (32.24% of the assembled genome) of sequences were identified as repeat elements, and 23,730 protein-coding genes were predicted based on multiple approaches. More than 97% of BUSCO genes were identified in the A. japonicus genome. The high-quality genome assembled in this work not only provides a valuable genomic resource for future population genetics, conservation biology and selective breeding studies of A. japonicus but also lays a solid foundation for the study of Sciaenidae evolution.

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