A high‐quality chromosome‐level genome assembly of a generalist herbivore,
            Trichoplusia ni

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 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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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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Improving the chromosome-level genome assembly of the Siamese fighting fish (Betta splendens) in a university Master’s course

10.1101/2020.03.06.981332 ◽

2020 ◽

Author(s):

Stefan Prost ◽

Malte Petersen ◽

Martin Grethlein ◽

Sarah Joy Hahn ◽

Nina Kuschik-Maczollek ◽

...

Keyword(s):

Genome Assembly ◽

High Throughput Sequencing ◽

Siamese Fighting Fish ◽

Betta Splendens ◽

High Quality ◽

Sequencing Platform ◽

Sequencing Technologies ◽

Oxford Nanopore ◽

Long Read ◽

Chromosome Level

AbstractBackgroundEver 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 behaviour. We updated the current genome assembly by generating a new long-read nanopore-based assembly with subsequent scaffolding to chromosome-level using previously published HiC data.FindingsThe use of 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 previously published HiC 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 95.8% complete BUSCO genes from the Actinopterygii dataset indicating a high quality of the assembly.ConclusionWe 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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Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome

BMC Genomics ◽

10.1186/s12864-020-07027-6 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Yiqian Li ◽

Wenyan Nong ◽

Tobias Baril ◽

Ho Yin Yip ◽

Thomas Swale ◽

...

Keyword(s):

Hong Kong ◽

Genome Assembly ◽

Homeobox Genes ◽

Homeobox Gene ◽

Gene Clusters ◽

Gene Organization ◽

Recent Analysis ◽

High Quality ◽

Protein Coding ◽

Chromosome Level

Abstract Background Homeobox-containing genes encode crucial transcription factors involved in animal, plant and fungal development, and changes to homeobox genes have been linked to the evolution of novel body plans and morphologies. In animals, some homeobox genes are clustered together in the genome, either as remnants from ancestral genomic arrangements, or due to coordinated gene regulation. Consequently, analyses of homeobox gene organization across animal phylogeny provide important insights into the evolution of genome organization and developmental gene control, and their interaction. However, homeobox gene organization remains to be fully elucidated in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians. Results Here, we present a high-quality chromosome-level genome assembly of the Hong Kong oyster, Magallana hongkongensis (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~ 758 Mb, scaffold N50 = 72.3 Mb). Our genome assembly was scaffolded using Hi-C reads, facilitating a larger scaffold size compared to the recently published M. hongkongensis genome of Peng et al. (Mol Ecol Resources, 2020), which was scaffolded using the Crassostrea gigas assembly. A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated in our genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data for other mollusc lineages. Conclusions The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally. Transposable element content is comparable to that found in other mollusc species, contrary to the conclusion of another recent analysis. Also, our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a number of the homeobox gene clusters, like the Hox/ParaHox clusters, are undergoing dispersal in molluscs such as this oyster.

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Chromosomal-level assembly of Juglans sigillata genome using Nanopore, BioNano, and Hi-C analysis

GigaScience ◽

10.1093/gigascience/giaa006 ◽

2020 ◽

Vol 9 (2) ◽

Cited By ~ 3

Author(s):

De-Lu Ning ◽

Tao Wu ◽

Liang-Jun Xiao ◽

Ting Ma ◽

Wen-Liang Fang ◽

...

Keyword(s):

Genome Assembly ◽

Reference Genome ◽

Juglans Regia ◽

Future Research ◽

High Quality ◽

Illumina Hiseq ◽

A Genome ◽

Contact Frequency ◽

Juglans Sigillata ◽

Chromosome Level

Abstract Background Juglans sigillata, or iron walnut, belonging to the order Juglandales, is an economically important tree species in Asia, especially in the Yunnan province of China. However, little research has been conducted on J. sigillata at the molecular level, which hinders understanding of its evolution, speciation, and synthesis of secondary metabolites, as well as its wide adaptability to its plateau environment. To address these issues, a high-quality reference genome of J. sigillata would be useful. Findings To construct a high-quality reference genome for J. sigillata, we first generated 38.0 Gb short reads and 66.31 Gb long reads using Illumina and Nanopore sequencing platforms, respectively. The sequencing data were assembled into a 536.50-Mb genome assembly with a contig N50 length of 4.31 Mb. Additionally, we applied BioNano technology to identify contacts among contigs, which were then used to assemble contigs into scaffolds, resulting in a genome assembly with scaffold N50 length of 16.43 Mb and contig N50 length of 4.34 Mb. To obtain a chromosome-level genome assembly, we constructed 1 Hi-C library and sequenced 79.97 Gb raw reads using the Illumina HiSeq platform. We anchored ∼93% of the scaffold sequences into 16 chromosomes and evaluated the quality of our assembly using the high contact frequency heat map. Repetitive elements account for 50.06% of the genome, and 30,387 protein-coding genes were predicted from the genome, of which 99.8% have been functionally annotated. The genome-wide phylogenetic tree indicated an estimated divergence time between J. sigillata and Juglans regia of 49 million years ago on the basis of single-copy orthologous genes. Conclusions We provide the first chromosome-level genome for J. sigillata. It will lay a valuable foundation for future research on the genetic improvement of J. sigillata.

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Telomere to telomere genome assembly of Fusarium musae F31, causal agent of crown rot disease of banana.

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-05-21-0127-a ◽

2021 ◽

Author(s):

Luca Degradi ◽

Valeria Tava ◽

Andrea Kunova ◽

Paolo Cortesi ◽

Marco Saracchi ◽

...

Keyword(s):

Genome Assembly ◽

Species Complex ◽

Crown Rot ◽

Fusarium Fujikuroi ◽

Valuable Resource ◽

High Quality ◽

Long Reads ◽

Fusarium Fujikuroi Species Complex ◽

Rot Disease ◽

Chromosome Level

Fusarium musae van Hove causes crown rot of banana and it is also associated to clinical fusariosis. A chromosome-level genome assembly of Fusarium musae F31 obtained combining Nanopore long reads and Illumina paired end reads resulted in 12 chromosomes plus one contig with overall N50 of 4.36 Mb, and is presented together with its mitochondrial genome (58072 bp). F31 genome includes telomeric regions for 11 of the 12 chromosomes representing the most complete genome available in the Fusarium fujikuroi species complex. The high-quality assembly of the F31 genome will be a valuable resource for studying the pathogenic interactions occurring between F. musae and banana. Moreover, it represents an important resource for understanding the genome evolution in the Fusarium fujikuroi species complex.

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