Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas’s cat,<i>Otocolobus manul</i>

Flack, Nicole; Drown, Melissa K.; Walls, Carrie; Pratte, Jay; McLain, Adam T.; Faulk, Christopher

doi:10.1101/2022.11.30.518596

Cited by 6 publications

(7 citation statements)

References 150 publications

(156 reference statements)

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“…2021 ). Other pest insect genomes have recently been sequenced using nanopore-only approaches such as the black carpenter ant, Camponotus pennsylvanicus De Geer (Hymenoptera: Formicidae), and the coconut rhinoceros beetle, Oryctes rhinoceros [L.] (Coleoptera: Scarabaeidae) ( Faulk 2022 ; Filipović et al . 2022 ).…”

Section: Resultsmentioning

confidence: 99%

The genome of the soybean gall midge (Resseliella maxima)

Melotto

Jones

Bosley

et al. 2023

G3: Genes, Genomes, Genetics

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The cecidomyiid fly, soybean gall midge, Resseliella maxima Gagné, is a recently discovered insect that feeds on soybean plants in the Midwest US. Resseliella maxima larvae feed on soybean stems which may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble a R. maxima reference genome. The final genome assembly is 206 Mb with 64.88X coverage, consisting of 1009 contigs with an N50 size of 714 kb. The assembly is high quality with a BUSCO score of 87.8%. Genome-wide GC level is 31.60% and DNA methylation was measured at 1.07%. The R. maxima genome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated that R. maxima assembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge, Orseolia oryzae Wood-Mason. The R. maxima genome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.

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Section: Resultsmentioning

confidence: 99%

The genome of the soybean gall midge (Resseliella maxima)

Melotto

Jones

Bosley

et al. 2023

G3: Genes, Genomes, Genetics

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“…During the second phase of the project, 6 µg of the remaining HMW DNA and 7 µg of the spleen-extracted DNA were used as input for library preparations with the Oxford Nanopore Ligation Sequencing kit SQK-LSK109, split into three and two library preparations for each extraction, respectively. Modifications as described by Flack et al (2023) were implemented during the latter sequencing effort to prepare additional library material, allowing for multiple reloadings of the same library and flow cell between washes. Prepared libraries were stored at 4 ºC while awaiting sequencing.…”

Section: Methodsmentioning

confidence: 99%

De novogenome assembly for an endangered lemur using portable nanopore sequencing in rural Madagascar

Hauff,

Rasoanaivo,

Razafindrakoto

et al. 2024

Preprint

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As one of the most threatened mammalian taxa, lemurs of Madagascar are facing unprecedented anthropogenic pressures. To address conservation imperatives such as this, researchers have increasingly relied on conservation genomics to identify populations of particular concern. However, many of these genomic approaches necessitate high-quality genomes. While the advent of next generation sequencing technologies and the resulting reduction of associated costs have led to the proliferation of genomic data and high-quality reference genomes, global discrepancies in genomic sequencing capabilities often result in biological samples from biodiverse host countries being exported to facilities in the Global North, creating inequalities in access and training within genomic research. Here, we present the first reference genome for the endangered red-fronted brown lemur (Eulemur rufifrons) from sequencing efforts conducted entirely within the host country using portable Oxford Nanopore sequencing. Using an archivedE. rufifronsspecimen, we conducted long-read, nanopore sequencing at the Centre ValBio Research Station near Ranomafana National Park, in rural Madagascar, generating over 750 Gb of sequencing data from 10 MinION flow cells. Exclusively using this long-read data, we assembled 2.21 gigabase, 20,330-contig nuclear assembly with an N50 of 98.9 Mb and a 17,108 bp mitogenome. The nuclear assembly had 31x average coverage and was comparable in completeness to other primate reference genomes, with a 95.47% BUSCO completeness score for primate-specific genes. As the first reference genome forE. rufifronsand the only annotated genome available for the specioseEulemurgenus, this resource will prove vital for conservation genomic studies while our efforts exhibit the potential of this protocol to address research inequalities and build genomic capacity.

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“…Although nanopore reads are inherently less accurate than Illumina reads, we were still able to generate an accurate consensus, and its BUSCO protein score of 89.9% indicates good resolution of the assembly. Other nanopore-only assemblies have shown overall quality scores of Q45 (1 in 50,000 base error rate) (Flack et al, 2022), considered as a platinum status genome by the Vertebrate Genomes Project (Morin et al, 2020).…”

Section: Gene Annotationmentioning

confidence: 99%

The Genome of the Soybean Gall Midge (Resseliella maxima)

Melotto¹,

Jones²,

Bosley³

et al. 2023

Preprint

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The cecidomyiid fly, soybean gall midge,Resseliella maximaGagn, is a recently discovered insect that feeds on soybean plants in the Midwest US.Resseliella maximalarvae feed on soybean stems which may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble aR. maximareference genome. The final genome assembly is 206 Mb with 64.88X coverage, consisting of 1009 contigs with an N50 size of 714 kb. The assembly is high quality with a BUSCO score of 87.8%. Genome-wide GC level is 31.60% and DNA methylation was measured at 1.07%. TheR. maximagenome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated thatR. maximaassembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge,Orseolia oryzae(Wood-Mason). TheR. maximagenome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.

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Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas’s cat,Otocolobus manul

Cited by 6 publications

References 150 publications

The genome of the soybean gall midge (Resseliella maxima)

The genome of the soybean gall midge (Resseliella maxima)

De novogenome assembly for an endangered lemur using portable nanopore sequencing in rural Madagascar

The Genome of the Soybean Gall Midge (Resseliella maxima)

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