An annotated draft genome for <i>Radix auricularia</i> (Gastropoda, Mollusca)

Schell, Tilman; Feldmeyer, Barbara; Schmidt, Hanno; Greshake, Bastian; Tills, Oliver; Truebano, Manuela; Rundle, Simon D.; Paule, Juraj; Ebersberger, Ingo; Pfenninger, Markus

doi:10.1101/087254

Cited by 23 publications

(37 citation statements)

References 53 publications

(47 reference statements)

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“…2013 ). To evaluate if the assembled genome size for P. plurivora is a marked underestimate of true genome size, such as may occur due to a high repeat content, we calculated a genome size estimate using k-mer analysis of our sequence data ( Schell et al 2017 ). We used Jellyfish ( Marçais and Kingsford 2011 ) for generating the k-mer histograms with a k-mer value of 25 and minimum phred quality of reads at 20.…”

Section: Methodsmentioning

confidence: 99%

Draft Genome Sequence for the Tree PathogenPhytophthora plurivora

Vetukuri

Tripathy

et al. 2018

Genome Biology and Evolution

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Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome sequence of P. plurivora, originally isolated from diseased European beech (Fagus sylvatica) in Malmö, Sweden. When compared with other sequenced Phytophthora species, the P. plurivora genome assembly is relatively compact, spanning 41 Mb. This is organized in 1,919 contigs and 1,898 scaffolds, encompassing 11,741 predicted genes, and has a repeat content of approximately 15%. Comparison of allele frequencies revealed evidence for tetraploidy in the sequenced isolate. As in other sequenced Phytophthora species, P. plurivora possesses genes for pathogenicity-associated RXLR and Crinkle and Necrosis effectors, predominantly located in gene-sparse genomic regions. Comparison of the P. plurivora RXLR effectors with orthologs in other sequenced species in the same clade (Phytophthora multivora and Phytophthora capsici) revealed that the orthologs were likely to be under neutral or purifying selection.

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Section: Methodsmentioning

confidence: 99%

Draft Genome Sequence for the Tree PathogenPhytophthora plurivora

Vetukuri

Tripathy

et al. 2018

Genome Biology and Evolution

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“…The absence of peaks in the k-mer distribution histogram and low mean coverage of the draft genome may indicate insufficient sequencing depth caused by a large total genome size, and/or high heterozygosity which complicates the assembly. In the 1.6 Gbp genome of another gastropod, the big-ear radix, Radix auricularia, approximately 70% of the content consisted of repeats [51]. As far as we know, high levels of repetitiveness within molluscan genomes are common [52], and also makes de novo assembly using only short reads challenging [53].…”

Section: First Draft Genome For Pteropodsmentioning

confidence: 99%

Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance

et al. 2020

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Background: Pteropods are planktonic gastropods that are considered as bio-indicators to monitor impacts of ocean acidification on marine ecosystems. In order to gain insight into their adaptive potential to future environmental changes, it is critical to use adequate molecular tools to delimit species and population boundaries and to assess their genetic connectivity. We developed a set of target capture probes to investigate genetic variation across their large-sized genome using a population genomics approach. Target capture is less limited by DNA amount and quality than other genome-reduced representation protocols, and has the potential for application on closely related species based on probes designed from one species. Results: We generated the first draft genome of a pteropod, Limacina bulimoides, resulting in a fragmented assembly of 2.9 Gbp. Using this assembly and a transcriptome as a reference, we designed a set of 2899 genomewide target capture probes for L. bulimoides. The set of probes includes 2812 single copy nuclear targets, the 28S rDNA sequence, ten mitochondrial genes, 35 candidate biomineralisation genes, and 41 non-coding regions. The capture reaction performed with these probes was highly efficient with 97% of the targets recovered on the focal species. A total of 137,938 single nucleotide polymorphism markers were obtained from the captured sequences across a test panel of nine individuals. The probes set was also tested on four related species: L. trochiformis, L. lesueurii, L. helicina, and Heliconoides inflatus, showing an exponential decrease in capture efficiency with increased genetic distance from the focal species. Sixty-two targets were sufficiently conserved to be recovered consistently across all five species. Conclusion: The target capture protocol used in this study was effective in capturing genome-wide variation in the focal species L. bulimoides, suitable for population genomic analyses, while providing insights into conserved genomic regions in related species. The present study provides new genomic resources for pteropods and supports the use of target capture-based protocols to efficiently characterise genomic variation in small non-model organisms with large genomes.

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“…Assembly of the Illumina reads resulted in a genome of 189,075,353 bp (189 Mb) assembled in 7974 scaffolds. In contrast, the total genome size estimated using the method of Schell et al [ 36 ] (from the maximum depth of read coverage) was 304.74 Mb (Additional file 2 : Table S11). The N50 of the genome assembly was 89,502 and the proportion of Ns was of 2.63% (Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…aegypti which has an unusually large genome. There is however some discrepancy between the estimated size using the method of Schell et al [ 36 ], the size of the original assembly and the size once redundancy is removed. The difference in estimated and assembled sizes could be due to the high level of redundancy as this will spread the coverage across different regions of the genome assembly that would be otherwise collapsed after redundancy removal.…”

Section: Discussionmentioning

confidence: 99%

“…The final assembly was assessed using FRCbam v1.0 to confirm that an improvement in the reported error rate had occurred. Genome size was estimated using the number of total trimmed nucleotides which were used in the assembly divided by the maximum of the per-position coverage frequency distribution, after reads were mapped back to the assembly using BWA-MEM [ 36 ]. Kmer spectra were assessed using KAT ( https://kat.readthedocs.io/en/latest ).…”

Section: Methodsmentioning

confidence: 99%

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The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus

et al. 2018

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BackgroundThe new genomic technologies have provided novel insights into the genetics of interactions between vectors, viruses and hosts, which are leading to advances in the control of arboviruses of medical importance. However, the development of tools and resources available for vectors of non-zoonotic arboviruses remains neglected. Biting midges of the genus Culicoides transmit some of the most important arboviruses of wildlife and livestock worldwide, with a global impact on economic productivity, health and welfare. The absence of a suitable reference genome has hindered genomic analyses to date in this important genus of vectors. In the present study, the genome of Culicoides sonorensis, a vector of bluetongue virus (BTV) in the USA, has been sequenced to provide the first reference genome for these vectors. In this study, we also report the use of the reference genome to perform initial transcriptomic analyses of vector competence for BTV.ResultsOur analyses reveal that the genome is 189 Mb, assembled in 7974 scaffolds. Its annotation using the transcriptomic data generated in this study and in a previous study has identified 15,612 genes. Gene expression analyses of C. sonorensis females infected with BTV performed in this study revealed 165 genes that were differentially expressed between vector competent and refractory females. Two candidate genes, glutathione S-transferase (gst) and the antiviral helicase ski2, previously recognized as involved in vector competence for BTV in C. sonorensis (gst) and repressing dsRNA virus propagation (ski2), were confirmed in this study.ConclusionsThe reference genome of C. sonorensis has enabled preliminary analyses of the gene expression profiles of vector competent and refractory individuals. The genome and transcriptomes generated in this study provide suitable tools for future research on arbovirus transmission. These provide a valuable resource for these vector lineage, which diverged from other major Dipteran vector families over 200 million years ago. The genome will be a valuable source of comparative data for other important Dipteran vector families including mosquitoes (Culicidae) and sandflies (Psychodidae), and together with the transcriptomic data can yield potential targets for transgenic modification in vector control and functional studies.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5014-1) contains supplementary material, which is available to authorized users.

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An annotated draft genome for Radix auricularia (Gastropoda, Mollusca)

Cited by 23 publications

References 53 publications

Draft Genome Sequence for the Tree PathogenPhytophthora plurivora

Draft Genome Sequence for the Tree PathogenPhytophthora plurivora

Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance

The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus

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