Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes

Kinkar, Liina; Gasser, Robin B.; Webster, Bonnie L.; Rollinson, David; Littlewood, D. Timothy J.; Chang, Bill C.H.; Stroehlein, Andreas J.; Korhonen, Pasi K.; Young, Neil D.

doi:10.3390/ijms22041811

Cited by 26 publications

(32 citation statements)

References 70 publications

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“…We would also like to indicate that recent investigations on parasitic flatworms such as Echinococcus granulosus Batsch, 1786, Clonorchis sinensis Loos, 1907 and Schistosoma haematobium (Bilharz, 1852) using long-read technologies have shown considerable extra-lengths within these mitogenomes, as much as 18.5 kb long ( Kinkar et al, 2021 ; Kinkar et al, 2019 ; Kinkar et al, 2020 ). We tend to think that in the near future, long-read technologies might unveil similar features among Geoplanidae.…”

Section: Discussionmentioning

confidence: 91%

Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte

Justine

Gastineau

Gros³

et al. 2022

PeerJ

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Background New records of alien land planarians are regularly reported worldwide, and some correspond to undescribed species of unknown geographic origin. The description of new species of land planarians (Geoplanidae) should classically be based on both external morphology and histology of anatomical structures, especially the copulatory organs, ideally with the addition of molecular data. Methods Here, we describe the morphology and reproductive anatomy of a species previously reported as Diversibipalium “black”, and the morphology of a species previously reported as Diversibipalium “blue”. Based on next generation sequencing, we obtained the complete mitogenome of five species of Bipaliinae, including these two species. Results The new species Humbertium covidum n. sp. (syn: Diversibipalium “black” of Justine et al., 2018) is formally described on the basis of morphology, histology and mitogenome, and is assigned to Humbertium on the basis of its reproductive anatomy. The type-locality is Casier, Italy, and other localities are in the Department of Pyrénées-Atlantiques, France; some published or unpublished records suggest that this species might also be present in Russia, China, and Japan. The mitogenomic polymorphism of two geographically distinct specimens (Italy vs France) is described; the cox1 gene displayed 2.25% difference. The new species Diversibipalium mayottensis n. sp. (syn: Diversibipalium “blue” of Justine et al., 2018) is formally described on the basis of external morphology and complete mitogenome and is assigned to Diversibipalium on the basis of an absence of information on its reproductive anatomy. The type- and only known locality is the island of Mayotte in the Mozambique Channel off Africa. Phylogenies of bipaliine geoplanids were constructed on the basis of SSU, LSU, mitochondrial proteins and concatenated sequences of cox1, SSU and LSU. In all four phylogenies, D. mayottensis was the sister-group to all the other bipaliines. With the exception of D. multilineatum which could not be circularised, the complete mitogenomes of B. kewense, B. vagum, B. adventitium, H. covidum and D. mayottensis were colinear. The 16S gene in all bipaliine species was problematic because usual tools were unable to locate its exact position. Conclusion Next generation sequencing, which can provide complete mitochondrial genomes as well as traditionally used genes such as SSU, LSU and cox1, is a powerful tool for delineating and describing species of Bipaliinae when the reproductive structure cannot be studied, which is sometimes the case of asexually reproducing invasive species. The unexpected position of the new species D. mayottensis as sister-group to all other Bipaliinae in all phylogenetic analyses suggests that the species could belong to a new genus, yet to be described.

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Section: Discussionmentioning

confidence: 91%

Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte

Justine

Gastineau

Gros³

et al. 2022

PeerJ

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“…First, long-read data (SRA accession numbers SRR15400746 and SRR15400747; via Oxford Nanopore technology [60]) were used for initial contig assembly employing the program Canu v.1.9 [61], setting a genome size estimate of 400 Mb. Errors in these data were corrected using medaka_consensus in the Medaka package v.1.0.3 (https://github.com/nanoporetech/ medaka).…”

Section: Dna Sequencing and Genome Assemblymentioning

confidence: 99%

Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation

et al. 2022

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Urogenital schistosomiasis is caused by the blood fluke Schistosoma haematobium and is one of the most neglected tropical diseases worldwide, afflicting > 100 million people. It is characterised by granulomata, fibrosis and calcification in urogenital tissues, and can lead to increased susceptibility to HIV/AIDS and squamous cell carcinoma of the bladder. To complement available treatment programs and break the transmission of disease, sound knowledge and understanding of the biology and ecology of S. haematobium is required. Hybridisation/introgression events and molecular variation among members of the S. haematobium-group might effect important biological and/or disease traits as well as the morbidity of disease and the effectiveness of control programs including mass drug administration. Here we report the first chromosome-contiguous genome for a well-defined laboratory line of this blood fluke. An exploration of this genome using transcriptomic data for all key developmental stages allowed us to refine gene models (including non-coding elements) and annotations, discover ‘new’ genes and transcription profiles for these stages, likely linked to development and/or pathogenesis. Molecular variation within S. haematobium among some geographical locations in Africa revealed unique genomic ‘signatures’ that matched species other than S. haematobium, indicating the occurrence of introgression events. The present reference genome (designated Shae.V3) and the findings from this study solidly underpin future functional genomic and molecular investigations of S. haematobium and accelerate systematic, large-scale population genomics investigations, with a focus on improved and sustained control of urogenital schistosomiasis.

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“…This effect is more pronounced in tetraploid genomes, since they have more alternative haplotype versions of the same region. Long-read sequencing technologies such as PacBio ( Shearman et al 2020 ; Vollger et al 2020 ) and Nanopore ( Kuderna et al 2019 ; Low et al 2019 ; Kinkar et al 2021 ) aim to overcome the problem of heterozygosity, allowing more space for overlaps during assembly ( Jiao and Schneeberger 2017 ). Further sequencing technologies such as proximity ligation and optical mapping help resolving areas that are difficult to assemble ( Field et al 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety

Freire

Weisweiler

Guerreiro

et al. 2021

G3 Genes|Genomes|Genetics

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Potato (Solanum tuberosum L.) is one of the most important crops with a world-wide production of 370 million metric tons. The objectives of this study were (i) to create a high quality consensus sequence across the two haplotypes of a diploid clone derived from a tetraploid elite variety and assess the sequence divergence from the available potato genome assemblies, as well as among the two haplotypes; (ii) to evaluate the new assembly’s usefulness for various genomic methods and (iii) to assess the performance of phasing in diploid and tetraploid clones, using linked read sequencing technology. We used PacBio long reads coupled with 10x Genomics reads and proximity-ligation scaffolding to create the dAg1_v1.0 reference genome sequence. With a final assembly size of 812 Mb, where 750 Mb are anchored to 12 chromosomes, our assembly is larger than other available potato reference sequences and high proportions of properly paired reads were observed for clones unrelated by pedigree to dAg1. Comparisons of the new dAg1_v1.0 sequence to other potato genome sequences point out the high divergence between the different potato varieties and illustrate the potential of using dAg1_v1.0 sequence in breeding applications.

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Nanopore Sequencing Resolves Elusive Long Tandem-Repeat Regions in Mitochondrial Genomes

Cited by 26 publications

References 70 publications

Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte

Hammerhead flatworms (Platyhelminthes, Geoplanidae, Bipaliinae): mitochondrial genomes and description of two new species from France, Italy, and Mayotte

Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation

Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety

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