Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

Xu, Xiao; Bei, Jinlong; Xuan, Yibo; Chen, Jiayuan; Chen, Defu; Barker, Stephen C.; Kelava, Samuel; Zhang, Xiao-Ai; Gao, Shan; Chen, Ze

doi:10.1186/s12864-020-07060-5

Cited by 14 publications

(10 citation statements)

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“…Finally, 5′ and 3′ telomeric, subtelomeric, rDNA, Long Terminal Repeat retrotransposons (LTR-rts), low complexity, and other repeat regions were exactly determined and confirmed by human curation (see section “Materials and Methods”). The complete O. polymorpha HU-11/CBS4732 genome is a full-length genome, which is defined to has sequences ending at the 5′ and 3′ telomeric sites without gaps and ambiguous nucleotides ( Xu et al, 2020 ).…”

Section: Resultsmentioning

confidence: 99%

Full-Length Genome of an Ogataea polymorpha Strain CBS4732 ura3Δ Reveals Large Duplicated Segments in Subtelomeric Regions

et al. 2022

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BackgroundCurrently, methylotrophic yeasts (e.g., Pichia pastoris, Ogataea polymorpha, and Candida boindii) are subjects of intense genomics studies in basic research and industrial applications. In the genus Ogataea, most research is focused on three basic O. polymorpha strains-CBS4732, NCYC495, and DL-1. However, the relationship between CBS4732, NCYC495, and DL-1 remains unclear, as the genomic differences between them have not be exactly determined without their high-quality complete genomes. As a nutritionally deficient mutant derived from CBS4732, the O. polymorpha strain CBS4732 ura3Δ (named HU-11) is being used for high-yield production of several important proteins or peptides. HU-11 has the same reference genome as CBS4732 (noted as HU-11/CBS4732), because the only genomic difference between them is a 5-bp insertion.ResultsIn the present study, we have assembled the full-length genome of O. polymorpha HU-11/CBS4732 using high-depth PacBio and Illumina data. Long terminal repeat retrotransposons (LTR-rts), rDNA, 5′ and 3′ telomeric, subtelomeric, low complexity and other repeat regions were exactly determined to improve the genome quality. In brief, the main findings include complete rDNAs, complete LTR-rts, three large duplicated segments in subtelomeric regions and three structural variations between the HU-11/CBS4732 and NCYC495 genomes. These findings are very important for the assembly of full-length genomes of yeast and the correction of assembly errors in the published genomes of Ogataea spp. HU-11/CBS4732 is so phylogenetically close to NCYC495 that the syntenic regions cover nearly 100% of their genomes. Moreover, HU-11/CBS4732 and NCYC495 share a nucleotide identity of 99.5% through their whole genomes. CBS4732 and NCYC495 can be regarded as the same strain in basic research and industrial applications.ConclusionThe present study preliminarily revealed the relationship between CBS4732, NCYC495, and DL-1. Our findings provide new opportunities for in-depth understanding of genome evolution in methylotrophic yeasts and lay the foundations for the industrial applications of O. polymorpha CBS4732, NCYC495, DL-1, and their derivative strains. The full-length genome of O. polymorpha HU-11/CBS4732 should be included into the NCBI RefSeq database for future studies of Ogataea spp.

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Section: Resultsmentioning

confidence: 99%

Full-Length Genome of an Ogataea polymorpha Strain CBS4732 ura3Δ Reveals Large Duplicated Segments in Subtelomeric Regions

et al. 2022

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“…Amblyomma, Dermacentor, Haemaphysalis, Hyalomma, and Ixodes (Maruyama et al, 2014;Qin et al, 2014;Souza et al, 2018;Dinçer et al, 2019Dinçer et al, , 2022Jia et al, 2019;Meng et al, 2019;Pascoal et al, 2019;Sameroff et al, 2019;Temmam et al, 2019;Gondard et al, 2020;Gómez et al, 2020;Ternovoi et al, 2020b;Xu et al, 2020Xu et al, , 2021Bratuleanu et al, 2021;Li et al, 2021;Shi et al, 2021;Ogola et al, 2022), as well as two mosquito species (Qin et al, 2014;Parry et al, 2021). The local prevalence of JMTV RNA in tick species such as Hae.…”

Section: Tick-and Vertebrate-associated Jingmenviruses Jingmen Tick V...mentioning

confidence: 99%

“…In fact, JMTV was found in high prevalence in R. microplus from China (53–63%), Brazil (25–67%), Trinidad and Tobago (6–46%), and the French Antilles (24–77%) over the years ( Maruyama et al, 2014 ; Qin et al, 2014 ; Souza et al, 2018 ; Pascoal et al, 2019 ; Sameroff et al, 2019 ; Temmam et al, 2019 ; Gondard et al, 2020 ; Guo J. J. et al, 2020 ; Kobayashi et al, 2021 ; Xu et al, 2021 ). However, the nature of the samples containing JMTV RNA extends beyond this species and includes 25 additional tick species from several genera, Rhipicephalus, Amblyomma, Dermacentor, Haemaphysalis, Hyalomma , and Ixodes ( Maruyama et al, 2014 ; Qin et al, 2014 ; Souza et al, 2018 ; Dinçer et al, 2019 , 2022 ; Jia et al, 2019 ; Meng et al, 2019 ; Pascoal et al, 2019 ; Sameroff et al, 2019 ; Temmam et al, 2019 ; Gondard et al, 2020 ; Guo J. J. et al, 2020 ; Gómez et al, 2020 ; Ternovoi et al, 2020b ; Xu et al, 2020 , 2021 ; Bratuleanu et al, 2021 ; Li et al, 2021 ; Shi et al, 2021 ; Ogola et al, 2022 ), as well as two mosquito species ( Qin et al, 2014 ; Parry et al, 2021 ). The local prevalence of JMTV RNA in tick species such as Hae.…”

Section: Tick- and Vertebrate-associated Jingmenvirusesmentioning

confidence: 99%

Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses

2022

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Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.

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“…Next-generation sequencing (NGS) plays a critical role in understanding the genetic diversity, molecular epidemiology, and transmission chain of virus outbreaks [21][22][23]. Several NGS approaches, including sequence-independent single-primer amplification, small RNA deep sequencing, and target enrichment methods have been utilized for whole-genome sequencing (WGS) of emerging viruses with low viral copy numbers [24][25][26][27]. The MinION system (Oxford Nanopore Technologies, London, UK) is a portable device for real-time sequencing in field situations or hospitals [28,29].…”

Section: Introductionmentioning

confidence: 99%

Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea

et al. 2022

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Background Whole-genome sequencing plays a critical role in the genomic epidemiology intended to improve understanding the spread of emerging viruses. Dabie bandavirus, causing severe fever with thrombocytopenia syndrome (SFTS), is a zoonotic tick-borne virus that poses a significant public health threat. We aimed to evaluate a novel amplicon-based nanopore sequencing tool to obtain whole-genome sequences of Dabie bandavirus, also known as SFTS virus (SFTSV), and investigate the molecular prevalence in wild ticks, Republic of Korea (ROK). Principal findings A total of 6,593 ticks were collected from Gyeonggi and Gangwon Provinces, ROK in 2019 and 2020. Quantitative polymerase chain reaction revealed the presence of SFSTV RNA in three Haemaphysalis longicornis ticks. Two SFTSV strains were isolated from H. longicornis captured from Pocheon and Cheorwon. Multiplex polymerase chain reaction-based nanopore sequencing provided nearly full-length tripartite genome sequences of SFTSV within one hour running. Phylogenetic and reassortment analyses were performed to infer evolutionary relationships among SFTSVs. Phylogenetic analysis grouped SFTSV Hl19-31-4 and Hl19-31-13 from Pocheon with sub-genotype B-1 in all segments. SFTSV Hl20-8 was found to be a genomic organization compatible with B-1 (for L segment) and B-2 (for M and S segments) sub-genotypes, indicating a natural reassortment between sub-genotypes. Conclusion/Significance Amplicon-based next-generation sequencing is a robust tool for whole-genome sequencing of SFTSV using the nanopore platform. The molecular prevalence and geographical distribution of SFTSV enhanced the phylogeographic map at high resolution for sophisticated prevention of emerging SFTS in endemic areas. Our findings provide important insights into the rapid whole-genome sequencing and genetic diversity for the genome-based diagnosis of SFTSV in the endemic outbreak.

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Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

Cited by 14 publications

References 28 publications

Full-Length Genome of an Ogataea polymorpha Strain CBS4732 ura3Δ Reveals Large Duplicated Segments in Subtelomeric Regions

Full-Length Genome of an Ogataea polymorpha Strain CBS4732 ura3Δ Reveals Large Duplicated Segments in Subtelomeric Regions

Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses

Whole-genome sequencing and genetic diversity of severe fever with thrombocytopenia syndrome virus using multiplex PCR-based nanopore sequencing, Republic of Korea

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