Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation

AbstractThe cryptic parasite Sparganum proliferum proliferates in humans and invades tissues and organs. Only scattered cases have been reported, but S. proliferum infection is always fatal. However, S. proliferum’s phylogeny and life cycle remain enigmatic. To investigate the phylogenetic relationships between S. proliferum and other cestode species, and to examine the mechanisms underlying pathogenicity, we sequenced the entire genomes of S. proliferum and a closely related non–life-threatening tapeworm Spirometra erinaceieuropaei. Additionally, we performed larvae transcriptome analyses of S. proliferum plerocercoid to identify genes involved in asexual reproduction in the host. The genome sequences confirmed that the S. proliferum has experienced a clearly distinct evolutionary history from S. erinaceieuropaei. Moreover, we found that nonordinal extracellular matrix coordination allows asexual reproduction in the host, and loss of sexual maturity in S. proliferum are responsible for its fatal pathogenicity to humans. Our high-quality reference genome sequences should be valuable for future studies of pseudophyllidean tapeworm biology and parasitism.

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Genome Analysis of the Fatal Tapeworm Sparganum Proliferum Uncovers the Cryptic Life Cycle and Mechanisms Underlying Aberrant Larval Proliferation

10.21203/rs.3.rs-78313/v1 ◽

2020 ◽

Author(s):

Taisei Kikuchi ◽

Mehmet Dayi ◽

Vicky Hunt ◽

Atsushi Toyoda ◽

Yasunobu Maeda ◽

...

Keyword(s):

Life Cycle ◽

Asexual Reproduction ◽

Sexual Maturity ◽

Evolutionary History ◽

Reference Genome ◽

Cestode Species ◽

Genome Sequences ◽

High Quality ◽

Future Studies ◽

Life Threatening

Abstract The cryptic parasite Sparganum proliferum proliferates in humans and invades tissues and organs. Only scattered cases have been reported, but S. proliferum infection is always fatal. However, S. proliferum’s phylogeny and life cycle remain enigmatic. To investigate the phylogenetic relationships between S. proliferum and other cestode species, and to examine the mechanisms underlying pathogenicity, we sequenced the entire genomes of S. proliferum and a closely related non–life-threatening tapeworm Spirometra erinaceieuropaei. Additionally, we performed larvae transcriptome analyses of S. proliferum plerocercoid to identify genes involved in asexual reproduction in the host. The genome sequences confirmed that the S. proliferum has experienced a clearly distinct evolutionary history from S. erinaceieuropaei. Moreover, we found that nonordinal extracellular matrix coordination allows asexual reproduction in the host, and loss of sexual maturity in S. proliferum are responsible for its fatal pathogenicity to humans. Our high-quality reference genome sequences should be valuable for future studies of pseudophyllidean tapeworm biology and parasitism.

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Genome analysis of the fatal tapeworm Sparganum proliferum unravels the cryptic lifecycle and mechanisms underlying the aberrant larval proliferation

10.1101/2020.05.19.105387 ◽

2020 ◽

Author(s):

Taisei Kikuchi ◽

Mehmet Dayi ◽

Vicky L. Hunt ◽

Atsushi Toyoda ◽

Yasunobu Maeda ◽

...

Keyword(s):

Extracellular Matrix ◽

Asexual Reproduction ◽

Sexual Maturity ◽

Reference Genome ◽

Cestode Species ◽

Genome Sequences ◽

High Quality ◽

Genetic Sequence ◽

Future Studies ◽

Underlying Mechanisms

AbstractBackgroundThe cryptic parasite Sparganum proliferum proliferates in humans and invades tissues and organs. Only scattered cases have been reported, but S. proliferum infection is always fatal. However, the S. proliferum phylogeny and lifecycle are still an enigma.ResultsTo investigate the phylogenetic relationships between S. proliferum and other cestode species, and to examine the underlying mechanisms of pathogenicity, we sequenced the entire S. proliferum genome. Additionally, S. proliferum plerocercoid larvae transcriptome analyses were performed to identify genes involved in asexual reproduction in the host. The genome sequences confirmed that the S. proliferum genetic sequence is distinct from that of the closely related Spirometra erinaceieuropaei. Moreover, nonordinal extracellular matrix coordination allows for asexual reproduction in the host and loss of sexual maturity in S. proliferum is related to its fatal pathogenicity in humans.ConclusionsThe high-quality reference genome sequences generated should prove valuable for future studies of pseudophyllidean tapeworm biology and parasitism.

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Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins

F1000Research ◽

10.12688/f1000research.9765.1 ◽

2016 ◽

Vol 5 ◽

pp. 2631 ◽

Cited By ~ 26

Author(s):

Jinhui Shen ◽

Qian Cong ◽

Lisa N. Kinch ◽

Dominika Borek ◽

Zbyszek Otwinowski ◽

...

Keyword(s):

Complete Genome ◽

Evolutionary History ◽

Reference Genome ◽

Pieris Rapae ◽

Defense Mechanism ◽

Butterfly Species ◽

Computational Simulations ◽

Median Length ◽

Future Studies ◽

Anti Cancer

The Small Cabbage White (Pieris rapae) is originally a Eurasian butterfly. Being accidentally introduced into North America, Australia, and New Zealand a century or more ago, it spread throughout the continents and rapidly established as one of the most abundant butterfly species. Although it is a serious pest of cabbage and other mustard family plants with its caterpillars reducing crops to stems, it is also a source of pierisin, a protein unique to the Whites that shows cytotoxicity to cancer cells. To better understand the unusual biology of this omnipresent agriculturally and medically important butterfly, we sequenced and annotated the complete genome from USA specimens. At 246 Mbp, it is among the smallest Lepidoptera genomes reported to date. While 1.5% positions in the genome are heterozygous, they are distributed highly non-randomly along the scaffolds, and nearly 20% of longer than 1000 base-pair segments are SNP-free (median length: 38000 bp). Computational simulations of population evolutionary history suggest that American populations started from a very small number of introduced individuals, possibly a single fertilized female, which is in agreement with historical literature. Comparison to other Lepidoptera genomes reveals several unique families of proteins that may contribute to the unusual resilience of Pieris. The nitrile-specifier proteins divert the plant defense chemicals to non-toxic products. The apoptosis-inducing pierisins could offer a defense mechanism against parasitic wasps. While only two pierisins from Pieris rapae were characterized before, the genome sequence revealed eight, offering additional candidates as anti-cancer drugs. The reference genome we obtained lays the foundation for future studies of the Cabbage White and other Pieridae species.

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Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates

Genes ◽

10.3390/genes11010050 ◽

2020 ◽

Vol 11 (1) ◽

pp. 50

Author(s):

Axel Barlow ◽

Stefanie Hartmann ◽

Javier Gonzalez ◽

Michael Hofreiter ◽

Johanna L. A. Paijmans

Keyword(s):

Clustering Analysis ◽

Error Rates ◽

Sequencing Error ◽

Genome Sequences ◽

High Quality ◽

Short Read ◽

Future Studies ◽

Sequencing Coverage ◽

Simplifying Assumptions ◽

Population Clustering

A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.

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Evidence of multiple genome duplication events in Mytilus evolution

10.1101/2021.08.17.456601 ◽

2021 ◽

Author(s):

Ana Corrochano-Fraile ◽

Andrew Davie ◽

Stefano Carboni ◽

Michaël Bekaert

Keyword(s):

Whole Genome Duplication ◽

Evolutionary History ◽

Reference Genome ◽

Genome Duplication ◽

Correct Identification ◽

High Quality ◽

Sequencing Technologies ◽

Abiotic Stressors ◽

Duplication Events ◽

First Time

Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia. Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences. The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises.

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Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management

BMC Genomics ◽

10.1186/s12864-021-07899-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Georgina Samaha ◽

Claire M. Wade ◽

Hamutal Mazrier ◽

Catherine E. Grueber ◽

Bianca Haase

Keyword(s):

Population Structure ◽

Evolutionary History ◽

Reference Genome ◽

Domestic Cat ◽

Snow Leopard ◽

Panthera Tigris ◽

Sequence Coverage ◽

Genomic Context ◽

Model Species ◽

High Quality

Abstract Background While recent advances in genomics has enabled vast improvements in the quantification of genome-wide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits. This has been attributed to the resources and infrastructure required to develop essential genomic datasets such as reference genomes. In the absence of a high-quality reference genome, cross-species alignments can provide reliable, cost-effective methods for single nucleotide variant (SNV) discovery. Here, we demonstrated the utility of cross-species genome alignment methods in gaining insights into population structure and functional genomic features in cheetah (Acinonyx jubatas), snow leopard (Panthera uncia) and Sumatran tiger (Panthera tigris sumatrae), relative to the domestic cat (Felis catus). Results Alignment of big cats to the domestic cat reference assembly yielded nearly complete sequence coverage of the reference genome. From this, 38,839,061 variants in cheetah, 15,504,143 in snow leopard and 13,414,953 in Sumatran tiger were discovered and annotated. This method was able to delineate population structure but limited in its ability to adequately detect rare variants. Enrichment analysis of fixed and species-specific SNVs revealed insights into adaptive traits, evolutionary history and the pathogenesis of heritable diseases. Conclusions The high degree of synteny among felid genomes enabled the successful application of the domestic cat reference in high-quality SNV detection. The datasets presented here provide a useful resource for future studies into population dynamics, evolutionary history and genetic and disease management of big cats. This cross-species method of variant discovery provides genomic context for identifying annotated gene regions essential to understanding adaptive and deleterious variants that can improve conservation outcomes.

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Genome sequence data of Leptosphaerulina arachidicola, a causal agent of peanut scorch spot in China

Plant Disease ◽

10.1094/pdis-08-21-1824-a ◽

2021 ◽

Author(s):

Yu-Ting Sheng Sheng ◽

Xiao-Li Yu ◽

Ting-Ting Mao ◽

Juan Zhang ◽

Xiao-Tong Guo ◽

...

Keyword(s):

Genome Size ◽

Genome Sequence ◽

Yield Loss ◽

Reference Genome ◽

Sequence Data ◽

High Quality ◽

Future Studies ◽

Significant Yield ◽

High Quality Genome ◽

Severe Leaf

Peanut scorch spot caused by Leptosphaerulina arachidicola is one of the most severe leaf diseases of peanut that causes significant yield loss. Here, we report the first high quality genome sequence of L. arachidicola JB313 isolated from an infected peanut leaf in China. The genome size is 47.66 Mb, consisting of 65 scaffolds (N50 length = 1.58 Mb) with a G+C content of 49.05%. The information in this report will provide a reference genome for future studies on peanut scorch spot pathogen in peanut.

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Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada

Microbiology Resource Announcements ◽

10.1128/mra.00625-19 ◽

2019 ◽

Vol 8 (41) ◽

Cited By ~ 2

Author(s):

Shari Tyson ◽

Christy-Lynn Peterson ◽

Adam Olson ◽

Shaun Tyler ◽

Natalie Knox ◽

...

Keyword(s):

Escherichia Coli ◽

Shiga Toxin ◽

Reference Genome ◽

Genome Sequences ◽

High Quality ◽

Content Type ◽

Food Animal ◽

Bovine Strain ◽

Human Infections ◽

Reference Genomes

We report high-quality closed reference genomes for 1 bovine strain and 10 human Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from serogroups O26, O45, O91, O103, O104, O111, O113, O121, O145, and O157. We also report draft assemblies, with standardized metadata, for 360 STEC strains isolated from watersheds, animals, farms, food, and human infections.

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Rites of Passage

10.1093/oso/9780198702603.003.0007 ◽

2018 ◽

Author(s):

Axel Michaels

Keyword(s):

Life Cycle ◽

Old Age ◽

Sexual Maturity ◽

Rites Of Passage ◽

Life And Death ◽

Transformational Process ◽

Local Contexts ◽

Vulnerable Community ◽

History Of ◽

The Individual

This chapter examines the classical Hindu life-cycle rites, the term saṃskāra and its history, and the main sources (Gṛhyasūtras and Dharma texts). It presents a history of the traditional saṃskāras and variants in local contexts, especially in Nepal. It describes prenatal, birth and childhood, initiation, marriage, old-age, death, and ancestor rituals. Finally, it analyzes the transformational process of these life-cycle rituals in the light of general theories on rites of passage. It proposes, in saṃskāras, man equates himself with the unchangeable and thus seems to counteract the uncertainty of the future, of life and death, since persons are confronted with their finite existence. For evidently every change, whether social or biological, represents a danger for the cohesion of the vulnerable community of the individual and society. These rituals then become an attempt of relegating the effects of nature or of mortality: birth, teething, sexual maturity, reproduction, and dying.

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Numerical Analysis on Performance of the Middle-Pressure Jet Grouting Method for Ground Improvement

Geosciences ◽

10.3390/geosciences11080313 ◽

2021 ◽

Vol 11 (8) ◽

pp. 313

Author(s):

Shinya Inazumi ◽

Sudip Shakya ◽

Takahiro Komaki ◽

Yasuharu Nakanishi

Keyword(s):

Life Cycle ◽

Comparative Analysis ◽

Ground Improvement ◽

Cement Slurry ◽

Mechanical Agitation ◽

High Quality ◽

Jet Grouting ◽

Computer Aided ◽

Improvement Method ◽

Cae System

This study focused on the middle-pressure jet grouting method, which has a complicated development mechanism for the columnar soil-improved body, with the aim of establishing a computer-aided engineering (CAE) system that can simulate the performance on a computer. Furthermore, in order to confirm the effect of middle-pressure jet grouting with mechanical agitation and mixing, a comparative analysis was performed with different jet pressures, the development situation was visualized, and the performance of this method was evaluated. The results of MPS-CAE as one of the CAE systems showed that the cement slurry jet ratio in the planned improvement range, including the periphery of the mixing blade, by the middle-pressure jet grouting together with the mechanical agitation and mixing was increased and a high quality columnar soil-improved body was obtained. It is expected that the introduction of CAE will contribute to the visualization of the ground, and that CAE will be an effective tool for the visual management of construction for ground improvement and the maintenance of improved grounds during the life cycle of the ground-improvement method.

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