No detectable signal for ongoing genetic recombination in SARS-CoV-2

The COVID-19 pandemic has led to an unprecedented global sequencing effort of its viral agent SARS-CoV-2. The first whole genome assembly of SARS-CoV-2 was published on January 5 2020. Since then, over 150,000 high-quality SARS-CoV-2 genomes have been made available. This large genomic resource has allowed tracing of the emergence and spread of mutations and phylogenetic reconstruction of SARS-CoV-2 lineages in near real time. Though, whether SARS-CoV-2 undergoes genetic recombination has been largely overlooked to date. Recombination-mediated rearrangement of variants that arose independently can be of major evolutionary importance. Moreover, the absence of recombination is a key assumption behind the application of phylogenetic inference methods. Here, we analyse the extant genomic diversity of SARS-CoV-2 and show that, to date, there is no detectable hallmark of recombination. We assess our detection power using simulations and validate our method on the related MERS-CoV for which we report evidence for widespread genetic recombination.

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Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab337 ◽

2021 ◽

Author(s):

Yuanchao Liu ◽

Longhua Huang ◽

Huiping Hu ◽

Manjun Cai ◽

Xiaowei Liang ◽

...

Keyword(s):

Genome Assembly ◽

Southwest China ◽

Reference Genome ◽

Biological Activities ◽

Single Copy ◽

The Tibetan Plateau ◽

Whole Genome ◽

High Quality ◽

Pharmacological Activities ◽

Genetic Studies

Abstract Ganoderma leucocontextum, a newly discovered species of Ganodermataceae in China, has diverse pharmacological activities. G. leucocontextum was widely cultivated in southwest China, but the systematic genetic study has been impeded by the lack of a reference genome. Herein, we present the first whole-genome assembly of G. leucocontextum based on the Illumina and Nanopore platform from high-quality DNA extracted from a monokaryon strain (DH-8). The generated genome was 50.05 Mb in size with a N50 scaﬀold size of 3.06 Mb, 78,206 coding sequences and 13,390 putative genes. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 96.55% of the 280 Fungi BUSCO genes. Furthermore, differences in functional genes of secondary metabolites (terpenoids) were analyzed between G. leucocontextum and G. lucidum. G. leucocontextum has more genes related to terpenoids synthesis compared to G. lucidum, which may be one of the reasons why they exhibit different biological activities. This is the first genome assembly and annotation for G. leucocontextum, which would enrich the toolbox for biological and genetic studies in G. leucocontextum.

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The de novo genome of the “Spanish” slug Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Panpulmonata): massive expansion of transposable elements in a major pest species

10.1101/2020.11.30.403303 ◽

2020 ◽

Author(s):

Zeyuan Chen ◽

Özgül Doğan ◽

Nadège Guiglielmoni ◽

Anne Guichard ◽

Michael Schrödl

Keyword(s):

Transposable Elements ◽

Genome Assembly ◽

De Novo ◽

Repetitive Sequences ◽

Land Snails ◽

Whole Genome ◽

Pest Species ◽

High Quality ◽

Genome Duplication Event ◽

Arion Vulgaris

AbstractBackgroundThe “Spanish” slug, Arion vulgaris Moquin-Tandon, 1855, is considered to be among the 100 worst pest species in Europe. It is common and invasive to at least northern and eastern parts of Europe, probably benefitting from climate change and the modern human lifestyle. The origin and expansion of this species, the mechanisms behind its outstanding adaptive success and ability to outcompete other land slugs are worth to be explored on a genomic level. However, a high-quality chromosome-level genome is still lacking.FindingsThe final assembly of A. vulgaris was obtained by combining short reads, linked reads, Nanopore long reads, and Hi-C data. The genome assembly size is 1.54 Gb with a contig N50 length of 8.6 Mb. We found a recent expansion of transposable elements (TEs) which results in repetitive sequences accounting for more than 75% of the A. vulgaris genome, which is the highest among all known gastropod species. We identified 32,518 protein coding genes, and 2,763 species specific genes were functionally enriched in response to stimuli, nervous system and reproduction. With 1,237 single-copy orthologs from A. vulgaris and other related mollusks with whole-genome data available, we reconstructed the phylogenetic relationships of gastropods and estimated the divergence time of stylommatophoran land snails (Achatina) and Arion slugs at around 126 million years ago, and confirmed the whole genome duplication event shared by them.ConclusionsTo our knowledge, the A. vulgaris genome is the first land slug genome assembly published to date. The high-quality genomic data will provide valuable genetic resources for further phylogeographic studies of A. vulgaris origin and expansion, invasiveness, as well as molluscan aquatic-land transition and shell formation.

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A high‐quality walnut genome assembly reveals extensive gene expression divergences after whole‐genome duplication

Plant Biotechnology Journal ◽

10.1111/pbi.13350 ◽

2020 ◽

Vol 18 (9) ◽

pp. 1848-1850 ◽

Cited By ~ 2

Author(s):

Junpei Zhang ◽

Wenting Zhang ◽

Feiyang Ji ◽

Jie Qiu ◽

Xiaobo Song ◽

...

Keyword(s):

Gene Expression ◽

Genome Assembly ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Whole Genome ◽

High Quality

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Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)

GigaScience ◽

10.1093/gigascience/giz112 ◽

2019 ◽

Vol 8 (9) ◽

Cited By ~ 11

Author(s):

Yu Xing ◽

Yang Liu ◽

Qing Zhang ◽

Xinghua Nie ◽

Yamin Sun ◽

...

Keyword(s):

Single Molecule ◽

Genome Assembly ◽

Genetic Improvement ◽

De Novo ◽

Draft Genome ◽

Whole Genome Sequence ◽

Whole Genome ◽

High Quality ◽

Chinese Chestnut ◽

Castanea Mollissima

AbstractBackgroundThe Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima.FindingsWe produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago.ConclusionsThe high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

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Chromosome-Level Genome Assembly and Annotation of a Sciaenid Fish, Argyrosomus japonicus

Genome Biology and Evolution ◽

10.1093/gbe/evaa246 ◽

2021 ◽

Vol 13 (2) ◽

Author(s):

Linlin Zhao ◽

Shengyong Xu ◽

Zhiqiang Han ◽

Qi Liu ◽

Wensi Ke ◽

...

Keyword(s):

Genome Assembly ◽

Wide Distribution ◽

High Quality ◽

Protein Coding ◽

Repeat Elements ◽

Long Reads ◽

The Family ◽

Solid Foundation ◽

Genomic Resource ◽

Chromosome Level

Abstract Argyrosomus japonicus is an economically and ecologically important fish species in the family Sciaenidae with a wide distribution in the world’s oceans. Here, we report a high-quality, chromosome-level genome assembly of A. japonicus based on PacBio and Hi-C sequencing technology. A 673.7-Mb genome containing 282 contigs with an N50 length of 18.4 Mb was obtained based on PacBio long reads. These contigs were further ordered and clustered into 24 chromosome groups based on Hi-C data. In addition, a total of 217.2 Mb (32.24% of the assembled genome) of sequences were identified as repeat elements, and 23,730 protein-coding genes were predicted based on multiple approaches. More than 97% of BUSCO genes were identified in the A. japonicus genome. The high-quality genome assembled in this work not only provides a valuable genomic resource for future population genetics, conservation biology and selective breeding studies of A. japonicus but also lays a solid foundation for the study of Sciaenidae evolution.

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Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation

GigaScience ◽

10.1093/gigascience/giaa148 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Monica M Sheffer ◽

Anica Hoppe ◽

Henrik Krehenwinkel ◽

Gabriele Uhl ◽

Andreas W Kuss ◽

...

Keyword(s):

Genome Assembly ◽

Range Expansion ◽

Reference Genome ◽

De Novo ◽

Sequencing Data ◽

High Quality ◽

Proximity Ligation ◽

Genomic Resource ◽

Paired End Sequencing ◽

Chromosome Level

Abstract Background Argiope bruennichi, the European wasp spider, has been investigated intensively as a focal species for studies on sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. Therefore, we assembled a high-quality chromosome-level reference genome of the European wasp spider as a tool for more in-depth future studies. Findings We generated, de novo, a 1.67 Gb genome assembly of A. bruennichi using 21.8× Pacific Biosciences sequencing, polished with 19.8× Illumina paired-end sequencing data, and proximity ligation (Hi-C)-based scaffolding. This resulted in an N50 scaffold size of 124 Mb and an N50 contig size of 288 kb. We found 98.4% of the genome to be contained in 13 scaffolds, fitting the expected number of chromosomes (n = 13). Analyses showed the presence of 91.1% of complete arthropod BUSCOs, indicating a high-quality assembly. Conclusions We present the first chromosome-level genome assembly in the order Araneae. With this genomic resource, we open the door for more precise and informative studies on evolution and adaptation not only in A. bruennichi but also in arachnids overall, shedding light on questions such as the genomic architecture of traits, whole-genome duplication, and the genomic mechanisms behind silk and venom evolution.

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A chromosome-level genome assembly for the Eastern Fence Lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology

10.1101/2020.06.06.138248 ◽

2020 ◽

Author(s):

Aundrea K. Westfall ◽

Rory S. Telemeco ◽

Mariana B. Grizante ◽

Damien S. Waits ◽

Amanda D. Clark ◽

...

Keyword(s):

Behavioral Ecology ◽

Genome Assembly ◽

Evolutionary Ecology ◽

Whole Genome ◽

Sceloporus Undulatus ◽

High Quality ◽

Whole Genome Analysis ◽

Genomic Resources ◽

Eastern Fence Lizard ◽

Chromosome Level

AbstractHigh-quality genomic resources facilitate population-level and species-level comparisons to answer questions about behavioral ecology, morphological and physiological adaptations, as well as the evolution of genomic architecture. Squamate reptiles (lizards and snakes) are particularly diverse in characteristics that have intrigued evolutionary biologists, but high-quality genomic resources for squamates are relatively sparse. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. We present a high-quality chromosome-level reference genome assembly, SceUnd1.0, (utilizing 10X Genomics Chromium, HiC, and PacBio data) and tissue/developmental stage transcriptomes for the Eastern Fence Lizard, Sceloporus undulatus. We performed synteny analysis with other available squamate chromosome-level assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes in S. undulatus. Using this new S. undulatus genome assembly we conducted reference-based assemblies for 34 other Sceloporus species to improve draft nuclear genomes assemblies from 1% coverage to 43% coverage on average. Across these species, typically >90% of reads mapped for species within 20 million years divergence from S. undulatus, this dropped to 75% reads mapped for species at 35 million years divergence. Finally we use RNAseq and whole genome resequencing data to compare the three assemblies as references, each representing an increased level of sequencing, cost and assembly efforts: Supernova Assembly with data from10X Genomics Chromium library; HiRise Assembly that added data from HiC library; and PBJelly Assembly that added data from PacBio sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq, but the chromosome-level scaffolds provided by the addition of the HiC data allowed the reference to be used for other whole genome analysis, including synteny and whole genome association mapping analyses. The addition of PacBio data provided negligible gains. Overall, these new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology.

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Dense sampling of bird diversity increases power of comparative genomics

Nature ◽

10.1038/s41586-020-2873-9 ◽

2020 ◽

Vol 587 (7833) ◽

pp. 252-257 ◽

Cited By ~ 2

Author(s):

Shaohong Feng ◽

Josefin Stiller ◽

Yuan Deng ◽

Joel Armstrong ◽

Qi Fang ◽

...

Keyword(s):

Genomic Diversity ◽

Bird Diversity ◽

Whole Genome ◽

Weak Selection ◽

Specific Variation ◽

Single Base Pair ◽

Genomic Resource ◽

Dense Sampling ◽

Dense Representation ◽

Genome Dataset

AbstractWhole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

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Chromosome-level reference genome of the European wasp spider Argiope bruennichi: a resource for studies on range expansion and evolutionary adaptation

10.1101/2020.05.21.103564 ◽

2020 ◽

Cited By ~ 2

Author(s):

Monica M. Sheffer ◽

Anica Hoppe ◽

Henrik Krehenwinkel ◽

Gabriele Uhl ◽

Andreas W. Kuss ◽

...

Keyword(s):

Genome Assembly ◽

Range Expansion ◽

Reference Genome ◽

De Novo ◽

Sequencing Data ◽

High Quality ◽

Proximity Ligation ◽

Genomic Resource ◽

Paired End Sequencing ◽

Chromosome Level

AbstractBackgroundArgiope bruennichi, the European wasp spider, has been studied intensively as to sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. Therefore, we assembled a high-quality chromosome-level reference genome of the European wasp spider as a tool for more in-depth future studies.FindingsWe generated, de novo, a 1.67Gb genome assembly of A. bruennichi using 21.5X PacBio sequencing, polished with 30X Illumina paired-end sequencing data, and proximity ligation (Hi-C) based scaffolding. This resulted in an N50 scaffold size of 124Mb and an N50 contig size of 288kb. We found 98.4% of the genome to be contained in 13 scaffolds, fitting the expected number of chromosomes (n = 13). Analyses showed the presence of 91.1% of complete arthropod BUSCOs, indicating a high quality of the assembly.ConclusionsWe present the first chromosome-level genome assembly in the class Arachnida. With this genomic resource, we open the door for more precise and informative studies on evolution and adaptation in A. bruennichi, as well as on several interesting topics in Arachnids, such as the genomic architecture of traits, whole genome duplication and the genomic mechanisms behind silk and venom evolution.

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A Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing

Viruses ◽

10.3390/v13101994 ◽

2021 ◽

Vol 13 (10) ◽

pp. 1994

Author(s):

Mariangela Stefania Fiori ◽

Daria Sanna ◽

Fabio Scarpa ◽

Matteo Floris ◽

Antonello Di Nardo ◽

...

Keyword(s):

African Swine Fever Virus ◽

Phylogenetic Reconstruction ◽

African Swine Fever ◽

Control Measures ◽

Genomic Diversity ◽

Economic Losses ◽

Small Scale ◽

Whole Genome ◽

Evolutionary Patterns ◽

Genetic Substructure

African swine fever virus (ASFV) is the etiological agent of the devastating disease African swine fever (ASF), for which there is currently no licensed vaccine or treatment available. ASF is defined as one of the most serious animal diseases identified to date, due to its global spread in regions of Africa, Europe and Asia, causing massive economic losses. On the Italian island of Sardinia, the disease has been endemic since 1978, although the last control measures put in place achieved a significant reduction in ASF, and the virus has been absent from circulation since April 2019. Like many large DNA viruses, ASFV mutates at a relatively slow rate. However, the limited availability of whole-genome sequences from spatial-localized outbreaks makes it difficult to explore the small-scale genetic structure of these ASFV outbreaks. It is also unclear if the genetic variability within outbreaks can be captured in a handful of sequences, or if larger sequencing efforts can improve phylogenetic reconstruction and evolutionary or epidemiological inference. The aim of this study was to investigate the phylogenetic patterns of ASFV outbreaks between 1978 and 2018 in Sardinia, in order to characterize the epidemiological dynamics of the viral strains circulating in this Mediterranean island. To reach this goal, 58 new whole genomes of ASFV isolates were obtained, which represents the largest ASFV whole-genome sequencing effort to date. We provided a complete description of the genomic diversity of ASFV in terms of nucleotide mutations and small and large indels among the isolates collected during the outbreaks. The new sequences capture more than twice the genomic and phylogenetic diversity of all the previously published Sardinian sequences. The extra genomic diversity increases the resolution of the phylogenetic reconstruction, enabling us to dissect, for the first time, the genetic substructure of the outbreak. We found multiple ASFV subclusters within the phylogeny of the Sardinian epidemic, some of which coexisted in space and time.

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