Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes

The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

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Genomic Analysis of Sarcomyxa edulis Reveals the Basis of Its Medicinal Properties and Evolutionary Relationships

Frontiers in Microbiology ◽

10.3389/fmicb.2021.652324 ◽

2021 ◽

Vol 12 ◽

Author(s):

Fenghua Tian ◽

Changtian Li ◽

Yu Li

Keyword(s):

Single Molecule ◽

De Novo ◽

Genomic Analysis ◽

Single Copy ◽

Whole Genome Sequence ◽

Type I ◽

Whole Genome ◽

Uridine Diphosphate ◽

Protein Coding ◽

Medicinal Value

Yuanmo [Sarcomyxa edulis (Y.C. Dai, Niemelä & G.F. Qin) T. Saito, Tonouchi & T. Harada] is an important edible and medicinal mushroom endemic to Northeastern China. Here we report the de novo sequencing and assembly of the S. edulis genome using single-molecule real-time sequencing technology. The whole genome was approximately 35.65 Mb, with a G + C content of 48.31%. Genome assembly generated 41 contigs with an N50 length of 1,772,559 bp. The genome comprised 9,364 annotated protein-coding genes, many of which encoded enzymes involved in the modification, biosynthesis, and degradation of glycoconjugates and carbohydrates or enzymes predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I polyketide, siderophore, and fatty acids, which are responsible for the pharmacodynamic activities of S. edulis. We also identified genes encoding 1,3-β-glucan synthase and endo-1,3(4)-β-glucanase, which are involved in polysaccharide and uridine diphosphate glucose biosynthesis. Phylogenetic and comparative analyses of Basidiomycota fungi based on a single-copy orthologous protein indicated that the Sarcomyxa genus is an independent group that evolved from the Pleurotaceae family. The annotated whole-genome sequence of S. edulis can serve as a reference for investigations of bioactive compounds with medicinal value and the development and commercial production of superior S. edulis varieties.

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Structural and functional characterization of a putative de novo gene in Drosophila

Nature Communications ◽

10.1038/s41467-021-21667-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Andreas Lange ◽

Prajal H. Patel ◽

Brennen Heames ◽

Adam M. Damry ◽

Thorsten Saenger ◽

...

Keyword(s):

De Novo ◽

Functional Characterization ◽

Comparative Genomic ◽

Noncoding Dna ◽

Protein Coding ◽

Ancestral Sequences ◽

De Novo Gene ◽

Genomic Studies ◽

Biochemical Genetic

AbstractComparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from noncoding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus. Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and circular dichroism (CD) data, we show that Goddard protein contains a large central α-helix, but is otherwise partially disordered. We find similar results for Goddard’s orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddard’s structure appears to have been maintained with only minor changes over millions of years.

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Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400563 ◽

2019 ◽

Vol 9 (10) ◽

pp. 3057-3066 ◽

Cited By ~ 2

Author(s):

Eoin O’Connor ◽

Jamie McGowan ◽

Charley G. P. McCarthy ◽

Aniça Amini ◽

Helen Grogan ◽

...

Keyword(s):

Genome Sequence ◽

Agaricus Bisporus ◽

Genomic Analysis ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Whole Genome ◽

Protein Coding ◽

Single Strain ◽

Protein Coding Genes ◽

Starting Point

Agaricus bisporus is an extensively cultivated edible mushroom. Demand for cultivation is continuously growing and difficulties associated with breeding programs now means strains are effectively considered monoculture. While commercial growing practices are highly efficient and tightly controlled, the over-use of a single strain has led to a variety of disease outbreaks from a range of pathogens including bacteria, fungi and viruses. To address this, the Agaricus Resource Program (ARP) was set up to collect wild isolates from diverse geographical locations through a bounty-driven scheme to create a repository of wild Agaricus germplasm. One of the strains collected, Agaricus bisporus var. bisporus ARP23, has been crossed extensively with white commercial varieties leading to the generation of a novel hybrid with a dark brown pileus commonly referred to as ‘Heirloom’. Heirloom has been successfully implemented into commercial mushroom cultivation. In this study the whole genome of Agaricus bisporus var. bisporus ARP23 was sequenced and assembled with Illumina and PacBio sequencing technology. The final genome was found to be 33.49 Mb in length and have significant levels of synteny to other sequenced Agaricus bisporus strains. Overall, 13,030 putative protein coding genes were located and annotated. Relative to the other A. bisporus genomes that are currently available, Agaricus bisporus var. bisporus ARP23 is the largest A. bisporus strain in terms of gene number and genetic content sequenced to date. Comparative genomic analysis shows that the A. bisporus mating loci in unifactorial and unsurprisingly highly conserved between strains. The lignocellulolytic gene content of all A. bisporus strains compared is also very similar. Our results show that the pangenome structure of A. bisporus is quite diverse with between 60–70% of the total protein coding genes per strain considered as being orthologous and syntenically conserved. These analyses and the genome sequence described herein are the starting point for more detailed molecular analyses into the growth and phenotypical responses of Agaricus bisporus var. bisporus ARP23 when challenged with economically important mycoviruses.

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Comparative Genomics of Clinical Isolates of the Emerging Tick-Borne Pathogen Neoehrlichia mikurensis

Microorganisms ◽

10.3390/microorganisms9071488 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1488

Author(s):

Anna Grankvist ◽

Daniel Jaén-Luchoro ◽

Linda Wass ◽

Per Sikora ◽

Christine Wennerås

Keyword(s):

Vascular Endothelium ◽

De Novo ◽

Phylogenetic Analyses ◽

Geographic Origin ◽

Comparative Genomic ◽

Whole Genome ◽

Illumina Hiseq ◽

Protein Coding ◽

Ehrlichia Ruminantium ◽

Protein Coding Genes

Tick-borne ‘Neoehrlichia (N.) mikurensis’ is the cause of neoehrlichiosis, an infectious vasculitis of humans. This strict intracellular pathogen is a member of the family Anaplasmataceae and has been unculturable until recently. The only available genetic data on this new pathogen are six partially sequenced housekeeping genes. The aim of this study was to advance the knowledge regarding ‘N. mikurensis’ genomic relatedness with other Anaplasmataceae members, intra-species genotypic variability and potential virulence factors explaining its tropism for vascular endothelium. Here, we present the de novo whole-genome sequences of three ‘N. mikurensis’ strains derived from Swedish patients diagnosed with neoehrlichiosis. The genomes were obtained by extraction of DNA from patient plasma, library preparation using 10x Chromium technology, and sequencing by Illumina Hiseq-4500. ‘N. mikurensis’ was found to have the next smallest genome of the Anaplasmataceae family (1.1 Mbp with 27% GC contents) consisting of 845 protein-coding genes, every third of which with unknown function. Comparative genomic analyses revealed that ‘N. mikurensis’ was more closely related to Ehrlichia chaffeensis than to Ehrlichia ruminantium, the opposite of what 16SrRNA sequence-based phylogenetic analyses determined. The genetic variability of the three whole-genome-sequenced ‘N. mikurensis’ strains was extremely low, between 0.14 and 0.22‰, a variation that was associated with geographic origin. No protein-coding genes exclusively shared by N. mikurensis and E. ruminantium were identified to explain their common tropism for vascular endothelium.

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Structural and functional characterization of a putative de novo gene in Drosophila

10.1101/2021.01.18.427054 ◽

2021 ◽

Author(s):

Andreas Lange ◽

Prajal H. Patel ◽

Brennen Heames ◽

Adam M. Damry ◽

Thorsten Saenger ◽

...

Keyword(s):

De Novo ◽

Functional Characterization ◽

Comparative Genomic ◽

Protein Coding ◽

Ancestral Sequences ◽

De Novo Gene ◽

Genomic Studies ◽

Biochemical Genetic ◽

Α Helix

AbstractComparative genomic studies have repeatedly shown that new protein-coding genes can emerge de novo from non-coding DNA. Still unknown is how and when the structures of encoded de novo proteins emerge and evolve. Combining biochemical, genetic and evolutionary analyses, we elucidate the function and structure of goddard, a gene which appears to have evolved de novo at least 50 million years ago within the Drosophila genus.Previous studies found that goddard is required for male fertility. Here, we show that Goddard protein localizes to elongating sperm axonemes and that in its absence, elongated spermatids fail to undergo individualization. Combining modelling, NMR and CD data, we show that Goddard protein contains a large central α-helix, but is otherwise partially disordered. We find similar results for Goddard’s orthologs from divergent fly species and their reconstructed ancestral sequences. Accordingly, Goddard’s structure appears to have been maintained with only minor changes over millions of years.

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Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica

Scientific Data ◽

10.1038/s41597-019-0201-8 ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 8

Author(s):

Fen Zhang ◽

Wei Li ◽

Cheng-wen Gao ◽

Dan Zhang ◽

Li-zhi Gao

Keyword(s):

Rna Editing ◽

De Novo ◽

Comparative Genomic ◽

Protein Coding ◽

Tea Tree ◽

Repeat Sequences ◽

Genomic Studies ◽

Cp Genome ◽

Mt Genome

Abstract Tea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. In this study, we de novo assembled the chloroplast (cp) and mitochondrial (mt) genomes of C. sinensis var. assamica cv. Yunkang10 into a circular contig of 157,100 bp and two complete circular scaffolds (701719 bp and 177329 bp), respectively. We correspondingly annotated a total of 141 cp genes and 71 mt genes. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878 bp and 149 bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are ~4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamica presented in this study will become an important resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.

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Genome Sequence of Streptococcus agalactiae Strain H002, Serotype III, Isolated in China from a Pregnant Woman

Genome Announcements ◽

10.1128/genomea.01109-15 ◽

2015 ◽

Vol 3 (5) ◽

Cited By ~ 2

Author(s):

Rui Wang ◽

Liping Li ◽

Fuguang Luo ◽

Wanwen Liang ◽

Xi Gan ◽

...

Keyword(s):

Pregnant Woman ◽

Genome Sequence ◽

Streptococcus Agalactiae ◽

Whole Genome Sequence ◽

Comparative Genomic ◽

Whole Genome ◽

Genomic Studies ◽

Important Addition

Here, we report the first whole-genome sequence of Streptococcus agalactiae strain H002, serotype III, isolated in China from a woman 32 weeks pregnant. This sequence represents an important addition to the published genomes and will promote comparative genomic studies of S. agalactiae spp. isolated from diverse regions, particularly when compared with Chinese strains.

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Whole-Genome Sequence ofEscherichia coliSerotype O157:H7 Strain EDL932 (ATCC 43894)

Genome Announcements ◽

10.1128/genomea.00647-16 ◽

2016 ◽

Vol 4 (4) ◽

Cited By ~ 2

Author(s):

Gaylen A. Uhlich ◽

George C. Paoli ◽

Chin-Yi Chen ◽

Bryan J. Cottrell ◽

Xinmin Zhang ◽

...

Keyword(s):

Escherichia Coli ◽

Genome Sequence ◽

Shiga Toxin ◽

Whole Genome Sequence ◽

Hemorrhagic Colitis ◽

Comparative Genomic ◽

Whole Genome ◽

Outbreak Strain ◽

E Coli ◽

Genomic Studies

The genome sequence ofEscherichia coliserotype O157:H7 EDL933, a ground beef isolate from a 1983 hemorrhagic colitis outbreak, is a standard reference for comparative genomic studies of Shiga toxin-producingE. colistrains. Here, we report the genome sequence of a patient stool isolate from that outbreak, strain EDL932.

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Quorum sensing and genomic studies of a marine bacterium Vibrio variabilis strain T01

10.7287/peerj.preprints.1029v1 ◽

2015 ◽

Author(s):

Kok-Gan Chan ◽

Nur Izzati Mohamad

Keyword(s):

Quorum Sensing ◽

Coastal Waters ◽

Marine Bacterium ◽

Cell Communication ◽

Whole Genome ◽

Whole Genome Analysis ◽

Protein Coding ◽

Signalling Molecule ◽

Genomic Studies ◽

Rna Genes

Vibrio variabilis strain T01 was isolated from the coastal waters in Hulu Selangor, Malaysia and its genome sequenced. This curved gram-negative bacterium shows cell-to-cell communication properties. The characteristics of the sequenced genome and its annotation processes are described here. The finished assembled whole genome of T01T exhibits genome size of 4,529,728 bp in 83 contigs with 46.22% G+C content, 4053 protein coding genes and 94 RNA genes. The whole genome analysis revealed the presence of quorum sensing signalling molecule synthase gene (luxM) which is crucial to understand the quorum sensing dependent phenotypes in this isolate.

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