Seeing the whole picture: What molecular ecology is gaining from whole genomes

AbstractOver the past years, large consortia have been established to fuel the sequencing of whole genomes of many cancer patients. Despite the increased abundance in tools to study the impact of SNVs, non-coding SVs have been largely ignored in these data. Here, we introduce svMIL2, an improved version of our Multiple Instance Learning-based method to study the effect of somatic non-coding SVs disrupting boundaries of TADs and CTCF loops in 1646 cancer genomes. We demonstrate that svMIL2 predicts pathogenic non-coding SVs with an average AUC of 0.86 across 12 cancer types, and identifies non-coding SVs affecting well-known driver genes. The disruption of active (super) enhancers in open chromatin regions appears to be a common mechanism by which non-coding SVs exert their pathogenicity. Finally, our results reveal that the contribution of pathogenic non-coding SVs as opposed to driver SNVs may highly vary between cancers, with notably high numbers of genes being disrupted by pathogenic non-coding SVs in ovarian and pancreatic cancer. Taken together, our machine learning method offers a potent way to prioritize putatively pathogenic non-coding SVs and leverage non-coding SVs to identify driver genes. Moreover, our analysis of 1646 cancer genomes demonstrates the importance of including non-coding SVs in cancer diagnostics.

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Whole genomes reveal multiple candidate genes and pathways involved in the immune response of dolphins to a highly infectious virus

Molecular Ecology ◽

10.1111/mec.15873 ◽

2021 ◽

Author(s):

Kimberley C. Batley ◽

Jonathan Sandoval‐Castillo ◽

Catherine Kemper ◽

Nikki Zanardo ◽

Ikuko Tomo ◽

...

Keyword(s):

Immune Response ◽

Candidate Genes ◽

Infectious Virus ◽

Whole Genomes

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Development of Molecular Markers for Detection of Acidovorax citrulli Strains Causing Bacterial Fruit Blotch Disease in Melon

International Journal of Molecular Sciences ◽

10.3390/ijms20112715 ◽

2019 ◽

Vol 20 (11) ◽

pp. 2715 ◽

Cited By ~ 1

Author(s):

Md. Rafiqul Islam ◽

Mohammad Rashed Hossain ◽

Hoy-Taek Kim ◽

Denison Michael Immanuel Jesse ◽

Md. Abuyusuf ◽

...

Keyword(s):

Infected Leaf ◽

Bacterial Fruit Blotch ◽

Early Disease Detection ◽

Acidovorax Citrulli ◽

Seed Health ◽

Field Samples ◽

Whole Genomes ◽

Pathogenesis Related ◽

Primer Sets ◽

Inoculation Assay

Acidovorax citrulli (A. citrulli) strains cause bacterial fruit blotch (BFB) in cucurbit crops and affect melon significantly. Numerous strains of the bacterium have been isolated from melon hosts globally. Strains that are aggressively virulent towards melon and diagnostic markers for detecting such strains are yet to be identified. Using a cross-inoculation assay, we demonstrated that two Korean strains of A. citrulli, NIHHS15-280 and KACC18782, are highly virulent towards melon but avirulent/mildly virulent to the other cucurbit crops. The whole genomes of three A. citrulli strains isolated from melon and three from watermelon were aligned, allowing the design of three primer sets (AcM13, AcM380, and AcM797) that are specific to melon host strains, from three pathogenesis-related genes. These primers successfully detected the target strain NIHHS15-280 in polymerase chain reaction (PCR) assays from a very low concentration of bacterial gDNA. They were also effective in detecting the target strains from artificially infected leaf, fruit, and seed washing suspensions, without requiring the extraction of bacterial DNA. This is the first report of PCR-based markers that offer reliable, sensitive, and rapid detection of strains of A. citrulli causing BFB in melon. These markers may also be useful in early disease detection in the field samples, in seed health tests, and for international quarantine purposes.

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Genomic analyses unveil helmeted guinea fowl (Numida meleagris) domestication in West Africa

Genome Biology and Evolution ◽

10.1093/gbe/evab090 ◽

2021 ◽

Author(s):

Quan-Kuan Shen ◽

Min-Sheng Peng ◽

Adeniyi C Adeola ◽

Ling Kui ◽

Shengchang Duan ◽

...

Keyword(s):

West Africa ◽

De Novo ◽

Guinea Fowl ◽

Chromatin Interaction ◽

De Novo Genome Assembly ◽

Numida Meleagris ◽

Whole Genomes ◽

Genomic Analyses ◽

Related Wild Species ◽

Wild Progenitors

Abstract Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

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Engineered yeast genomes accurately assembled from pure and mixed samples

Nature Communications ◽

10.1038/s41467-021-21656-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Joseph H. Collins ◽

Kevin W. Keating ◽

Trent R. Jones ◽

Shravani Balaji ◽

Celeste B. Marsan ◽

...

Keyword(s):

Genetic Engineering ◽

Metagenomic Sequencing ◽

Long Reads ◽

Whole Genomes ◽

Genome Features ◽

Engineered Yeast ◽

Yeast Genomes ◽

Yeast Genetic ◽

Yeast Plasmids ◽

Assembly Software

AbstractYeast whole genome sequencing (WGS) lacks end-to-end workflows that identify genetic engineering. Here we present Prymetime, a tool that assembles yeast plasmids and chromosomes and annotates genetic engineering sequences. It is a hybrid workflow—it uses short and long reads as inputs to perform separate linear and circular assembly steps. This structure is necessary to accurately resolve genetic engineering sequences in plasmids and the genome. We show this by assembling diverse engineered yeasts, in some cases revealing unintended deletions and integrations. Furthermore, the resulting whole genomes are high quality, although the underlying assembly software does not consistently resolve highly repetitive genome features. Finally, we assemble plasmids and genome integrations from metagenomic sequencing, even with 1 engineered cell in 1000. This work is a blueprint for building WGS workflows and establishes WGS-based identification of yeast genetic engineering.

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The ontogeny of molecular ecology

Molecular Ecology ◽

10.1111/j.1365-294x.2006.03016.x ◽

2006 ◽

Vol 15 (10) ◽

pp. 2687-2689 ◽

Cited By ~ 3

Author(s):

JOHN C. AVISE

Keyword(s):

Molecular Ecology

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Molecular Ecology and Evolution: Approaches and Applications.—B. Schierwater, B. Streit, G. P. Wagner, and R. DeSalle (eds.).

Systematic Biology ◽

10.1093/sysbio/47.1.176 ◽

1998 ◽

Vol 47 (1) ◽

pp. 176-179

Author(s):

Neil W. Blackstone ◽

Steven A. Nadler

Keyword(s):

Molecular Ecology

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Robust and scalable inference of population history from hundreds of unphased whole genomes

Nature Genetics ◽

10.1038/ng.3748 ◽

2016 ◽

Vol 49 (2) ◽

pp. 303-309 ◽

Cited By ~ 206

Author(s):

Jonathan Terhorst ◽

John A Kamm ◽

Yun S Song

Keyword(s):

Population History ◽

Whole Genomes ◽

Scalable Inference

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Bacteriocins of Non-aureus Staphylococci Isolated from Bovine Milk

Applied and Environmental Microbiology ◽

10.1128/aem.01015-17 ◽

2017 ◽

Vol 83 (17) ◽

Cited By ~ 24

Author(s):

Domonique A. Carson ◽

Herman W. Barkema ◽

Sohail Naushad ◽

Jeroen De Buck

Keyword(s):

Staphylococcus Aureus ◽

Bacterial Infections ◽

Genome Mining ◽

Bovine Milk ◽

Gene Clusters ◽

Antibiotic Use ◽

Content Type ◽

Treatment And Prevention ◽

Whole Genomes

ABSTRACT Non-aureus staphylococci (NAS), the bacteria most commonly isolated from the bovine udder, potentially protect the udder against infection by major mastitis pathogens due to bacteriocin production. In this study, we determined the inhibitory capability of 441 bovine NAS isolates (comprising 26 species) against bovine Staphylococcus aureus. Furthermore, inhibiting isolates were tested against a human methicillin-resistant S. aureus (MRSA) isolate using a cross-streaking method. We determined the presence of bacteriocin clusters in NAS whole genomes using genome mining tools, BLAST, and comparison of genomes of closely related inhibiting and noninhibiting isolates and determined the genetic organization of any identified bacteriocin biosynthetic gene clusters. Forty isolates from 9 species (S. capitis, S. chromogenes, S. epidermidis, S. pasteuri, S. saprophyticus, S. sciuri, S. simulans, S. warneri, and S. xylosus) inhibited growth of S. aureus in vitro, 23 isolates of which, from S. capitis, S. chromogenes, S. epidermidis, S. pasteuri, S. simulans, and S. xylosus, also inhibited MRSA. One hundred five putative bacteriocin gene clusters encompassing 6 different classes (lanthipeptides, sactipeptides, lasso peptides, class IIa, class IIc, and class IId) in 95 whole genomes from 16 species were identified. A total of 25 novel bacteriocin precursors were described. In conclusion, NAS from bovine mammary glands are a source of potential bacteriocins, with >21% being possible producers, representing potential for future characterization and prospective clinical applications. IMPORTANCE Mastitis (particularly infections caused by Staphylococcus aureus) costs Canadian dairy producers $400 million/year and is the leading cause of antibiotic use on dairy farms. With increasing antibiotic resistance and regulations regarding use, there is impetus to explore bacteriocins (bacterially produced antimicrobial peptides) for treatment and prevention of bacterial infections. We examined the ability of 441 NAS bacteria from Canadian bovine milk samples to inhibit growth of S. aureus in the laboratory. Overall, 9% inhibited growth of S. aureus and 58% of those also inhibited MRSA. In NAS whole-genome sequences, we identified >21% of NAS as having bacteriocin genes. Our study represents a foundation to further explore NAS bacteriocins for clinical use.

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