Jumping genes are the exciting part of the Poison Frog Genome

The genome of the strawberry poison frog, Oophaga pumilio, has just been sequenced and the results show that it hosts a wide array of transposable elements, “jumping genes,” virus-like, repetitive sequences that copy themselves inside of genomes. The poison frog has a genome that is twice the size of the human genome, and two-thirds of it is composed of transposable elements. In addition, there is evidence that many of these transposable elements have recently horizontally transferred into the genome.

Genomic Takeover by Transposable Elements in the Strawberry Poison Frog

Rogers RL, Zhou L, Chu C, Márquez R, Corl A, Linderoth T, Freeborn L, MacManes MD, Xiong Z, Zheng J, Guo C, Xun X, Kronforst MR, Summers K, Wu Y, Yang H, Richards-Zawacki CL, Zhang G2, & Nielsen R

Abstract—We sequenced the genome of the strawberry poison frog, Oophaga pumilio, at a depth of 127.5× using variable insert size libraries. The total genome size is estimated to be 6.76 Gb, of which 4.76 Gb are from high copy number repetitive elements with low differentiation across copies. These repeats encompass DNA transposons, RNA transposons, and LTR retrotransposons, including at least 0.4 and 1.0 Gb of Mariner/Tc1 and Gypsy elements, respectively. Expression data indicate high levels of gypsy and Mariner/Tc1 expression in ova of O. pumilio compared with Xenopus laevis. We further observe phylogenetic evidence for horizontal transfer (HT) of Mariner elements, possibly between fish and frogs. The elements affected by HT are present in high copy number and are highly expressed, suggesting ongoing proliferation after HT. Our results suggest that the large amphibian genome sizes, at least partially, can be explained by a process of repeated invasion of new transposable elements that are not yet suppressed in the germline. We also find changes in the spliceosome that we hypothesize are related to permissiveness of O. pumilio to increases in intron length due to transposon proliferation. Finally, we identify the complement of ion channels in the first genomic sequenced poison frog and discuss its relation to the evolution of autoresistance to toxins sequestered in the skin.

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Finding Ancient Ancestors in Modern DNA

Digging ancient signals out of modern human genomes

With new genome analysis tools, scientists have made significant advances in our understanding of modern humans' origins and ancient migrations.

But trying to find ancient DNA, let alone prove that the ancient DNA is ancestral to a population living today is extremely challenging.

A new study in Molecular Biology and Evolution (MBE) adds to this understanding by reconstructing artificial genomes with the analyses of the genome of 565 contemporary South Asian individuals to extract ancient signals that recapitulate the long history of human migration and admixture in the region.

"All in all, our results provide a proof-of-principle for the feasibility of retrieving ancient genetic signals from contemporary human subjects, as if they were genomes from the past embedded in amber," said Luca Pagani, the research coordinator of the study.

The study was led by Burak Yelmen and Mayukh Mondal from the Institute of Genomics of the University of Tartu, Estonia and coordinated by Luca Pagani from the same institution and from the University of Padova, Italy.

"The genetic components we managed to extract from modern genomes are invaluable, given the shortage of ancient DNA available from South Asian human remains, and allow us to elucidate the genetic composition of the ancient populations that inhabited the area," said Burak Yelmen, co-first author of the study.

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New Database of Dog Genomes

Researchers create the largest global catalog of variations in the dog genome

By Prabarna Ganguly, Ph.D.
Science Writer/Editor, NHGRI

In 2019, 'King' the Wire Fox Terrier won the Westminster Dog Show in Madison Square Garden, having competed against 2,800 dogs from 203 breeds. The sheer number of dog breeds points toward the major role played by genetics in shaping such variation in dogs.

In a new study, researchers at the National Human Genome Research Institute (NHGRI) have generated the largest catalog of genetic variants associated with physical traits for domesticated dog breeds. The findings, published in Nature Communication, will help researchers assess if variants associated with dog body structure, behavior and life span could also be implicated in related human diseases.

"This study included data from more than 722 dogs and 144 modern breeds," says Dr. Ostrander, NIH Distinguished Investigator and senior author of the paper. "Through the results, we've learned some of the fascinating genetics behind the variability observed in the world's 450 dog breeds."

After humans initially selected for specific traits during dog breeding centuries ago, dogs have since formed traits and characteristics spontaneously over time. Jocelyn Plassais, a postdoctoral researcher in Dr. Ostrander's laboratory and lead author of the study explained that dogs naturally develop disorders that are common to humans, such as various forms cancers, infections and even diabetes. In addition, a vast number of regions within the dog genome remain similar to the human genome. Thus, dog genomes can provide insight into the biological mechanisms of human health and disease.

The researchers used whole genome sequencing and genome-wide association studies to identify genomic variants associated with sixteen observable characteristics. Most of the blood samples from dogs were taken via The Dog Genome Project, a citizen science initiative that relies on donations from motivated dog owners.

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Nanopore pioneers ultrafast tumor analyses

Same-day genomic and epigenomic analysis of brain tumors

via GIPHY

A plethora of technologies are currently required to assess different genomic and epigenomic alterations; however, the associated costs and long turnaround times combined with extensive infrastructure and training requirements have, to date, hindered their implementation1 . To address these challenges, Dr. Philippe Euskirchen and co-workers at the ICM Brain and Spine Institute, France, assessed the potential of nanopore sequencing technology to deliver comprehensive and cost-effective characterisation of genetic alterations in brain cancer samples — including analysis of copy number (CN) alterations, epigenetic base modifications, and single nucleotide variations (SNVs)1,2. Furthermore, all nanopore sequencing workflows were designed to go from sample to result within a single day.

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Birds illustrate how genomics can make things harder, even if it makes things better

What’s in a Name? How Genome Mapping Can Make It Harder to Tell Species Apart

Rebecca Heisman, Living Bird

If you had opened a copy of the Sibley Guide to Birds when it was first published in the year 2000 and flipped to the section on wood-warblers, you would have found 13 pages devoted to members of a single genus: Dendroica, Latin for tree-dweller. Dendroica’s inhabitants included 21 colorful species—such as Magnolia, Blackburnian, and Cerulean Warblers—dear to the hearts of many birders.

Open a copy of the second edition of the Sibley Guide today, and Dendroica is nowhere to be found.

There hasn’t been a mass extinction in the intervening years. The wood-warbler species are all still there, but filed under a different genus name, Setophaga. Instead, there has been a major shift in how ornithologists sort and classify bird species, and the genus name Dendroica was a casualty.

Decisions about how North American bird species are classified and what is and is not considered a species are made every summer by a special committee of the American Ornithological Society. An AOS committee bases its judgments on the best available science. But the science is rapidly expanding. Like many other branches of biology, ornithologists are trying to make sense of a flood of new information flowing from the latest advances in genome mapping. Today, avian geneticists can dive deep into genomes to unveil the molecular differences underlying variation between birds.

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New Genome Assembler Makes Progress on Fundamental Problem

Assembly of long, error-prone reads using repeat graphs

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin & Pavel A. Pevzner

Nature Biotechnology (Research Article)

Abstract—Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than short-read data, most long-read assembly algorithms do not provide the repeat characterization necessary for producing optimal assemblies. Here, we present Flye, a long-read assembly algorithm that generates arbitrary paths in an unknown repeat graph, called disjointigs, and constructs an accurate repeat graph from these error-riddled disjointigs. We benchmark Flye against five state-of-the-art assemblers and show that it generates better or comparable assemblies, while being an order of magnitude faster. Flye nearly doubled the contiguity of the human genome assembly (as measured by the NGA50 assembly quality metric) compared with existing assemblers

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Snake venom genomics provides important insights

New insights into chromosome evolution, venom regulation in snakes

How do snake genomes direct the production of deadly venom toxins and other key extreme features of snakes?

Snake genomes encode the secrets to their unique and often extreme adaptations, but genome resources for snakes and other reptiles have lagged behind their mammal and bird counterparts.

In a new paper, a team of biologists led by Todd Castoe, associate professor of biology at The University of Texas at Arlington, addressed these questions by generating and analyzing the first most complete chromosome-level genome for a snake – the prairie rattlesnake (Crotalus viridis). Their work, “The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes,” is published in the April issue of Genome Research, the scientific journal published by Cold Spring Harbor Laboratory.

Cockroaches thrive with extra-large genomes

American cockroaches thrive in cities, thanks to their incredibly long genomes

“Few insects have a reputation for grossing people out as thoroughly as the American cockroach. The so-called water bugs, which thrive indoors on fermenting and rotting foods, are rich sources of disease-causing bacteria. Now, researchers have sequenced their genome for the first time—and have uncovered some of the secrets to their uncanny ability to survive in our urban jungles.

Compared with other insects, the genome of the American cockroach (Periplaneta americana) is the second largest sequenced to date after the locust. Like the locust, much of the cockroach genome, some 60%, is made of repetitive elements—sequences of DNA that occur over and over. And compared with three other species in its family—the German cockroach and two termite species—it is actually more closely related to the termites.“

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George Smith on what's to gain from looking into the genomes of extinct furry elephants

Decoding a Mammoth with George Church

Join Harvard DNA pioneer George Church and Chris Smith in conversation as they discuss gene cloning, DNA sequencing, decoding the mammoth genome, the risks posed by fossil viruses lurking in extinct genomes, the prospects of xenotransplantation, and safety of gene therapy, and the risks of human CRISPR. The discussion was recorded on March 15th, live in front of a studio audience at the Hello Tomorrow Summit, in Paris, 2019...

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Next Next Gen Detection of Structural Variants

Accurate detection of complex structural variations using single-molecule sequencing

Fritz J. Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad, Arndt von Haeseler, and Michael C. Schatz

Nature Methods (Research article)

Abstract—Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. Addressing this need, we introduce open-source methods for long-read alignment (NGMLR; https://github.com/philres/ngmlr) and structural variant identification (Sniffles; https://github.com/fritzsedlazeck/Sniffles) that provide unprecedented sensitivity and precision for variant detection, even in repeat-rich regions and for complex nested events that can have substantial effects on human health. In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches. NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings.

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We'll need AI to deal with coming wave of genome data

Getting smart about artificial intelligence

By: Alison Cranage, Science writer

“Genomics is set to become the biggest source of data on the planet, overtaking the current leading heavyweights – astronomy, YouTube and Twitter. Genome sequencing currently produces a staggering 25 petabytes of digital information per year. A petabyte is 1015 bytes, or about 1,000 times the average storage on a personal computer. And there is no sign of a slowdown.”

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A discussion of the limitations of a single, static reference genome

Buffalo gave us spicy wings and the ‘book of life.’ Here’s why that’s undermining personalized medicine

“The human reference genome, largely completed in 2001, has achieved near-mythic status. It is “the book of life,” the “operating manual for Homo sapiens.” But the reference genome falls short in ways that have become embarrassing, misleading, and, in the worst cases, emblematic of the white European dominance of science — shortcomings that are threatening the dream of genetically based personalized medicine.“

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Population-specific genome structure variation coverage in GenomeWeb

Human Genome Structural Variation Patterns Vary by Population, Optical Mapping Study Shows

NEW YORK (GenomeWeb) – Some large structural variants in the human genome exhibit population-specific patterns, according to a new analysis of more than 150 genome maps.

Large structural variants — those that are bigger than 2 kilobases — are difficult to detect, especially as short-read sequencing technologies are the most commonly used tools in genomic analysis.

For their study, Pui-Yan Kwok from the University of California, San Francisco and his colleagues analyzed optical genome maps generated for more than 150 individuals representing more than two dozen populations. A phylogenetic analysis of these maps indicated that some SVs and CNVs show variable population patterns. The researchers were also able to characterize SVs in typically intractable regions of the genome, including spots not covered by the human reference genome. Their results were published yesterday in Nature Communications.

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Flesh-Eating Bacteria’s Genomic/Transcriptomic Trigger Found

Coordinating the sort of full-spectrum analysis more commonly deployed in cancer research, scientists based at Houston Methodist examined flesh-eating strains of Streptococcus pyogenesboth genomically and transcriptomally. Once the scientists had amassed an unusually large data set, they sifted through it with artificial intelligence tools and discovered a novel virulence mechanism. In addition to explaining how a run-of-the-mill strep infection can turn into a devastating flesh-eating disease, the mechanism may guide efforts to develop vaccines and therapies.

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