Advances in technology have allowed geneticists to sequence a slew of unique animal, plant, and fungi to species over the past thirty years. Public databases currently house tens of thousands of eukaryotic genome assemblies, but a relative few include an estimate of the total genome size for their respective species. Genome size (or C-value) varies widely, even at the species level, largely due to noncoding DNA, which is often dismissed as “junk” DNA. The standard metrics used to characterize assemblies don’t get at size and chromosome number—the fundamental structure of genomes. Without this foundational information, a new study in GENETICS asks: “Are our genome assemblies good enough?”

To determine whether existing assemblies match the estimated genome size for their corresponding species, author Carl Hjelmen designed an R script to pull information from four NCBI databases: Assembly, BioSample, Sequence Read Archive (SRA), and Taxonomy. Starting from the >40,000 available eukaryotic genome assemblies, he analyzed the ~15,000 animal, plant, and fungi genomes that had existing size estimates. He also used karyotype databases to determine the haploid chromosome number for mammals, dipterans, coleopterans, amphibians, polyneopterans.

Taking into account Kingdom, the sequencing platform used, and common assembly statistics, Hjelmen devised a metric called “Proportional difference from genome size” to determine how closely a given assembly length came to matching the estimated genome size. If the assembly was within 10% of the estimate, he considered it “good.” 

He found that almost half of the assemblies analyzed were outside of 10% of the genome size estimate for their species. Most were smaller than the estimates, suggesting that some assemblies are missing information. The larger the genome size, the more dramatic the deviation tended to be—which wasn’t surprising considering that larger eukaryotic genomes often carry more of that so-called “junk” DNA. (Nongenic DNA—a friendlier way to describe the regions of the genome that don’t code for proteins—might turn out to be more informative than its reputation would suggest, points out Hjelmen.)

Hjelmen also discovered a positive relationship between late-replicating heterochromatin and assembly/genome size deviation. When genomes contained more heterochromatin, the assembly was more likely to be missing DNA; he argues that this “lost information” should be highly sought after when studying populations and their health. And though the results were modest, long-read technologies appeared more likely to assemble genomes near that 10% cutoff.

This study points out the limitations of widely used genome metrics like N50 (which narrowly measures contiguity) and BUSCO value (which describes completeness of core sets of genes). To shrink this analytic gap, Hjelmen proposes a new structural unit: “PN50,” or proportional N50 value, which contextualizes N50 values by relating them to estimated genome size and haploid chromosome number. Adding PN50 to the current mix of metrics could increase the rigor of genome research, offering insight into the less-studied structural components of assemblies and supporting universal assembly comparison.

Like a genetic time capsule, mitochondria contain the secrets of their ancient bacterial origins in their own genomes (mtDNA), separate from the nuclear genomes (nucDNA) that tend to be in the spotlight. mtDNA is especially vulnerable to UV damage as the cellular powerhouses are located in the cytoplasm, near the thin cell membrane. While UV damage to nuclear DNA triggers the nucleotide excision repair (NER) pathway to replace the damaged segment, mtDNA has more limited repair mechanisms and may instead rely on degradation to mitigate the damage.

Recent research published in the May issue of GENETICS by Waneka et al. revisits this assumption, reporting evidence that mitochondria may have unique DNA repair pathways to address UV damage in Arabidopsis thaliana and Saccharomyces cerevisiae.

UV damage produces cyclobutane pyrimidine dimers (CPDs), which result in bulky distortions in the DNA structure. In response, NER creates single-stranded incisions upstream and downstream of the dimer to excise the damaged fragment, which is then replaced by a polymerase using the opposite strand as a template.

The excision process results in damage-containing oligonucleotides with distinct size distributions, which is a useful characteristic for investigating damage repair. Bacterial NER produces fragments of ~10 to 13 nt, while eukaryotic nuclear NER produces fragments of ~23 to 30 nt. In an approach called excision repair sequencing (XR-seq), antidamage antibodies recognize and capture the fragments for subsequent sequencing analysis, allowing researchers to map the locations of active DNA repair across the genome.

To explore the effects of UV damage on mitochondrial DNA in plants, yeast, and flies, Waneka et al. analyzed previously published XR-seq datasets from UV-irradiated A. thaliana, S. cerevisiae, and D. melanogaster S2 cells. They found that mtDNA fragments had distinct size distributions compared to nucDNA fragments. In S. cerevisiae, the mtDNA fragments were predominantly 26 nt in size, while in A. thaliana, they were 28 nt. Both species also had additional fragment peaks at regular size intervals—2 nt in S. cerevisiae and 4 nt in A. thaliana. In D. melanogaster, however, mtDNA fragments did not follow the same size patterns.

Among the most frequent fragments, the CPDs were located in common positions relative to the read end. This suggests that UV damage results in mtDNA fragments of specific sizes and positions relative to the damaged location—a known characteristic of NER.

However, Waneka et al. also presented an alternative explanation, hypothesizing that the distinct fragment sizes could also be produced by a yet uncharacterized damage-induced mtDNA degradation pathway. They emphasized that many questions remain as the bacterial origins of mtDNA make it difficult to predict which genes may be involved in the response to UV damage.

What we do know is that the accumulation of mutations in mtDNA can contribute to metabolic and neurodegenerative diseases, and that UV damage to mtDNA is linked to skin aging and melanoma. Thus, further research is needed to understand the yet-unrevealed damage-induced NER and/or degradation mechanisms which may protect mitochondrial DNA. Either of these possibilities point to the exciting prospect of novel maintenance or processing in response to exogenous damage.

Look at any list of the top 10 most aggressive animals, and you will undoubtedly find a mugshot of the North American wolverine. Although much smaller than most of the other animals accompanying it on such lists—such as the hippopotamus and the wild boar—this feisty member of the weasel family has been a protagonist in popular myths, even serving as inspiration for superhero characters and as mascots of sports teams. A wide range of cultural, social, economic, and psychological factors influence human-wolverine relations. In many Indigenous societies, the wolverine is a respected cultural keystone species and is often viewed as a trickster. Unfortunately, these solitary carnivores rely on cold temperatures and snowy environments for their reproduction and survival, so their future remains uncertain in a warming world.

A new study published in the August issue of G3: Genes|Genomes|Genetics provides geneticists and conservation biologists with a high-quality, chromosome-level genome assembly of the wolverine, including extensive annotation of genes involved in behavior and immune responses to pathogens. The authors’ goal goes far beyond the wolverine: they seek to provide similar high-quality assemblies for other species predicted to be impacted by increasing global temperatures. This means setting the benchmark for a workflow that offers the best compromise possible when balancing cost, time, simplicity, accuracy, and completeness for long-read assembly and genome annotation. 

“Our goal is to replace the existing short-read assemblies and increase the quality standards for new reference genomes in light of current sequencing technologies,” says lead author Si Lok.

Improving the standards of genome assembly in the current era

The DNA sequenced in the report comes from a 30-year-old tissue sample of a male wolverine specimen from the Kugluktak (Coppermine) region of Nunavut. Lok and colleagues use PacBio contiguous long-reads (CLR) mode, which typically provides maximal read length at a reasonable cost; however, it is prone to 15-20% pseudo-random errors. To mitigate such inaccuracies while maintaining the numerous benefits of this approach, the authors used a two-step workflow for genome assembly: 1) the uncorrected CLRs are assembled using Flye assembler, followed by a polishing regimen with high-quality Illumina short reads, and 2) the subsequent scaffolding of the assembly against assemblies of related family members.

“It took us nearly two years to optimize a workflow that produces a final genome assembly comprising well less than 1000 contigs—about 10–100 times better than those found in most genome reports—at a cost of under $10,000,” says Lok. The cost is going down all the time.

This new workflow leads to striking completeness and accuracy: 99.98% of the current BUSCO set of 9,226 genes used to assess assembly quality are complete at exon-level in the wolverine assembly, placing it in the top tier of assemblies produced from long-reads. Lok hopes that their report shows how cost-effective, accurate, and complete sequencing and assembly can be nowadays. “No future genome reports should be less than chromosome-level, given the current technologies.”

Conservation genomics meets wolverine behavior

The new article also provides the first full-length mitochondrial genome assembly for the North American wolverine, as well as a tabulation of potential microsatellite markers for the wolverine. Since monitoring population size and distribution, reproductive success, and gene flow in wild populations often relies on analyses of mitochondrial DNA and microsatellites, the authors hope to provide a resource for developing these and other species-specific genomic markers.

In addition, Lok and colleagues annotated genes whose orthologs have been associated with aggressive traits in other organisms—an adaptation to drive competition for food and mates— and the key components of innate immune responses. “Environmental disruptions from climate change will increase vulnerabilities to new pathogens,” says Lok.

“We are in the process of reporting genomes for other species predicted to be heavily affected by climate change in efforts to support their conservation and ecological relationships, such as that of the Canada lynx and the snowshoe hare,” says Lok. He wishes this report to set a minimum standard of quality for future genome reports and resources for conservation biologists.

Guest post by Nina Wolff pays tribute to long-standing GSA member Margaret Lieb.

Margaret (Peggy) Lieb died on March 8, 2018 in South Pasadena, California at the age of 94. After attending schools in New Rochelle, NY, she graduated magna cum laude from Smith College, and subsequently studied with  H.J. Muller at Indiana University and with Francis Ryan at Columbia University, where she received her PhD degree. Following postdoctoral studies at Caltech in the laboratory of Max Delbruck, and in Paris at the Pasteur and Radium Institutes, Lieb taught at Brandeis University and then moved to the Medical School of the University of Southern California where she continued her research and teaching for 45 years. After her retirement, she continued to be active as an Emerita member of the faculty, and as a garden docent at the Huntington Museum and Botanical Garden.

While at Caltech, Lieb published one of the first studies of phage lambda, and subsequently isolated and characterized a large number of mutations in the repressor gene of the phage. Her studies of lysogenization indicated that the active repressor was a dimer, a conclusion later confirmed by biochemical studies in other laboratories. While mapping mutations in the lambda repressor gene, she observed that excess recombination (negative interference) was associated with mutations arising from the deamination of 5-methylcytosine. This led to the identification of a novel mismatch repair gene (vsr) in E. coli – a gene that is adjacent to the gene for cytosine methylase. The Vsr function reduces the probability of mutations that occur due to spontaneous deamination of 5meC. Although genes related to vsr appear to be limited to bacteria, the search for genes like vsr in eukaryotes, where 5-methycytosine has important regulatory functions, has led others to the discovery of additional specific repair activities in higher organisms.

In 1972-1973, Lieb served as Program Directory of the Genetic Biology program of the National Science Foundation. She was elected Chairman of the Virology Division of the ASM in 1975, and served on the editorial boards of Journal of Virology and GENE. She was a Fellow of the American Association for the Advancement of Science (AAAS).

Peggy Lieb maintained an active interest in the research of her colleagues, and will also be missed by the students and post-doctoral fellows who spent time in her lab. Her high standards of performance in the classroom and in the lab were challenging and also appreciated by those who knew her.

Mutations that disrupt the gene BRCA2 dramatically increase the odds of developing breast and ovarian cancer—but such mutations aren’t enough to cause cancer on their own. To turn normal cells cancerous, some of BRCA2’s genetic interactors must also mutate. In an article recently published in GENETICS, Ding et al. sought to identify some of these genes.

BRCA2 is a tumor suppressor gene that normally helps cells maintain genome integrity, which is why its loss can lead to mutations in other genes and eventually to cancer. But losing BRCA2 function also cripples a cell’s ability to proliferate—making cancer less likely to develop, not more. One possible explanation for this seeming contradiction is that additional mutations in other genes allow cells without functional BRCA2 to survive and become dangerous.

To find such genetic interactors, the researchers screened a mouse cell line in which disabling both copies of the mouse version of BRCA2 (Brca2) is lethal, enabling them to look for genetic changes that would allow cells with no functional Brca2 to survive. Their screen turned up Gipc3, which was not known to be involved with Brca2 or breast cancer; it was instead associated with certain types of deafness.

Gipc3 doesn’t simply compensate for Brca2 mutants’ defects in DNA repair. The researchers observed that, although overexpressing Gipc3 allowed cells to survive without functional Brca2, it wasn’t enough to protect them from DNA-breaking ionizing radiation. This made the group suspect that other genes are also involved.

Ding et al. looked for proteins that bind the protein encoded by Gipc3 (GIPC3), collecting proteins that physically associate with GIPC3 and using mass spectrometry to identify them. They found that signaling proteins APPL1 and APPL2 appear to bind GIPC3, but the analysis couldn’t show for certain that they’re involved in the pathway of interest. Using existing structural data, they predicted which parts of GIPC3 may be important for binding APPL1 and APPL2, reasoning that if they could disrupt these interactions, they could see whether the two proteins worked with GIPC3 to allow cells without functional Brca2 to survive.

They found that when APPL1 and APPL2 are unable to properly bind GIPC3, most cells don’t survive Brca2 loss, indicating that APPL1 and APPL2 are critical for GIPC3’s role in protecting these cells. APPL1 and APPL2 have many functions in the cell, and it’s unclear how they work with GIPC3, which is a topic for future study. This work adds Gipc3 to a growing list of genetic Brca2 interactors that may play a role in development of breast and ovarian cancer, adding another fragment to the complex genetic story of how ordinary cells become cancerous.

CITATION:

Ding, X.; Philip, S.; Martin, B.; Pang, Y.; Burkett, S.; Swing, D.; Pamala, C.; Ritt, D.; Zhou, M.; Morrison, D.; Ji, X.; Sharan, S. Survival of BRCA2-Deficient Cells Is Promoted by GIPC3, a Novel Genetic Interactor of BRCA2.
GENETICS, 207(4), 1335-1345.
DOI: 10.1534/genetics.117.30035
http://www.genetics.org/content/207/4/1335

When a mutation arises in an egg or sperm cell, it could be evolutionarily important. But if a mutation occurs in somatic tissue instead, the result could be cancer. Mutations in the germline and soma not only have contrasting consequences, they also arise at different rates that may reflect the balance of DNA damage and repair pathways in different tissue types. In the September issue of GENETICS, Chen et al. predict gene mutation rates in different tissues and find that high expression increases mutation rates in the germline, but not in somatic tissue.  

The first step was to obtain a reliable estimate of the mutation rate in both germ cells and somatic tissues. The researchers relied on a set of germline mutations, previously identified using exome data from thousands of sets of parents and children. Any variation that was unique to the children must be caused by germline mutation in either the father or mother. To identify somatic mutations, the researchers analyzed three different cancer samples that included whole exome sequence of both normal and malignant cells. Variation unique to either tissue type predates the tumor and should be due to somatic mutations.

A statistical model that evaluated how well various factors predict the mutation rate revealed a key difference. In germ cells, a high gene expression level was linked to a higher mutation rate, but the opposite was observed in somatic tissues. Though the magnitude of the effect varied in the three different cancer types, there was always a negative correlation with expression. Other factors also contributed differently to mutation in the germline and somatic tissues, including GC content for the germline and replication timing in the soma.

Gene expression level probably affects mutation rate because the DNA double helix unzips to accommodate transcription machinery, making the individual strands more vulnerable to mutagens, and because there is a dedicated repair mechanism to fix DNA damage that occurs in transcribed regions. The opposite effects of expression level on mutation rates suggests germline and somatic tissues have marked differences in the balance between damage and repair. For example, expression may be more mutagenic in the germline, or repair mechanisms may be more efficient in the soma. There could even be unidentified DNA damage repair processes that are unique to certain tissues. Though somatic mutations can’t be passed down to the next generation like germline mutations, they are the root cause of most cancers. Quickly and correctly repairing this DNA damage is vital for an organism’s survival.

CITATION:

Contrasting Determinants of Mutation Rates in Germline and Soma

Chen Chen, Hongjian Qi, Yufeng Shen, Joseph Pickrell, and Molly Przeworski

GENETICS September 1, 2017. 207 (1): 255-267

https://doi.org/10.1534/genetics.117.1114

http://www.genetics.org/content/207/1/255

In the ruins of the Chernobyl Nuclear Power Plant—an area deemed unsafe for humans for the next 20,000 years after a catastrophic failure—life thrives. Fungi that reside there, along with other organisms that can survive large radiation doses, must have strategies to cope with the DNA-damaging effects of living at a meltdown site. In the April issue of GENETICS, Repar et al. report that radiation-resistant prokaryotes tend to have higher rates of genome rearrangements—a sign of improperly repaired double-strand breaks in DNA—than related species do, meaning that even these hardy organisms can’t fully prevent or fix radiation-induced DNA damage.

The failure to repair all DNA damage doesn’t result from lack of trying. Prior research showed that Deinococcus radiodurans, one of the most radiation-resistant organisms identified to date, has a special method for repairing double-strand breaks in DNA, and along with several other radiation-resistant prokaryotes, it can patch its genome back together after hundreds of double-strand breaks. Variation in the DNA repair machinery is under positive selection in radiation-resistant bacteria but not in related nonresistant bacteria, indicating that there’s a need to optimize these genes’ functions to cope with radiation.

Despite their adaptations to radiation bombardment, these species’ genomes are more shuffled around than their more radiation-sensitive relatives’ are. This suggests it’s not possible to prevent or patch up all the damage, even with super-charged DNA repair, but it’s also conceivable that the increased rate of genome rearrangements might actually be beneficial in conditions of stress. The rearrangements could cause mutations that allow the radiation-resistant organisms to survive in their dangerous environments. But Repar et al. found that radiation-resistant organisms were no different from their nonresistant cousins in selection for genome organization (i.e., against genome rearrangements), implying that their high rate of rearrangements does not affect their ability to adapt to radiation stress. Ultimately, although these extremophiles are uniquely skilled at fixing their genomes, they still end up with battle scars.

CITATION:

Repar, J.; Supek, F.; Klanjscek, T.; Warnecke, T.; Zahradka, K.; Zahradka, D. Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria.
GENETICS, 205(4), 1677-1689.
DOI: 10.1534/genetics.116.196154
http://www.genetics.org/content/205/4/1677

Short-read sequencing has fueled the acceleration of genetic research But though these next-generation methods are fast and efficient, they can’t do everything well. One important area in which short-reads fall short is detecting structural variants (SV), where chunks of the genome are deleted, inserted, repeated, inverted, or in some other way shuffled around compared to the reference sequence. Such variants play a significant role in natural genetic variation, and cause many genetic diseases. But the global significance of structural variants is not well understood because they are harder to systematically detect than single nucleotide polymorphisms (SNPs), the type of variation targeted by short-read sequencing.

In the January issue of GENETICS, Mak et al. show that mapping long DNA fragments on nanochannel arrays can be used to survey structural variation across individual genomes. Applying the method to examine a human “trio” (mother, father, and child) from the 1000 Genomes Project, they identified seven times as many large insertions and deletions than previously found by sequencing approaches.

The method uses the commercial Irys technology to analyze large DNA fragments (greater than 150 kilobases) by first fluorescently labeling the DNA using an enzyme that nicks one of the strands every time it encounters a specific sequence motif. The labeled DNA fragments are then imaged in a nanochannel array. These arrays stretch out each DNA fragment uniformly within a tiny silicon groove, allowing the distance between each site-specific label to be measured.

The labeling patterns of the DNA molecules allow the overall structure of the fragment to be mapped. So, for example, deletion of a chunk of sequence might appear as loss of a signature pattern. In essence, the high-tech method is reminiscent of the trusty restriction map of the molecular genetics era—in which sequence-specific restriction enzymes cut DNA into defined fragments that could be used to infer the large-scale arrangement of sequence.

One major advantage of the nanochannel method is speed, says senior author Pui-Yan Kwok (University of California, San Francisco). “Mapping usually involves cloning, so you’re making a library, picking colonies, doing digests, putting the pieces back together; it can take forever. With our method, pretty much everything is finished in days,” says Kwok.

Kwok’s group developed the original nick-labeling technique and published proof-of-principle experiments in 2012. The new paper demonstrates how the method can be implemented for mapping structural variation across a genome. The authors generated genome maps of cell lines from three individuals: the 1000 genomes project CEU trio, which is a family whose genomes have been extensively characterized by sequencing methods. Using genomes from parents and a child allows researchers to cross-check that variants show Mendelian inheritance, and allows them to identify haplotypes (the set of variants that lie together on one chromosome of a pair). The genome maps revealed more than 1500 insertions and deletions greater than 5 kilobases in size, compared to the 215 previously found in the well-studied trio. Among the new variants, the team identified five deletions that may influence disease susceptibility. These deletions are homozygous (present in both copies of the genome) and remove all or substantial parts of genes associated with susceptibility to cancers, psoriasis, certain bacterial infections, and resistance to malaria.

While the results are impressive, the method has its limitations, reminds Kwok. It provides only a birds-eye view of the genome, not the base pair resolution delivered by sequencing. That means other methods will still be needed to hone in on important details. Secondly, the method can’t analyze DNA samples isolated by standard techniques because long enough DNA fragments can only be prepared by starting with intact cells. The method also can’t detect all kinds of structural variants. For instance, it can’t identify those smaller than about five kilobases. “There are also some places in the genome that are just too complex even for this method,” says Kwok.

Nonetheless, there are many potential applications. “Many of the plant and animal genome researchers are interested in this approach, to look for big structural variants without needing a lot of other experiments,” says Kwok. His group has been developing clinical applications for analyzing microdeletion syndromes like DiGeorge syndrome, which are diseases caused by relatively small structural variants that are not easy to dissect with conventional approaches.

But the overall goal, says Kwok, is to combine the long-range information provided by nanochannel-based genome mapping with the high resolution of short-read sequencing, while bridging the gap with intermediate methods (e.g. approaches that yield longer sequence reads or that can resolve whole-genome haplotypes). By combining short, medium, and long range approaches, Kwok’s group aims to efficiently generate high quality genome assemblies with single base pair resolution.

“I think we need a more complete picture of the genome,” says Kwok. “People often go for the fastest and cheapest technology rather than the technology that will give them the best information. It’s important to step back a bit and ask: ‘What am I trying to learn from this genome?’”

CITATION

Mak, A. C., Lai, Y. Y., Lam, E. T., Kwok, T. P., Leung, A. K., Poon, A., … & Andrews, W. (2016). Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays. Genetics, 202(1), 351-362. doi: 10.1534/genetics.115.183483

http://genetics.org/content/202/1/351.full

If you’ve ever watched a procedural crime-solving show on television, you’re sure to have seen a lab tech magically produce results from a complicated assay in mere minutes. If you’re a wet lab scientist, you’ve probably found yourself wishing that “CSI technology” were real so you didn’t have to spend your whole day running PCRs and gels.

In this month’s issue of GENETICS, Wei and Williams, from the Montefiore Medial Center at the Albert Einstein College of Medicine, use sequencing technology that seems akin to science fiction to rapidly detect aneuploidy in just hours – an advance that could greatly improve the current state of clinical sequencing.

The study features the minION – a nanopore-based sequencer that reads and records DNA sequence in real time from very long reads. The minION sequencer is small – not much bigger than a USB thumb drive – and plugs directly into the computer that will be used to analyze the data. Inside the sequencer, nanopores create channels for DNA or other molecules to pass through a membrane that has an electric potential. When molecules pass through the nanopores, they disrupt the potential in a characteristic manner, which gives a known pattern in the read-out that lets them be identified. (Oxford Nanopore Technologies has an excellent animation explaining the technology in detail here.)

Wei and Williams developed a sample preparation and data-analysis method that uses the minION sequencer to produce rapid, real-time sequencing of short pieces of DNA, a change from the extremely long reads originally used in nanopore sequencing. Their methodology allowed them to detect aneuploidy, including trisomies and sex-chromosome abnormalities, in prenatal and miscarriage samples in less than four hours.

This methodology could potentially allow clinicians to detect aneuploidy in time-sensitive samples in just a few hours, for less than a thousand dollars – something that could only have been dreamt of even a decade ago. With exciting new methodologies, science fiction is on its way to science fact, and it’s picking up speed all the time.

CITATION

Wei S., Williams Z. 2016. Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology. GENETICS, 202(1):37-44. doi: 10.1534/genetics.115.182311 http://www.genetics.org/content/202/1/37

When sharp-eyed 20-year-old Calvin Bridges entered Columbia University in 1909, the word “gene” had just been coined. At that time, the term was profoundly abstract, referring to “factors” or “conditions” that could be glimpsed only through the window of statistical analysis.

Seven years later, Bridges and his colleagues had brought these mysterious factors firmly down to earth, pinning them to a concrete location in the cell. Bridges’s groundbreaking 1916 PhD thesis was the first article ever published in GENETICS and presented the final confirmation that genes lie on chromosomes. In a special 100th anniversary Perspectives article in the January 2016 issue of GENETICS, Barry Ganetzky and Scott Hawley describe the background of this seminal work and trace its lasting impact on modern research.

At Columbia, Bridges joined a group of energetic young scientists who inhabited Thomas Hunt Morgan’s tiny “Fly Room” and studied the fruit fly Drosophila melanogaster. Beginning in 1910, Morgan and his students began to realize the chromosome theory of inheritance first proposed by Theodor Boveri and Walter Sutton aligned perfectly with their observations in Drosophila. But although the parallels between the inheritance of chromosomes and genes were convincing, it took an imaginative leap from Bridges to provide an example that unambiguously tied inheritance of specific genes to a specific chromosome.

January cover artist Alexander Cagan’s take on Bridges 1916.

Bridges had been working on sex-linked traits when he noticed rare flies that deviated from the usual rules of heredity. These were females that had inherited all their sex-linked traits from their mothers, and males with all the sex-linked traits from their fathers. Rather than ignoring these exceptions as meaningless flukes, Bridges hypothesized they were the result of an error in the distribution of the sex-linked X chromosome during meiosis. If the two homologous X chromosomes failed to separate during the first phase of meiosis, the resulting egg would contain either both of the X chromosomes, or neither (a single X is normal). Based on this idea, Bridges predicted that the offspring of the exceptional females would include XXY daughters — a configuration that had never been seen before. Sure enough, under the microscope, some of the flies clearly carried two X’s and a Y.

Detail of Plate 1 from Bridges 1916b. Top sketch shows the three autosomes (including the pair of “dot” chromosomes) of a wild-type female, plus a pair of X chromosomes. Bottom sketch shows chromosomes from a daughter of an “exceptional” mother (i.e. one that inherited sex-linked traits only from her own mother). An additional J-shaped Y chromosome is clearly visible.

Bridges’s GENETICS article lay the groundwork for much of the century of genetics that followed, not only by confirming the chromosome theory of inheritance, but by providing the foundation for our understanding of sex determination and meiosis. After this momentous start, Bridges went on to shape the field in many other important ways, including leading the effort to map thousands of Drosophila genes to the bands visible in preparations of giant salivary gland polytene chromosomes. For this contribution, Ganetzky and Hawley refer to Bridges as the founding father of modern genomics. He also used his skill as an inventor (his hobby was building a futuristic car called “the Lightning Bug”) to make it easier to work with Drosophila, introducing the binocular microscope, synthetic fly food, anesthesia, and designing custom incubators and culture bottles.

When Morgan eventually won the 1933 Nobel Prize in Physiology or Medicine for “his discoveries concerning the role played by the chromosome in heredity,” he acknowledged the vital contributions of Bridges and close colleague Alfred Sturtevant by sharing the prize money with their children.

For more on the 100th anniversary of GENETICS, visit the freshly redesigned journal website. For more about the work and life of Bridges, check out Cold Spring Harbor Laboratory’s absorbing online exhibit Calvin Blackman Bridges Unconventional Geneticist (1889-1938). Subscribe to Genes to Genomes for much more on the 100th anniversary of GENETICS!

CITATIONS:

Bridges, C. B. (1916). Non-disjunction as proof of the chromosome theory of heredity. Genetics, 1(1), 1-52.

http://www.genetics.org/content/1/1/1.full.pdf+html

Bridges, C. B. (1916). Non-disjunction as proof of the chromosome theory of heredity (concluded). Genetics, 1(2), 107-163
http://www.genetics.org/content/1/2/107.full.pdf+html