October issue cover: What’s going on here?

Posted on 25 Oct 2016 by Brooke LaFlamme

{credit}Convergent cabbages by Keyong Chang{/credit}

For all of October, we at Nature Genetics have been admiring the lovely cabbages on our cover. The image, created by photographer Keyong Chang, was contributed by the authors of the study on page 1218 of the issue.

But what is the story behind these pretty green cabbages?

Xiaowu Wang, corresponding author of the study, gave us a behind-the-scenes look at the process that led to the picture on our cover.

The image conveys the main idea of the study, namely that Brassica oleracea (cabbage, left) and Brassica rapa (Chinese cabbage, right) have taken similar evolutionary paths to arrive at their similar, but distinct, appearances. During domestication, farmers selected for cabbages of both species to have the large, leafy heads for which they are known. As shown in the study, the farmers were unknowingly selecting for orthologous genes in these two species. Continue reading →

August issue cover: What’s going on here?

Posted on 22 Aug 2016 by Brooke LaFlamme

Rhinopithecus bieti{credit}Yong-cheng Long{/credit}

This month’s cover image is inspired by the paper on page 947 reporting the reference genome sequence of the black snub-nosed monkey, the second snub-nosed monkey genome paper published in Nature Genetics. The golden snub-nosed monkey genome was published in 2014.

In their paper, Li Yu and colleagues present the de novo genome sequence assembly of Rhinopithecus bieti as well as whole genome resequencing of all four other snub-nosed monkey species. All five species are among the world’s most endangered primate species. Three species, R. bieti, R. roxellana and R. strykeri, live at very high altitudes—above 3,000 meters. R. bieti lives exclusively on the Yunnan and Tibetan plateaus. The other two species, R. brelichi and R. avunculus, inhabit lowland regions. The authors compared the genome sequences between these species to identify genomic regions showing evidence of positive selection that could be related to living at high altitudes.

The photograph on the cover image was taken by one of the study’s co-authors, Dr. Yong-Cheng Long, who was profiled by the Nature Conservancy for his work on conservation of R. bieti (also called the Yunnan golden monkey by the locals). We asked Dr. Long to tell us a little about the monkey shown in the picture.

“The monkey is [a] male, whose name is ‘Big Guy’, and he is feeding on some leaves,” he said by email. “The Big Guy used to have 4 wives (about 6 years ago) and now has only 2, as he is getting old and is not strong enough to hold all of them because the females are more likely to find a strong shoulder to cry on.”

Dr. Long said there are 57 R. bieti individuals in the habituated “Yunnan snuby” group, which is open to the public. Because many of the individuals in the area are fully habituated to human presence, it is not difficult to get photographs of them. The group is only a small portion of the largest natural monkey troop (approximately 1,000 in total) in the world. Dr. Long emphasized the impact that illegal poaching has had on the monkeys. “This species has been endangered by human’s killing, and the monkeys can certainly survive once the killing is stopped.” In China, 2016 is the Year of the Monkey, and it has turned out to also be a lucky year for these particular monkeys. “We found the monkey group has boomed,” said Dr. Long. “12 of the 57 are the infants born this year.”

Nature Genetics office mascot

The lead author of the study, Dr. Yu, became interested in studying these species because of his focus on conservation genetics of endangered mammals distributed in Yunnan Province, China. This is one of the core regions of biodiversity in the world. “The most notable among the endangered mammals distributed in Yunnan Province is R. bieti, which is found exclusively on Yunnan and Tibetan Plateau”, said Dr. Yu by email. “It is unique in that it is the only primate having a red mouth like most humans, which [is why it’s called] one of the most beautiful animals.” Dr. Yu also noted that it is the highest altitude-dwelling nonhuman primate. It can survive in very cold and hypoxic environments that other primates cannot tolerate. “So, I was deeply attracted by this mysterious and interesting species, and was eager to come to understand it.”

We at Nature Genetics are also celebrating the Chinese Year of the Monkey. Our office mascot is this golden snub-nosed monkey (right), which was produced for marketing purposes in China (I snagged one during a recent visit to the Shanghai office). Scanning a barcode on the monkey’s rear end (left) will take you to the publication of the R. roxellana (golden snub-nosed monkey) genome paper.

July issue cover: What’s going on here?

Posted on 22 Jul 2016 by Brooke LaFlamme

This month’s cover features the inspiring block-like karst mountains of the Li River between Guilin and Yangshuo in Guangxi province. The image was inspired by a study in this month’s issue reporting deep sequencing of the MHC region in individuals of Han Chinese ancestry. The study represents an important resource for the study of immune-related disorders in Asian populations. It also identifies loci associated with risk of psoriasis, thus demonstrating the power of this resource.

In addition to simply being a beautiful image evocative of the mountains in Guangxi province, the image also brings to mind the peaks that might be observed in many types of genomic data, such as Sanger sequencing reads, ChIP-seq peaks, etc.

Our own chief editor, Myles Axton, did first-hand research leading to the selection of this cover image. As he found, the Yulong River in Yangshuo is less muddy than the Li River and better for swimming and sightseeing from bamboo rafts (arrow indicates NG editor in the field).

Yulong River{credit}Myles Axton{/credit}

Myles holding a 20 yuan note with drawing of karst mountains.{credit}Myles Axton{/credit}

June issue cover: What’s going on here?

Posted on 24 Jun 2016 by Brooke LaFlamme

Carrot canang sari by Rachel Meyer

As June comes to a close, it’s time to look back at our June issue and ask “what’s going on here?” with the cover image. As you may have guessed, the image is related to the publication of the carrot genome sequence in this month’s issue.

The cover image was provided by Rachel Meyer, a scientist who was not a co-author of the genome paper. Dr. Meyer was previously a postdoctoral researcher with Michael Purugganan at NYU and is an AAAS Science and Technology Policy fellow. She is also a co-founder of Shoots & Roots in New York.

Dr. Meyer gave us the following information about the carrot canang sari on the June cover:

Celebrating the recent availability of rainbow carrots year-round in Washington DC, I cut them in various ways and laid them out in a public dirt plot between the sidewalk and the street that was still bare because Spring had barely started and planting was far from beginning. The cold kept the carrots nicely preserved for three days. The installation took about 6 hours, and the design itself was lifted from a Persian carpet, sharing an origin with some of the earliest domesticated carrots. I had no intention to leave the installation there but people in the busy U-street/Shaw district, coming home late at night from the bars, would stop and photograph it, and even some of the suits interrupted their morning power walks to work to investigate it. After a few days, to my surprise it was not rats, but a middle-aged man who had decimated the carrots for a meal.

Shelby Ellison, an author of the carrot genome article this cover references, did this research as part of her NSF Plant Genome Postdoctoral Fellowship. We were in the same class of Fellows together and became friends because we would look for cool restaurants around DC together during our brief visits to NSF for annual Plant Genome meetings. I’m grateful to be able to explore the subject of her science through installation.

For more about the carrot genome paper, see our previous blog post, featuring Q&A with the corresponding author.

May issue cover: What’s going on here?

Posted on 17 May 2016 by Brooke LaFlamme

This month’s cover image is inspired by the Article on p. 528 of this issue, by Jeff Wall, Nicola Illing, Nadav Ahituv and colleagues. The paper reports the genome of the bat Miniopterus natalensis and transcriptional dynamics in the developing bat wing. This species, one of a group known as vesper bats, is also known as the Natal long-fingered bat and is found in parts of Africa.

The image chosen for the cover is a frontal view of a bat embryo at a late stage of development (stage CS21) taken by study co-author Mandy Mason. This developmental stage is known as
“Translucent Wing”, as you can clearly see the skeletal structures in the wing and the membrane between the outstretched digits. The embryo in this image was stained with Alizarin red (maroon-red-pink) for bone and Alcian blue (blue-cyan) for cartilage. The image was actually taken as part of an earlier study to understand the progression of limb development in this species and to compare it with that of the mouse.

The current study presents not only the genome sequence of the Natal long-fingered bat, but also RNA-seq and ChIP-seq (for H3K27ac and H3K27me3) profiling of the developing limbs. The authors identified more than 7,000 genes that were differentially expressed between the forelimbs—the eventual wings—and the hindlimbs. Through comparative genomics analyses, they found nearly 3,000 regions showing evidence of accelerated evolution along the bat lineage that overlapped with H3K27ac peaks, suggesting that these are candidate enhancer regions for wing development. “This study offers a comprehensive resource for future work in comparative limb development,” co-author Mandy Mason told us. “Aside from the results that we have presented in this paper, these open datasets can be queried to help answer additional questions that may be asked by both our and other research groups.”

April issue cover: What’s going on here?

Posted on 26 Apr 2016 by Brooke LaFlamme

Tlalcacahuatl gold by Erin Dewalt

This month’s cover image is a visual tribute to the peanut and its importance to both the ancient civilizations of the Americas and modern agriculture. The genome sequences of the two progenitor species to the cultivated peanut were published in this month’s issue by David Bertioli and colleagues. The genome sequences are the first step to characterizing the genome of cultivated peanut, which was formed by the hybridization of these two species thousands of years ago. The genome sequences give us valuable clues about the evolution of these species. The authors also identified candidate genes for pest resistance, which could lead to advances in peanut cultivation in the future.

The image was inspired by a gold and silver necklace with beads in the shape of peanuts that was found in the tomb of the Great Lord of Sipan of the ancient Peruvian Moche culture. The necklace (c. 300) is now at the Museo Arqueológico Nacional Brüning in Peru. You can see an image of the necklace here and with more context here. The peanuts in the cover image have the same wavy shape as the beads in the necklace. The speckled texture and symmetric division of gold and silverish-blue in the cover image are also inspired by this ancient artifact.

Erin Dewalt, senior graphic designer for Nature Publishing Group, developed the image concept. She shows the peanuts underground, almost dangling from the plant above like beads. Peanut seeds develop underground after the flowers are fertilized. The ovary develops into a “peg” (gynophore) that drives back down into the soil, where it develops into the fruit that we cultivate as peanuts.

Peanut pegs growing into the soil. The tip of the peg, once buried, swells and develops into a peanut fruit. {credit}H. Zell via Wikimedia Commons{/credit}

The title of the image, Tlalcacahuatl gold, is a reference to the ancient Aztec name for peanut, tlalcacahuatl. But it is also a reference to the wealth represented by the peanut, both for ancient cultures and for modern agriculture. Because peanut plants fix nitrogen, thanks to the symbiotic bacteria in their root nodules, they return nutrients to the soil and improve cultivation of other crops (a fact famously advertised to farmers in the U.S. by George Washington Carver).

Tangential reading: The peanut necklace of the Great Lord of Sipan was almost lost to history forever. As this LA Times article from 1988 reported, grave robbers nearly made off with the treasures of the Lord of Sipan, including the necklace.

Highlighting genomes for DNA Day 2016

Posted on 25 Apr 2016 by Brooke LaFlamme

October 2015 cover “Histone butterflies” by Luisa Lente. Inspired by Salvador Dalí.

Today is national DNA day, celebrating the completion of the Human Genome Project in 2003 and the publication of the proposed structure of DNA in 1953 by James Watson and Francis Crick (PDF here).

This year for DNA day, we wanted to highlight papers reporting new genome sequences of organisms from peanuts to Papilio butterflies published in Nature Genetics over the last year. All reference genomes are published open access under a CC-BY licence. Continue reading →

March issue cover: What’s going on here?

Posted on 25 Mar 2016 by Brooke LaFlamme

Alamy photo “Talus cones on Svalbard”

March is already winding to a close, but we wanted to take a quick break to answer that most burning of all questions: what is going on with our cover this month?

On p.331 of this month’s issue, Owen Rackham and colleagues describe an algorithm called Mogrify that predicts transcription factor combinations for direct reprogramming between 173 human cell types and 134 tissues (see also the News and Views by Patrick Cahan).

Mogrify effectively paints a landscape of cell conversions and provides directions for getting from one point to another. This is often visualized using a variation on Waddington’s epigenetic landscape (for example, see “A deterministic map of Waddington’s epigenetic landscape for cell fate specification” by Bhattacharya et al.).

Visualization of Waddington’s epigenetic landscape{credit}Bhattacharya et al. BMC Syst Biol. 2011; 5: 85.{/credit}

The epigentic landscape as imagined by Waddington involves a marble (the cell) rolling down a hill with many alternate paths (cell fates).

You can imagine the image on the cover (depicting talus deposits on the surface of a mountain in Norway) as the epigenetic landscape, with the different cell fates rising out of the pluripotent state. In this case, there is no marble, because the cell and its fate (address on the landscape) are in fact the same thing. But similar to the talus cones, the cell’s fate is not unchangeable. As Mogrify makes clear, the cell has the potential to transform into many different cell types, regardless of its current address on the landscape. We just have to understand the map to help it get there.

Other articles related to Mogrify:

Breakthrough in human cell transformation could revolutionise regenerative medicine (University of Bristol press release)

Serendipity’s touch on cell conversions (Duke-NUS)

February issue cover: What is going on here?

Posted on 12 Feb 2016 by Catherine Potenski

This month, our cover portrays a trifecta of pollinators and the different flowers from which they feed. Centrally, you see a hawkmoth (left) and a hummingbird (right), with a bee watching the proceedings from above. They are very different organisms and all three pollinate different species of Petunia. The color, scent and morphology of the flowers all contribute to attracting the respective pollinators. The evolution of various floral traits dictates pollinator preference, leading to diversity and speciation of the plants.

The genetics underlying these changes are fascinating to explore. In this current issue, Cris Kuhlemeier and colleagues identified a gene controlling ultra violet (UV) light absorbance of flowers in three species of Petunia. The level of UV absorbance is inversely correlated with color; flowers with high levels of UV-absorbance are white or light colored, while flowers that do not absorb UV are more deeply colored, usually purple or red.

Using QTL analysis and a transposon mutagenesis screen, Kuhlemeier and colleagues discovered a gene that encodes a transcription factor that regulates UV absorbance levels. They characterized the locus in the different Petunia species and found mutations responsible for increased or decreased UV absorbance.

The genetic changes at this locus led to changes in UV absorbance with concomitant changes in flower color; these correlate with changes in pollinator identity. As such, bees and hummingbirds pollinate colorful flowers with low UV absorbance, while the nocturnal hawkmoth pollinates high UV absorbing white flowers. That is why the hummingbird is seen sipping from a red flower, while the hawkmoth helps itself to the white.

For more information and background on this interesting work, see our Q&A with the authors and the News and Views by Erich Grotewold.

Artist Erin Dewalt was inspired by classical drawings of flowers to help her illustrate this example of “Petunia pollinators”.

January issue cover: What’s going on here?

Posted on 24 Jan 2016 by Brooke LaFlamme

Happy New Year! Ok, we know it’s a little belated, but there’s still time to talk about the cover of our January issue.

This month’s cover image shows two male ruffs. The more colorful male on the left is an Independent male, the most common of the three types of ruff males. In this image, he is dominating a subordinate Satellite male as part of a mating display to attract females. For more context on the amazing mating behavior of the ruff, check out this video and some of the news coverage about the papers published in this issue (including this Nature News article. We also really like this one at The Guardian).

The genetic basis of the three male morphs found in this species was elucidated in large part in two studies published in this issue by Terry Burke and colleagues and Leif Andersson and colleagues. Both groups sequenced the genomes of the ruff and found a large inversion present in the two rarer male types, the Satellites and Faeders, that controls the appearance and mating behavior of the male. (See also the News and Views by Chris Jiggins and our editorial highlighting the studies).

The image shown on the cover was provided by photographer Torsten Green-Petersen. For more gorgeous bird pictures from this photographer (including more ruffs!), see his website at https://www.fagelnsblick.com/.

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