Experience with genome assemblies would also be advantageous.
Nominations and applications are welcome and whilst scientific qualifications are paramount, we would particularly appreciate nominations and applications from suitably qualified researchers from underrepresented groups (including women, ethnic minority scientists, scientists with disabilities and other underrepresented groups). Please email nominations/applications by October 15th, 2020 to firstname.lastname@example.org with the following items:
Cover letter stating the reasons for your nomination, of if applying for yourself, your interest in the role and familiarity with the journals,
Abbreviated CV (Education, Publications, Outreach) if you have it.
We are really excited to get a sneak peak into the story behind a new Special Feature in Molecular Ecology Resources focusing on the use of genomic techniques to better understand natural history collections. In this Special Feature, the authors led by Assistant Professor Lua Lopez, compiled a broad range of studies using a variety of methods to illustrate the enormous potential of museum samples to answer question fundamental to molecular ecology. See below for a video interview with Lua and the article. Check out the great set of articles in the special feature here.
What led you to put together a special issue on this topic?
My first contact with ancient genomics was during my postdoc at PSU at the Lasky Lab. As soon as I started looking for literature to help me get the project started I realized that, except in the field of human ancient genomics, information was scattered and it was not easy to find methodological papers for wet-lab or bioinformatics of this type of data. We were lacking a strong foundation of studies using a combination of ancient, historical and modern samples stored in museums. Because of all this I wanted to put together an issue compiling a critical mass of studies using Natural History Collections (NCH) to advance the field of evolutionary biology. Although I had been thinking for a while about this, I only adventured to put this together when two new postdocs also working with NHC samples joined the lab, Dr. Kathryn Turner and Dr. Emilly Bellis. The three of us, together with our postdocsupervisor Jesse Lasky, decided it was time to get this running and I am very excited with the result.
2. Of the papers in the special feature, can you identify any broad trends?
All papers provide a significant advance in important methodological steps (from DNA extraction to data analysis) facilitating the use of NHC sample in evolutionary studies. The data used to test the methods in these papers provide a glimpse of the new research avenues that NHC samples can open.
3. What did you find the most surprising about the papers in this feature?
It was incredible to see how many fields can benefit from using NHC samples. This issue does not only cover methodological aspects but it shows how NHC samples can help answer long-standing questions in the fields of metagenomics, epigenetics, conservation genomics, evolutionary ecology and phylogenetics.
4. What do you recommend to researchers trying to collect genomic data from natural history collections?
Contact as many NHCs as you can. There are still many collections that are not digitized and being aware of what is available that can have a large impact in your experimental design. If this is your first time working with NHC samples, team up, genetic studies with NCH samples can be a big challenge (high risk, high reward). Having someone with experience to guide you is going to be one of the best things you can do to ensure the success of your research.
5. What do you think are crucial next research steps to effectively utilizing natural history collections?
I strongly believe that the next steps include digitizing NHC collections and archiving DNA data. Many NHC samples are not yet digitized and researchers looking a particular species can only obtain a partial picture of what’s available for their studies. The accuracy we have to answer particular questions is, in most cases, determined by the samples we have access to (i.e. number of samples, geographical and temporal distribution). In addition, any genetic data obtained from NHC samples should be publicly available. By having access to larger data sets we can not only increase the accuracy of our results but we can also better predict future scenarios.
6. What (if any) method advances are needed?
In the past 10-20 years, we have improved enormously in our wet lab protocols and bioinfomatics but the intrinsic nature of DNA from NHC samples means that we still have a long way to go. Ideally, we want standardize protocols for large taxonomic groups and identify what kind of factors have a larger impact in DNA damage. This also applies for pipelines for data analysis, in general the more standardized protocols are the best, it will hep us comparing results among studies and trying to identify broad evolutionary patters.
7. What would your message be for students about to start their first research projects on this topic?
Understand what kind of samples you have in your hands. It’s not only about how old they are, it’s also about how where they preserve after sampling and during storage, where are they coming from, how much material you have, etc. Many factors are going to influence the success of obtaining DNA of enough quality for downstream analysis. And the same goes for the data analysis, make sure you are considering the particular nature of the genetic data that you are analyzing. NHC samples are precious and destructive sampling cannot be done lightly. So, always do a test run and ask all the questions that you have.
In this interview, Professor Bo Dong tells us about his team’s recent study exploring the genomic basis of environmental adaptation in the leathery sea squirt (Styela clava), a highly invasive species of tunicate that has adapted to a broad range of environments. In this study, the authors assembled a chromosomal-level genome and transcriptome of the leathery sea squirt and undertook in situ hybridization and drug inhibition experiments in order to elucidate molecular mechanisms of adaptation. Continue reading to find out what the team found and why it matters, and click here to read the article.
What led to your interest in this topic / what was the motivation for this study?
Our lab works on organ morphogenesis and developmental genomics using an ascidian model. When we collected animals at the sea in Qingdao, China, we found many leathery sea squirts. Previous research has found that the leathery sea squirt is invasive across the globe, and impacts on both marine biodiversity and aquaculture industries. Therefore, we were interested in revealing the genomic basis of its adaptation. In addition, the Wellcome Sanger Institute, in celebration of its 25th anniversary, created a poll of species where the winners would have their genomes decoded. The leathery sea squirt was included in the ‘Dangerous Zone’ category of the poll, and although it did not win this strengthened our determination to decode its genome.
What difficulties did you run into along the way?
In order to obtain a better genome assembly, we used the PacBio sequencing and combined this with Hi-C approach. Because of the small size of leathery sea squirt adults, we tried many times to get enough high-quality DNA from one individual for library construction. In addition, the approaches for functional analysis is fairly limited in this ascidian species. We tried different ways to do dechorionation or microinject the DNA into the eggs, but it was not working well. We are continuing our work on this now.
What is the biggest or most surprising finding from this study?
Compared with the classical ascidian model species Ciona robusta, we found that Styela clava has a genome double the size but with comparable gene number. Another intriguing finding is that cold-shock protein genes were transferred horizontally into the S. clava genome from bacteria. Transfer of these genes provides one of the possible molecular mechanisms for S. clava to adapt the environmental stress, particularly low-temperature stress.
Moving forward, what are the next steps for this research?
We obtained the genetic information and molecular network of environmental adaptation and metamorphosis of leathery sea squirts through high quality genome assembly. Next, we are focusing on two further aspects of this project: 1) we are further digging into the signaling molecules that control the larval metamorphosis experimentally and 2) we plan to reveal the mechanisms for gene transfer from bacteria to ascidians.
What would your message be for students about to start their first research projects in this topic?
First, you should know clearly what kinds of scientific questions you want to ask by genome assembly approaches. Second, try to discuss your research projects with scientists with different backgrounds to adjust your research strategies and analyze your results. Third, compare your genome data with the data from other species to see if your conclusion is a universal one.
What have you learned about science over the course of this project?
Animals are so smart. They use different and unexpected strategies to adapt to environmental stress. Genomic approaches are a powerful way to elucidate the biological mechanisms of adaptation. Experimental results are often different from your expectations.
Describe the significance of this research for the general scientific community in one sentence.
The present study provides a chromosomal-level genome for understanding environmental adaptation in invasive tunicates.
Describe the significance of this research for your scientific community in one sentence.
Our study provides the chromosomal-level genome resources of leathery sea squirt (S. clava) and a comprehensive genomic basis for understanding environmental adaptation and larval metamorphosis.
Wei, Jiankai, et al. “Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava).” Molecular Ecology Resources (2020). doi.org/10.1111/1755-0998.13209