Along with Prozac and the polymerase chain reaction (PCR), shotgun sequencing has become widely recognized as one of the top pivotal medical discoveries of the past 50 years. This powerful technology has made it possible to ascertain the entire nucleotide sequence of an organism. Furthermore, with advances in Next Generation Sequencing (NGS) technologies, many laboratories around the world now can run their own sequencing experiments. Since fungal genomes are relatively small and compact, fungi have quickly become the most sequenced eukaryotic taxon. Researchers from diverse subdisciplines can analyze these genomic sequences and decipher their functional elements, which has led to many discoveries in basic fungal biology, taxonomy, population genetics, evolution, and beyond. Yet, along with opportunities, the deluge of sequence data presents many technical, logistical and regulatory challenges that often prevent researchers from using the data most effectively.
How can fungal biologists ensure open access to living cultures of strains and species that have been sequenced to date? The article by Kevin McCluskey provides an excellent review of the strain collection, long-term storage and dissemination practices developed at one of the most respected fungal culture collections in the USA – the Fungal Genetic Stock Center. Ensuring unrestricted access to these strains is critical for the reproducibility and integrity of sequence data, which will serve as a foundation for many post-genomic studies. Unfortunately, public databases contain many sequences attributed to the wrong strain or even species, presumably caused by a strain mix-up during serial strain transfer. To avoid these costly and embarrassing mistakes, sequenced strains need to be deposited in professionally maintained culture collections (It is worth pointing out that, as a bonus, deposition in such a collection also results in a significant increase in citation of the original sequencing study!).
In this issue, we also highlight the work of researchers who tackle other daunting issues associated with the wealth and complexity of NGS sequence data. Scientists from three major sequencing centers, the Broad Institute, the Joint Genome Institute (JGI) and the J. Craig Venter Institute (JCVI), offer recommendations and report their findings in fungal genome sequencing, annotation and analysis. The comprehensive review of eukaryotic genome annotation by Brian Haas and colleagues will be instrumental when you need to define your strategies at the beginning of any genome project. Finally, do not miss Barbara Robbert's and Tatiana Tatusova's review of the genomic resources and tools available at the National Center for Biotechnology Information at NIH, the world largest collection of biological sequence data and data mining tools. These online tools are especially useful for individual fungal biology laboratories without a large IT infrastructure, servers, software or the computational expertise required for analysis of large sequence data sets.
NGS technologies offer immense transformational value to all areas of fungal biology; however, sequence data management and analysis is becoming progressively more complicated. Whether you are a seasoned genomics warrior or a recent recruit, learning how to harness these powerful technologies may take much longer than expected. We all have a lot to learn. Yet, as the saying goes, a journey of a thousand miles begins with a single step.
Wishing you a wonderful journey,
Dr Li-Jun Ma
Email: [email protected]
Dr Joan W Bennett
Email: [email protected]
Dr Natalie D Fedorova
Email: [email protected]