Year: 2016
Type: article
Abstract: The International Plant and Animal Genome (PAG) meeting takes place in the middle of January each year in San Diego, California, and will hold its 25th meeting in 2017. The meeting covers recent developments and planned work related to plant and animal genomes and includes technical presentations, posters, industry exhibits, and workshops. PAG attracts more than 3000 biologists, bioinformaticians, and industry representatives from 50+ countries who present their latest contributions to genome research. The large crowds and packed schedule at PAG is exciting and lends a feeling of being on the cutting edge of the rapidly changing field of genomics and its associated technologies. All of this takes place in a laid-back California atmosphere: San Diego in January is usually sunny and warm and provides a welcome respite for PAG attendees who sit outside during meeting breaks soaking up the sun and exchanging ideas. PAG has an increasingly expanding focus on a range of topics related to the genomes of plants and animals. The scientific programs at PAG are organized into workshops: sessions of scientific presentations organized around a taxonomic group (e.g., arthropod genomics) or a conceptual theme (e.g., statistical genomics). In 2016, there were more than 150 workshops on the schedule for PAG, and new workshops are added each year. Workshop themes must be proposed by attendees and accepted by PAG organizers. Once accepted, workshops run for several years and are re-evaluated periodically. Each workshop includes at least five and sometimes many more 20-min talks on the designated topic, but they can also be used to facilitate discussion and working groups. Workshop speakers are usually identified and invited by workshop organizers. Self-nomination (speakers contacting the workshop organizers) is a usual and effective way to engage in a workshop. The length of the workshop varies by topic, with some workshops lasting 2 h and others spanning the length of a day or even multiple days. In addition to the 1800 talks presented in the workshops, there is a very large poster session; 1100 posters were presented at PAG in 2016. Marketed as “The Largest Ag-Genomics Meeting in the World” (www.intlpag.org), the historical focus of PAG has been on the genomics of domesticated plants and animals. However, with changing technology, concomitant drops in genome sequencing cost, and the growth of user-friendly and affordable analysis platforms, genomics research is expanding into nonmodel, noncrop systems. Accordingly, today PAG workshops span a broad range of categories including genomics of plants; genomics of animals and fungi; general topics in genomics; tools, techniques, and resources; and education and outreach. In addition, PAG includes multiple plenary lectures, each of which draws well over 1000 attendees. Many researchers attend PAG each year to contribute and take in the latest updates on their favorite taxon, plant functional group, or question in plant biology. In 2016, the species- or genus-specific workshops in plants included a wide range of biofuel and food crops and established and emerging model organisms (e.g., Brassica, Brachypodium). In addition to annual workshops on globally important crops (e.g., legumes, maize, rice, soybean, and wheat), it has been particularly exciting to see a growing number of workshops focus on perennial crops (cacao, grape, mango, palm), and other edible taxa that traditionally have received less attention from the global research community (e.g., flax, Lolium, oats, Sorghum, and millets). Workshops now include plants grown for vegetative tissues (cassava, sugar beet, sugar cane, sweet potato, yam) and plants grown for their edible seeds and fruits. Another rising theme at PAG is workshops that cover groups of plants united by a particular trait or use (e.g., bioenergy grasses, cool season legumes, forage feedstocks and turf, forest trees, fruit/nuts, functional genomics of C4 and CAM, grasslands, ornamentals, perennial grasses, root genomics, and weedy/invasive plants. Perhaps most exciting, talks in a number of workshops were organized around challenging genomic questions in specific plant genera, where speakers employ cutting-edge technologies to push the boundaries of our current understanding. These taxon-specific workshops focus on components of apomixes, the plant epigenome, phytobiomes, genomics of plant development, genomics of tissue regeneration in plants, graft genetics and genomics, and the phytoremediation genome. Each year a number of high-impact studies of plant genomes are reported at PAG providing important new insights into specific systems and genome biology in general. Recently, multiple genome sequencing efforts have revealed the complexity of plant genomes in terms of the differences in genome content across individuals or variety groups. These unique genomic features can be so small as to encompass only a one or a few genes, or as large as an entire chromosome, are sometimes referred to as the “private” or “dispensable” genome (vs. the “core” genome) of an individual or variety group; i.e., the parts of the genome not shared with the reference or with other conspecifics. It is possible to detect these differences when genomes are assembled de novo, rather than being assembled to a reference, so this genomic variation within species is being uncovered rapidly as sequencing and assembly techniques improve. While the idea of a dynamic genome is not new and has been explored extensively in microbes, the extent and impact of these small differences for more complex plant genomes is now being explored in a variety of plants, as presented for domesticated rice (Oryza sativa) in the International Rice Informatics Consortium workshop by Weibo Xie (Huazhong Agricultural University). Low-coverage sequencing of >1000 accessions followed by tests for a variety of traits revealed that the nonconstant elements of the genome might contribute substantially to agronomically important phenotypes in the crop (Yao et al., 2015; Xie, 2016). We hope that this type of detailed genomic investigation can soon be translated to nondomesticated plants to understand the relative importance of the disposable genome in the context of adaptation and fitness in the wild. A related challenge in genome assembly comes from highly heterozygous genomes that are difficult to assemble with short reads. To date, many genome builds in systems that are heterozygous in nature have focused on homozygous lines, but recently attention has turned to the challenge of sequencing highly heterozygous cultivars as well as wild species. For example, recent advances in the grape genome include the utilization of deep coverage (600×) short reads (Patel et al., 2016) and the incorporation of longer PacBio reads (Cantu et al., 2016, see below). Experimentation with computationally efficient assembly approaches (e.g., Jellyfish, Platanus, among others) facilitates comparative analysis of assembly metrics and speed. These steps forward are significant not only for these systems, but also for myriad naturally outcrossing systems where genome assembly has been hindered by heterozygous genomes. PAG also offers several workshops that focus on specific animal groups, although there are fewer workshops on basic questions on animal biology relative to those offered for plants. The following animal groups were the topics of PAG workshops in 2016: arthropods, avian genomics, buffalo, camelids, cat and dogs, cattle/sheep/goat, cattle, equines, poultry, and swine. Other animal-focused workshops covered animal epigenetics, animal genomics and adaptation to climate change, functional annotations of animal genomes, and another focused on the genomics of nonclassical model animals. For some animal taxa, talks about specific animals are scattered throughout different workshops with various themes (see below). For example, at PAG XXIV (2016), several presentations addressed the genomics of pigeons, which since Darwin have been an important icon of evolutionary biology. Beth Shapiro (University of California Santa Cruz) presented “Population Genomics of Passenger Pigeons” in the Degraded DNA and Paleogenomics workshop, illustrating the utility of using ancient DNA to understand the genomics, population variation, and evolutionary history of extinct organisms (Shapiro et al., 2016). In another session (Domestication Genomics), Michael Shapiro University of Utah presented “More Than Skin Deep: Limb Identity and the Origins of Feathered Feet in Domestic Pigeons” (Shapiro, 2016). This fascinating study looked at the genetic basis of variation in the morphology of pigeon feet; most pigeons have scaly feet, while some lineages have evolved feathered feet under domestication. This study demonstrated that the shift from scales to feathers in pigeon feet is due in part to a shift in expression from hindlimb-specific genes to expression of forelimb (i.e., wing)-specific genes. As our knowledge of individual genomes grows, general questions that transcend taxonomic boundaries emerge related to genome biology and the evolution of genomes. Correspondingly, an increasing number of PAG workshops are now organized around broad questions, and the focus is on scientific advances rather than on the taxonomic group or the technique. The number and scope of these question-focused workshops grow each year, and in 2016 there were 28 workshops organized around different questions. These included such topics as domestication genomics, ecological genomics, population and conservation genomics, speciation genomics, and systems genomics. Other workshops included the evolution of genome size, genomic features and chromosome functionality, and polyploidy. Some workshops address mechanisms underlying genome change such as noncoding RNA, organellar genetics, posttranscriptional gene regulation, sex chromosomes and sex determination, small RNA, the somatic genome, and transposable elements. Scientists have also organized workshops on degraded DNA and paleogenomics, genomics of gene banks, host–microbe interactions, and analysis and the role of the microbiome. These theme-based workshops are some of the best attended at PAG and usually include well-known, productive scientists as speakers. One example of a question-based workshop is Domestication Genomics, which we (Briana L. Gross and Allison J. Miller) have organized for the past 4 years. The aim of this workshop is to highlight recent advances in the domestication genomics of plants and animals by inviting a range of international speakers to share their work. Each year, six speakers have participated in the workshop, including several members/supporters of the Botanical Society of America: Andrew Doust (Oklahoma State University), Amy Litt (University of California Riverside), Rachel Meyer (National Science Foundation), Jonathan Wendel (Iowa State University), and Eric von Wettberg (Florida International University), among others. Some of the organisms featured in the Domestication Genomics workshop include apple, canines, cattle, chickpeas, eggplant, horse, pigeons, potato, and sunflower. Presenters in the Domestication Genomics workshop have shared work pinpointing the geographic origins of many of these and other domesticated plants and animals. Their talks have explored the complexity of the genomic basis of agriculturally important traits and the consequences of strong artificial selection on genetic diversity at a population level. Speakers have also tackled questions related to the origin and evolution of weeds in agricultural systems. An emerging theme in the Domestication Genomics workshop is the importance of surveying a broad and geographically representative sample of the wild relatives of domesticated organisms in comparative analyses. Another recurring theme is the large number of markers (most commonly single nucleotide polymorphisms) needed to test hypotheses about the genetic underpinnings of adaptive variation and to estimate population genetic changes under domestication, particularly in heterozygous taxa. Other PAG workshops often highlight the power of genomics in illuminating interesting and unique aspects of plant growth. For example, grafting, the union of different individuals or even different taxa, occurs in nature and is also an important component of woody crops such as grapes and apples, and even some herbaceous crops. In the Graft Genetics and Genomics workshop, Michitaka Notaguchi (Nagoya University) gave a presentation on the capacity for grafting across plant lineages (Notaguchi, 2016). The authors demonstrated that different Nicotiana species can be grafted to one another, to other Solanaceae genera, monocots, gymnosperms, and even a fern! In addition to addressing agriculturally relevant questions regarding graft compatibility, this work raises important basic questions about the conservation of plant anatomical structure and function across distantly related plant lineages. This workshop also featured recent advances by Gennaro Fazio's group (USDA–Agricultural Research Service) on the effects of apple rootstocks on apple scions including their morphology, physiology, and transcriptome (Fazio and Tworkoski, 2016). Recent advances in apple genomics facilitate the generation of markers for QTL and eQTL studies and the identification of rootstock-mediated gene expression in the scion. One of the most valuable aspects of attending PAG is the opportunity to learn about new tools, techniques, and resources available for the generation and analysis of genomic data. Private companies, organizations, as well as groups of scientists organize workshops and programs designed to demonstrate new technologies, bioinformatics pipelines and platforms, and their applications in genome biology and evolution. For example, at PAG 2016, the tools and techniques workshops included allele mining, analysis of complex genomes, bioinformatics, comparative genomics, computation and gene discovery, gene expression and analysis, gene introgression, genome annotation, genome management, proteomics, and QTL cloning. CoGe, Ensembl, Galaxy, Illumina, iPlant, JBrowse, JGI, NCBI, and the UCSC Genome Browser (among others) were on hand offering workshops and/or demonstrations highlighting updates and new functionality in their platforms. Besides these workshops, companies offering services related to DNA and RNA extraction, library preparation, sequencing, and bioinformatics, ionomics, metabolomics, metagenomics, proteomics, and high-throughput phenotyping offered displays in a massive exhibit hall. The more than 130 exhibits on display at PAG in 2016 provided scientists the opportunity to talk one-on-one with company representatives about their specific needs and projects. One of the emerging technologies in recent years is the PACbio sequencing platform, which can deliver long reads; average read lengths are up to 10 kb, and some long reads range to >40 kb in the newer systems. While the technology has been available for some time, the applications of the system to plant genomes are now being felt. In particular, this system has been used to resequence the 3.6 Gb genome of sunflower (Helianthus annuus). Although the genome was already sequenced using a combination of Illumina and other technologies, the recent expansion of transposable elements (TEs) in the sunflower genome made it difficult to assemble completely. This year, Nicolas Langlade (LIPM–INRA/CNRS) and colleagues (Gouzy et al., 2016) reported in the Compositae workshop on the use of PACbio technology to produce a de novo sequence and assembly of sunflower. The PACbio instruments gave an average read-length of 9.8 kb at 100× coverage, resulting in an N50 contig length of 524 kb and a comprehensive assembly without the gaps in the original genome version. This represents a massive step forward for a challenging plant genome (note that the sunflower genome is larger than the maize genome and that the TEs are young and undifferentiated, making it comparatively difficult). However, it should also be noted that this achievement required multiple PACbio sequences and a year of work (with full-time employees); thus, while the potential for truly deciphering increasing complex genomes does exist, it is still not a trivial task. Generally, PAG attracts principal investigators, postdocs, and industry representatives. Graduate students attend in relatively small numbers, and undergraduate students likely make up a small percentage of attendees. As a result, education and outreach workshops at PAG are geared toward laboratory heads and professors. In 2016, specific education and outreach workshops included Cultivating Broader Impact, iPlant Education: Genomics, DNA Barcoding, Resources and Programs for Undergraduate, and Teaching Genetics, Genomics, and Biotechnology. Education and Outreach is relatively new at PAG and is an important area for potential expansion; perhaps a workshop highlighting how PAG attendees are teaching/conducting outreach would be useful. In addition, specific events for undergraduate and graduate student attendees might expand participation and also seed the next generation of PAG supporters. Popular events at PAG are the approximately seven plenary lectures, which take place throughout the meeting. Each lecture features a prominent speaker who gives a broad overview of a major issue or new advance in genomics. Some favorites in recent years included Beth Shapiro (University of California, Santa Cruz) who spoke about using ancient DNA to reconstruct the evolutionary history of polar bears and James Ostell (National Center for Biotechnology Information, USA) who recounted the history and looked toward the future of storing and accessing genomic data, the amount of which is growing exponentially each year. John Quackenbush (Harvard T.H. Chan School of Public Health) explained the ways in which network approaches connecting genotypes and phenotypes can uncover biological processes. These popular, well-attended lectures are held in a huge ballroom that holds at least 1000 people, with slides projected on four screens and numerous televisions. The International Plant and Animal Genome meeting offers an opportunity to catch up on the latest advances in the genomics of specific plant and animal groups, to follow the development of specific questions within genomics, to learn about the new technologies and their applications in understanding genome biology and evolution, and to network with colleagues and collaborators from around the world. Given the incredible pace at which genome access and analysis is changing, PAG is a great way to stay current in a friendly and exciting environment. Keeping up with advances in genomics is critical for research programs of many individual principal investigators. Beyond this, a meeting like PAG helps ensure that those training undergraduates, graduate students, and postdocs for academic and industry jobs are up to speed with the latest tools, technologies, and their applications in botany and beyond. And if you can't travel to San Diego for the meeting, you can always keep up with PAG on Twitter—thousands of tweets from the 2016 PAG meeting are available at #PAGXXIV.
Source: American Journal of Botany
DOI: 10.3732/ajb.1600143
Authors: Allison J. Miller, Briana L. Gross
Institutions: Saint Louis University, University of Minnesota, Duluth
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: bronze
OpenAlex ID: W2443327248