Scientists sequence plant DNA in the field to identify species within hours

first_imgArticle published by Sue Palminteri Popular in the CommunitySponsoredSponsoredOrangutan found tortured and decapitated prompts Indonesia probeEMGIES17 Jan, 2018We will never know the full extent of what this poor Orangutan went through before he died, the same must be done to this evil perpetrator(s) they don’t deserve the air that they breathe this has truly upset me and I wonder for the future for these wonderful creatures. So called ‘Mankind’ has a lot to answer for we are the only ones ruining this world I prefer animals to humans any day of the week.What makes community ecotourism succeed? In Madagascar, location, location, locationScissors1dOther countries should also learn and try to incorporateWhy you should care about the current wave of mass extinctions (commentary)Processor1 DecAfter all, there is no infinite anything in the whole galaxy!Infinite stupidity, right here on earth.The wildlife trade threatens people and animals alike (commentary)Anchor3dUnfortunately I feel The Chinese have no compassion for any living animal. They are a cruel country that as we knowneatbeverything that moves and do not humanily kill these poor animals and insects. They have no health and safety on their markets and they then contract these diseases. Maybe its karma maybe they should look at the way they live and stop using animals for all there so called remedies. DisgustingConservationists welcome China’s wildlife trade banThobolo27 JanChina has consistently been the worlds worst, “ Face of Evil “ in regards our planets flora and fauna survival. In some ways, this is nature trying to fight back. This ban is great, but the rest of the world just cannot allow it to be temporary, because history has demonstrated that once this coronavirus passes, they will in all likelihood, simply revert to been the planets worst Ecco Terrorists. Let’s simply not allow this to happen! How and why they have been able to degrade this planets iconic species, rape the planets rivers, oceans and forests, with apparent impunity, is just mind boggling! Please no more.Probing rural poachers in Africa: Why do they poach?Carrot3dOne day I feel like animals will be more scarce, and I agree with one of my friends, they said that poaching will take over the world, but I also hope notUpset about Amazon fires last year? Focus on deforestation this year (commentary)Bullhorn4dLies and more leisSponsoredSponsoredCoke is again the biggest culprit behind plastic waste in the PhilippinesGrapes7 NovOnce again the article blames companies for the actions of individuals. It is individuals that buy these products, it is individuals that dispose of them improperly. If we want to change it, we have to change, not just create bad guys to blame.Brazilian response to Bolsonaro policies and Amazon fires growsCar4 SepThank you for this excellent report. I feel overwhelmed by the ecocidal intent of the Bolsonaro government in the name of ‘developing’ their ‘God-given’ resources.U.S. allocates first of $30M in grants for forest conservation in SumatraPlanet4dcarrot hella thick ;)Melting Arctic sea ice may be altering winds, weather at equator: studyleftylarry30 JanThe Arctic sea ice seems to be recovering this winter as per the last 10-12 years, good news.Malaysia has the world’s highest deforestation rate, reveals Google forest mapBone27 Sep, 2018Who you’re trying to fool with selective data revelation?You can’t hide the truth if you show historical deforestation for all countries, especially in Europe from 1800s to this day. WorldBank has a good wholesome data on this.Mass tree planting along India’s Cauvery River has scientists worriedSurendra Nekkanti23 JanHi Mongabay. Good effort trying to be objective in this article. I would like to give a constructive feedback which could help in clearing things up.1. It is mentioned that planting trees in village common lands will have negative affects socially and ecologically. There is no need to even have to agree or disagree with it, because, you also mentioned the fact that Cauvery Calling aims to plant trees only in the private lands of the farmers. So, plantation in the common lands doesn’t come into the picture.2.I don’t see that the ecologists are totally against this project, but just they they have some concerns, mainly in terms of what species of trees will be planted. And because there was no direct communication between the ecologists and Isha Foundation, it was not possible for them to address the concerns. As you seem to have spoken with an Isha spokesperson, if you could connect the concerned parties, it would be great, because I see that the ecologists are genuinely interested in making sure things are done the right way.May we all come together and make things happen.Rare Amazon bush dogs caught on camera in BoliviaCarrot1 Feba very good iniciative to be fallowed by the ranchers all overSponsored Scientists can now rapidly read the genetic code of an organism, even a plant, in the field.A portable real-time DNA sequencer speeds the process of reading the genome—an organism’s complete set of DNA—with minimal equipment, enabling scientists to identify and distinguish between closely related plant species, in the field.Rapid species identification of plant and animal tissue samples could greatly assist trade inspections, biodiversity studies, invasive species detection, and field research. Scientists can now rapidly read the DNA of an organism—even a plant—anywhere.Researchers at the Royal Botanic Gardens, Kew, have recently reported on their use of a handheld real-time DNA sequencing device that allowed them to identify the various species of an entire field of plants far faster than could be done using previous methods.This was the first time genomic sequencing of plants has been performed in the field. They highlight the new opportunities that real-time nanopore sequencing (RTnS) offers for plant research and conservation.DNA sequencing equipment in the field lab in Snowdownia National Park in Wales, U.K.. Photo credit Royal Botanical Gardens, KewSpeeding the process of species identificationIdentifying similar-looking plants has traditionally been difficult and time-consuming, requiring plant samples to be collected in the field, transported to a lab, and analyzed with large, expensive equipment, a process that took weeks or months. The lengthy process limits how fast decisions can be made regarding species newly found in forest corridors or found in international shipments of plant or animal products.Students work to identify as many plant species as possible during a plant inventory. Photo credit: U.S. National Park ServiceReading the genetic code of a plant or an animal is regarded to be the most reliable way to identify its species. New DNA analysis technology has decreased the time and cost of identifying the species of a given organism. Technology to sequence DNA, which is used to determine the order of four base nucleotides—adenine, guanine, cytosine, and thymine—in a strand of DNA, has improved dramatically over the past decade. This order, or sequence, of these building blocks of an organism’s DNA is unique to each organism, so knowing the order of the DNA of a sample allows scientists to identify its species.DNA barcoding—the collection, extraction, sequencing, and translation of a species’ DNA into a unique digital barcode—is increasingly being used to identify species, assess composition of natural communities, and combat poaching and illegal wildlife trade. Research teams are testing applications of DNA barcoding for identifying closely related animal species, such as sharks and rays, as trade in some, but not all, species is illegal. Efforts are also ongoing to apply the technology to plant products that have been processed, such as timber.DNA barcodes for four species. The barcodes for the two butterflies are not identical but more similar to each other than to the birds. Image credit: Sitfu.com, CC-3.0The advantage of barcoding is its ability to read short strands of DNA, which is often what are  available to scientists analyzing environmental DNA (eDNA) from soil, water, or fecal samples. To compare species, the technology requires a recoverable segment of DNA that can serve as an identification marker across species. Scientists have identified the Cytochrome C Oxidase 1 or CO1 gene region of DNA as universally usable for animal species. However, the C01 gene region evolves too slowly in plants, so scientists are still searching for the single best gene region for plants. This has limited species identification of plants in the field.Improving the precision of species identificationReal-time nanopore sequencing (RTnS)—a relatively new DNA sequencing method—may enable rapid species identification at a relatively low cost and with minimal equipment. Nanopore sequencers add to the utility of barcoding because they can read longer strands of DNA with less preparation, such as PCR amplification or chemical labeling, of each sample.Laptops process genetic data in the tent that served as a portable field lab. Photo credit: Royal Botanical Gardens, KewStreamlining preparation makes the technology potentially cheaper, faster, and smaller than other DNA sequencers and, thus, useful for monitoring disease outbreaks, environmental changing, food safety, and antibiotic resistance. It also facilitates the sequencing of whole human, animal, and plant genomes.The capacity to read longer DNA strands gives the nanopore sequencer more genetic information to work with, which enables it to more precisely distinguish samples and thus more accurately identify their species.The Kew scientists used the MinION, a portable RTnS DNA sequencer from Oxford Nanopore Technologies, to analyze plant species in the U.K.’s Snowdonia National Park. This was the first time genomic sequencing of plants has been performed in the field.Researcher Alex Papadopolous working with test tubes in the portable plant DNA analysis lab. Photo credit: Royal Botanical Gardens, KewThe MinION runs off a USB cable attached to a laptop and is small enough to be portable for fieldwork. A tiny sample of blood, feces, plant tissue, or other sample is mixed with reagents and placed into the handheld device. It generates data about the sample’s DNA within minutes, which is a big advantage for investigating wildlife crimes and identifying the species of traded wildlife and plant products.MinION has been used in field surveys to sequence animal DNA to identify species, but plant species identification through DNA has been more difficult.“Identifying species correctly based on what they look like can be really tricky and needs expertise to be done well,” said Alexander Papadopulos, Kew scientist and co-author on the paper. “This is especially true for plants when they aren’t in flower or when they have been processed into a product.”The research team achieved its aim of identifying and distinguishing between two closely-related, similar-looking plant species of the genus Arabidopsis—Arabidopsis thaliana and A. lyrata—in a single day of collecting and sequencing samples entirely in the field.Arabidopsis lyrata flowering in the field. Snowdownia National Park, U.K.. Photo credit: Royal Botanical Gardens, KewAdding flexibility to species identificationThe new RTnS technology allowed the team to sequence random parts of the plants’ genomes, which avoids the time-consuming process of targeting specific regions of DNA, the more traditional approach for identifying species with DNA.“Our experiments show that by sequencing random pieces of the genome in the field, it’s possible to get very accurate species identification within a few hours of collecting a specimen,” said Papadopulos in a media release. “More traditional methods need a lot of lab equipment and have often only provided enough information to identify a sample to the genus level.”The researchers compared their field-generated DNA sequences to a freely available database of reference genome sequences, created using traditional methods, to make their identification. Once confirmed, the field-sequenced data can then themselves be used as reference samples for DNA sequences to help future identifications of those species in the field.Another Arabidopsis in flower. Photo credit: Alex PapadopolousIn their paper, the authors state, “Our analyses demonstrate that correctly identifying unknown reads from matches to a reference database with RTnS reads enables rapid and confident species identification.”Lead author of the paper Joe Parker said in a media release, “This research proves that we can now rapidly read the DNA sequence of an organism to identify it with minimum equipment. Rapidly reading DNA anywhere, at will, should become a routine step in many research fields. Despite hundreds of years of taxonomic research, it is still not always easy to work out which species a plant belongs to just by looking at it. Few people could correctly identify all the species in their own gardens.”ReferenceParker, J., Helmstetter, A. J., Devey, D., Wilkinson, T., & Papadopulos, A. S. (2017). Field-based species identification of closely-related plants using real-time nanopore sequencing. Scientific reports, 7(1), 8345. https://www.nature.com/articles/s41598-017-08461-5center_img DNA, Genetics, Plants, Research, Species, Technology, Wildtech last_img read more