plant genome sequencing

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P. tremula genome sequencing was performed on DNA extracted from propagated root cuttings of a single wild tree growing on the Umeå University campus (63° 49′17′′N, 20° 18′40′′E). ", Bowers JE et al (2012) "Development of a 10,000 Locus Genetic Map of the Sunflower Genome Based on Multiple Crosses. The v1 sequence contains 2.3 gigabases of sequence data. Almost 600 complete plant genome assemblies are now available in public repositories. State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, Bioinformatics Center, School of Computer and Information Engineering, Henan University, Kaifeng, China . "Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Poplar was the third plant genome to be published, and is now one of two published genomes of tree species (the other being papaya). ", Draft genome of the kiwifruit Actinidia chinensis, "Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. As a result, while only 534 megabases of the genome were assembled the genome spans >786 Mb of sequence (the extra 200 MB are NNNNNN's representing unassembled repeat sequences -- transposons -- of known length between sequenced regions of the genome). We sequenced the genome of wild radish (Raphanus raphanistrum), a Brassicaceae species that experienced a whole-genome triplication event prior to diverging from Brassica rapa. The Plant Genome is a gold open access journal that provides the latest advances and breakthroughs in plant genomics research, with special attention to innovative genomic applications that advance our understanding of plant biology that may have applications to crop improvement. Despite substantial gene gains in these two species compared with Arabidopsis thaliana and Arabidopsis lyrata, ∼70% of the orthologous groups experienced gene losses in R. raphanistrum and B. rapa, with most of the losses occurring prior to their divergence. Comparative analyses of S. baicalensis genome with those of other closely related members of the mint family reveals the likely genomic changes that led to evolution of a new metabolic pathway for synthesis of 4′-deoxyflavone bioactives in the skullcap family. In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. Knowledge of plant genomes initially lagged behind those of other kingdoms but has greatly increased with the development of new technologies for DNA sequencing; bioinformatic analysis, rather than data production, is increasingly the bottleneck to further knowledge. Wang K et al (2012) "The draft genome of a diploid cotton Gossypium raimondii" Nature Genetics doi:10.1038/ng.2371. As of this writing the BGI genome assembly doesn't appear to be available to download anywhere. The genome was sequenced to a depth of 20x using a combination of 454 and Sanger sequencing, and 50x using Illumina short read sequencing technology. The genome of Brassica rapa was published in Nature Genetics in September 2011 by a consortum of researchers lead by the Beijing Genomics Institute (BGI). These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement." The Chickpea (Cicer arietinum) is widely grown around the world although the centers of production and consumption are the middle east and India. PacBio is the only sequencing … Many fruits we think of as separate species can breed with each other, making it difficult to properly define species barriers. Genes on these atypical outlier chromosomes show lower GC content and a significant fraction of putative horizontal gene transfer genes. This study reports a chromosome-level reference genome sequence for the medicinal plant Scutellaria baicalensis (Huang Qin). When a species’ reference genome is available, whole-genome resequencing is an efficient approach for discovering genes, SNPs, and structural variants, … Analysis of orthologous gene sets identifies gene families that may be unique to conifers. While that doesn't mean it represents the ancestral state of flowering plants, comparing amborella to the major flowering plant lineages -- the eudicots, monocots, and magnoliids (the last of which still doesn't have even a single published genome, someone please get on that!) Jaillon, O., Aury, J., Noel, B., Policriti, A., Clepet, C., Casagrande, A., Choisne, N., Aubourg, S., Vitulo, N., Jubin, C., Vezzi, A., Legeai, F., Hugueney, P., Dasilva, C., Horner, D., Mica, E., Jublot, D., Poulain, J., Bruyère, C., Billault, A., Segurens, B., Gouyvenoux, M., Ugarte, E., Cattonaro, F., Anthouard, V., Vico, V., Del Fabbro, C., Alaux, M., Di Gaspero, G., Dumas, V., Felice, N., Paillard, S., Juman, I., Moroldo, M., Scalabrin, S., Canaguier, A., Le Clainche, I., Malacrida, G., Durand, E., Pesole, G., Laucou, V., Chatelet, P., Merdinoglu, D., Delledonne, M., Pezzotti, M., Lecharny, A., Scarpelli, C., Artiguenave, F., Pè, M., Valle, G., Morgante, M., Caboche, M., Adam-Blondon, A., Weissenbach, J., Quétier, F., & Wincker, P. (2007). Nature Genetics doi: [10.1038/ng.2569. However C. bursa-pastoris is a tetraploid with all the challenges to genome assembly and genetic analysis that entails. This project would generate large-scale plant genome data within the next five years (2017-2022), addressing fundamental questions about plant evolution. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle, "The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Genome sequence of the palaeopolyploid soybean Nature, 463 (7278), 178-183 DOI: 10.1038/nature08670. DNA and RNA data are utilized to annotate many genes and protein functions in the draft genome. We also report the draft sequence of the South American oil palm Elaeis oleifera, which has the same number of chromosomes (2n = 32) and produces fertile interspecific hybrids with E. guineensis2 but seems to have diverged in the New World. Here we generate the first chromosome-scale high-quality reference genome sequence for C. sativa and annotated 89,418 protein-coding genes, representing a whole-genome triplication event relative to the crucifer model Arabidopsis thaliana. Capsella is "the closest well-characterized genus" to arabidopsis and in fact the plants look rather similar to the eye of someone who doesn't study arabidopsis for a living. Check out the Pan-grass synteny project. Genome sequencing, assembling and annotation have been major priorities in plant genetics research during the past 20 years. Genome Paper: Tina T. Hu et al. is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (Vaccinium spp.) Resources from this version of the cucumber genome are available at this site. ), a member of family Rhamnaceae, is a major dry fruit and a traditional herbal medicine for more than one billion people. (2011) "The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants." Sequencing and assembling a complete plant genome has been seen as a daunting task. Results Assembly-to-assembly mapping and gene ID mapping to the previous TGAC v1 assembly, archived at Polyploid view enabled, allowing users to view alignments among multiple wheat components simultaneously Here we select Spirodela polyrhiza for whole-genome sequencing. RNA-Seq expression profiling showed that blueberry growth, maturation, and ripening involve dynamic gene expression changes, including coordinated up and down regulation of metabolic pathway enzymes, cell growth-related genes, and putative transcriptional regulators. Shi J et al (2013) "Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica, Arabidopsis and Other Angiosperm Species" doi: Nelson DR & Schuler MA (2013) "Cytochrome P450 Genes from the Sacred Lotus Genome". Baker, J. Coddington, K.A. Potatoes are arguably the second most important non-grass crop grown around the world. Angelique D'Hont et al (2012) "The banana (Musa acuminata) genome and the evolution of monocotyledonous plants." Lycophytes are often grouped with ferns as vascular non-seed producing plants. Two versions of the foxtail millet genome were generated independently by the Beijing Genomics Institute and the Joint Genomes Institute and published in the same issue of Nature Biotechnology: Zheng G et al. ", The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences, "Background: Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Further analyses of the jujube-specific genes and transcriptome data from 15 tissues reveal the molecular mechanisms underlying some specific properties of the jujube. The well-preserved hexaploid genome structure of C. sativa surprisingly mirrors those of economically important amphidiploid Brassica crop species from lineage II as well as wheat and cotton. The Genome Paper Ling HQ et al (2013) "Draft genome of the wheat A-genome progenitor Triticum urartu" Nature DOI: 10.1038/nature11997. 2015. Plant genomes are typically large, highly repetitive, and exhibit a wide variety of ploidy, making them challenging to sequence and assemble using traditional sequencing technologies. The decontaminated sequencing reads were used to predict the genome size, heterozygosity, and repetitive rate. Cyanogenic glycoside (CG) biosynthetic enzymes were highly expressed in green fruit, and a candidate CG detoxification enzyme was up regulated during fruit ripening. Assaf Distelfeld from Tel Aviv University discusses recently generated genome assemblies of wheat progenitors, and how this new resource can help improve wheat breeding. As plant genomes are generally giant, genome survey by next-generation sequencing offers an affordable way to characterize the genome before conducting costly long-read genome sequencing . Its high vitamin C content can be attributed to a unique high level expression of genes involved in both biosynthesis and regeneration. Foxtail millet was domesticated in China and is a more distant relative to maize and sorghum. Crop Plant, Dr Aakash Goyal (Ed. The assembly consists of 10,687 contigs of the total length of 43.4 Mb and includes 17,755 complete and partial protein-coding genes. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. Algae. The barley genome was assembled using a mixture of BAC-sequencing, anchoring to a high density genetic map, and syntenic path assembly. Clone 94006 was collected from the banks of a river just north of Syracuse, NY. TE_Nest ... (SR) proteins in maize using the Plant Genome Database PlantGDB". (The downside is BAC-by-BAC sequencing takes longer and costs more, which is why it isn't as common anymore). The results of this study will aid in future investigations of secondary metabolite pathways in Aquilaria and other non-model medicinal plants. The published castor bean genome is based on a 4.6x coverage of the genome using solexa sequencing. AU - Wilde, Gail. ",, "The American cranberry (Vaccinium macrocarpon Ait.) Unlike the clementine genome described below, the sweet orange genome project used DNA from a diploid individual, making the assembly of the genome somewhat more difficult as inconsistences between aligned sequences might simply be the result of variation between the two genome copies of that diploid individual. Have we missed a published genome sequence? Whole genome alignments to rice, brachypodium and barley. Salix purpurea is a close relative of the DOE flagship model tree species, Populus trichocarpa, in the family Salicaceae.". Sequencing involves determining the order of bases, the nucleotide subunits-adenine( A), guanine(G), cytosine(C) and thymine(T), found in DNA. Whereas next-generation sequencing technology is allowing the advancement of whole-genome sequencing, one major obstacle to the successful assembly from short-read sequence data of complex diploid (and higher ploidy) organisms is heterozygosity. Neem (Azadirachta indica) is a relative of relative of mahogany found in India and neighboring countries. ", The genome sequence of the orchid Phalaenopsis equestris. The genome of cannabis (Cannabis sativa) was published in Genome Biology in October 2011. The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. For more details visit phytozome's page on the genome. Initially Plant genome projects focused on a few model organisms Characterized by Small genomes or their amenability to genetic studies. Conclusions Here we present a high-quality sequence for the complex jujube genome, the first genome sequence of Rhamnaceae, using an integrated strategy. The first bacterial whole genome to be sequenced was of the bacterium Haemophilus influenzae. The complex jujube genome provides insights into fruit tree biology. indica) Science 2006 (5565), 79-92 DOI: 10.1126/science.1068037. De novo RNA sequencing (RNA-Seq) analysis of SW revealed the developmental regulation of genes involved in specialized metabolic processes that impact taste and flavor in beer. A total of 4,214 scaffolds from the genome sequence assembly were aligned into the genetic map. De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms. Phytozome is a plant comparative genomics portal wherein families of related genes representing the … Unassembled genomes are not included, nor are organelle only sequences. A second Thellungiella species was independently sequenced by the Chinese Academy of Sciences. The Beijing Genome Institute (BGI) has contributed consistently over the years starting with the rice genome, then ten additional genomes primarily based on Illumina technology, and now they have announced a large‐scale plant genome sequencing project. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. All DNA was extracted using a DNeasy Plant Mini Kit (Qiagen). These restrictions are outlines by the. Currently the two diploid progenitors have both been sequenced and the genome assemblies may be downloaded from the link below (also the source of the quoted text above). Cassava (Manihot esculenta) is the most important crop that most people in America and Europe have never heard of (except perhaps in the form of tapioca). Plant genome sequencing powered by Ion™ semiconductor sequencing offers fast, affordable genome and exome sequencing in plants. Our study provides insights into jujube-specific biology and valuable genomic resources for the improvement of Rhamnaceae plants and other fruit trees. (genome unpublished and not fully assembled). The sorghum genome was published in 2009. We demonstrate that K. flaccidum indeed produces several plant hormones and homologues of some of the signalling intermediates required for hormone actions in higher plants. International Medicago Genome Annotation Group's webpage. The columbine genome was sequenced to 8-fold coverage by JGI and a pre-publication release of the genome is available for download from phytozome (account creation/login required). We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. The castor bean (Ricinus communis) is an oilseed plant that is the source of castor oil and the deadly poison ricin. It is the first publicly available genome from within the asterid clade. Schmidt et al. The published strawberry genome consists of 7 chromosomes/pseudomolecules. Using this method, highly pure nuclear HMW DNA suitable for a long read sequencing can be extracted in 5-6 h from difficult plant samples. This version is available at Phytozome. While the current genome assembly covers only half the estimated genome size of the rubber tree (1.1 GB assembled from a 2.15 GB genome) and is highly fragmented (N50 = ~3,000), the authors present evidence that their assembly captures the majority of the rubber genome gene space. The genome was assembled into 12 pseodomolecules with the assistance of a genetic map. However, the molecular genetic basis for identifying DNA markers in hop for breeding and to study its domestication has been poorly established. Genome Paper: Krishnan NM et al (2012) "A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica" BMC Genomics DOI: 10.1186/1471-2164-13-464. Until that uncertainly is resolved they are presented as a separate branch within the Rosids. In additio, the recent history of maize has included not one but two blooms of transposon activity. "Polyploidization events are frequent among flowering plants, and the duplicate genes produced via such events contribute significantly to plant evolution. The initial release of the genome includes 691 MB of sequence data, and 41,204 protein coding genes located on the putative chromosome assemblies. Given those options and the international reach of the internet, it's probably safest to stick with the scientific name. The nuclear genome is composed of 44,592 protein-coding genes. Recent proposals are now contemplating the sequencing, assembly and annotation of the genomes of all of the world’s plant species; meanwhile, low coverage sequencing to measure diversity across collections and wild populations has already become commonplace for many species, especially those utilized as crops. Selaginella has the distinction of currently being the smallest sequenced plant genome (~110 megabases, smaller than Arabidopsis!) The first approach to second generation sequencing was pyrosequencing, commercialized by Roche (Basel, Switzerland) as the GS20 (Margulies et al., 2005). It turns out the chilli/sweet pepper is one of those species that too many people wanted to sequence. This assembled genome was used as a base to analyze further data generated from a hetrozygous line where a great deal of presence absence variation was detected. japonica) Science, 296 (5565), 92-100 DOI: 10.1126/science.1068275, Yu, J. et al. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Here we describe a high-quality genome assembly of the parents of the IL population. The usefulness of the sequence was demonstrated by the retrieval of N. benthamiana orthologs for 24 immunity-associated genes from other species including Ago2, Ago7, Bak1, Bik1, Crt1, Fls2, Pto, Prf, Rar1, and mitogen-activated protein kinases. The Chinese plum (or Japanese Apricot, basically europeans weren't creative at all about coming up with english names for asian produce) is, like peach, a member of the genus Prunus. ", Architecture and evolution of a minute plant genome Nature 2013, "Horseweed (Conyza canadensis), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. By continuing you agree to the use of cookies. The genome paper: They also promoted the evolution of human, animals, and the planet earth. (2002). and native grape (Vitis spp.). The current assembly is only to the scaffold level (no pseudomolecules) and consists of 302 megabases of sequence spread over 971 scaffolds. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance. The jujube (Ziziphus jujuba Mill. A. lyrata is self-incompatable, while A. thaliana reproduced primarily through self-fertilization. The objective of this work is to sequence and analyze its genome, and to present a comparative analysis with other known genomes of the green lineage. © 2018 Elsevier Ltd. All rights reserved. Add more details here. That is older than the dinosaurs! Oxford nanopore sequencing involves feeding a fragment of DNA through a tiny (nano)pore in a flowcell and determining the sequence of that DNA based on how current through that pore is changed by the … The version of the grape genome in CoGe contains ~500 megabases of sequence and 26346 annotated genes spread across 19 chromosomes. Genome paper: Eman K Al-Dous et al., (2011) "De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)." (2011) "The Arabidopsis lyrata genome sequence and the basis of rapid genome size change." Its seeds are high in protein and dietary fibre, but low in oil and starch. Have you used the information gathered together on this page to assist you in writing a publication? Strikingly, the sacred lotus has 16 COG2132 multi-copper oxidase family proteins with root-specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment. sinensis. The expression changes for cucurbitacin E and I are shown to be consistent with known responses of A. agallocha to biotic stress and a set of homologous genes in Arabidopsis thaliana related to cucurbitacin bio-synthesis is presented and validated through qRT-PCR.This study is the first attempt to identify cucurbitacin E and I from in vitro agarwood and the first draft genome for any species of Aquilaria. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. Re-sequencing of the plant and animal genome will identify genetic variations such as SNPs and InDels and discover other genetic changes of the sequenced species. In addition to being used in soups, breads, and as animal feed, barley is perhaps most widely known as at source of the malt used to produce most beer around the world. To our knowledge, this article represents the first published draft genome of an agricultural weed.". Robert … Our assembled genome contains 29,431 predicted protein-coding genes. --Nature Genetics Abstract. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Yet almost NO bananas are produced domestically in the USA. ", [The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation] Published in PNAS in 2007, Genome is available from Phytozome:!info?alias=Org_Olucimarinus. Selaginella moellendorffii is a lycophyte, an ancient branch of the plant tree of life. Genes were predicted using both sequencing of ESTs and homology to the genes of other sequenced plant species, resulting in a total of 25,385 protein coding genes. Based on kmer abundance the authors estimate the total genome size to be ~740 megabases in size. While these species belong to the same clade which diverged from the other arabidopsis-and-allies group, they have been evolving separately for approximately as long as the divergence between Arabidopsis and Brassica, indicating comparative genomics between the two species should be interesting. Drosophila melanogaster ' s whole genome was sequenced in 2000. Bolger ME(1), Weisshaar B(2), Scholz U(3), Stein N(3), Usadel B(4), Mayer KF(5). By adding in BAC and fosmid end sequences as well as a genetic map with 7,015 markers (that's a lot!) The researchers identified a whole genome duplication which occurred in bamboo between 7-12 million years ago. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes." BMC Genomics doi: 10.1186/1471-2164-14-75. Plant Genome Sequencing Accelerates Crop Research This webinar discusses the impact of high-quality, affordable de novo genome assemblies on crop research.

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