1000 Plant Genomes Project

Former international research effort vanc 6 February 2024 1000 Plant Genomes Project 2019 2008 onekp.com nowrap Alberta Innovates Technology Futures Alberta Agricultural Research Institute (AARI) Genome Alberta University of Alberta BGI China National GeneBank (CNGB) Musea Ventures (Somekh Family Foundation) The 1000 Plant Transcriptomes Initiative (1KP) was an international research effort to establish the most detailed catalogue of genetic variation in plants. It was announced in 2008 and headed by Gane Ka-Shu Wong and Michael Deyholos of the University of Alberta. The project successfully sequenced the transcriptomes (expressed genes) of 1,000 different plant species by 2014;Retrieved Feb. 25, 2010 Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GK Data access for the 1,000 Plants (1KP) project GigaScience 3 17 17 2014 25625010 4306014 10.1186/2047-217X-3-17 free its final capstone products were published in 2019. One Thousand Plant Transcriptomes Initiative One thousand plant transcriptomes and the phylogenomics of green plants Nature 574 7780 679–685 October 2019 31645766 6872490 10.1038/s41586-019-1693-2 Wong Gane Ka-Shu Soltis Douglas E. Leebens-Mack Jim Wickett Norman J. Barker Michael S. de Peer Yves Van Graham Sean W. Melkonian Michael May 4, 2016 Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants Annual Review of Plant Biology 71 741–765 10.1146/annurev-arplant-042916-041040 31851546 2020AnRPB..71..741W 209416841 1543-5008 free 1KP was a large-scale (involving many organisms) sequencing projects designed to take advantage of the wider availability of high-throughput ("next-generation") DNA sequencing technologies. The similar 1000 Genomes Project, for example, obtained high-coverage genome sequences of 1,000 individual people between 2008 and 2015, to better understand human genetic variation. Hayden EC International genome project launched Nature 451 7177 378–9 January 2008 18216809 10.1038/451378b 2008Natur.451R.378C 205035320 About IGSR and the 1000 Genomes Project http://www.internationalgenome.org/about IGSR: The International Genome Sample Resource October 2, 2018 The initiative provided a template for further planetary-scale genome projects, including the 10KP Project—sequencing the whole genomes of 10,000 plants,Cheng Shifeng Melkonian Michael Smith Stephen A. Brockington Samuel Archibald John M. Delaux Pierre-Marc Li Fay-Wei Melkonian Barbara Mavrodiev Evgeny V. Sun Wenjing Fu Yuan March 1, 2018 10KP: A phylodiverse genome sequencing plan GigaScience 7 3 1–9 10.1093/gigascience/giy013 5869286 29618049 and the Earth BioGenome Project—aiming to sequence, catalogue, and characterize the genomes of all of Earth's eukaryotic biodiversity.Lewin Harris A. Robinson Gene E. Kress W. John Baker William J. Coddington Jonathan Crandall Keith A. Durbin Richard Edwards Scott V. Forest Félix Gilbert M. Thomas P. Goldstein Melissa M. April 24, 2018 Earth BioGenome Project: Sequencing life for the future of life Proceedings of the National Academy of Sciences 115 17 4325–4333 10.1073/pnas.1720115115 0027-8424 5924910 29686065 2018PNAS..115.4325L free Goals 2002, the number of classified green plant species was estimated to be around 370,000, however, there are probably many thousands more yet unclassified. Pitman NC, Jørgensen PM 891010 Estimating the size of the world's threatened flora Science 298 5595 989 November 2002 12411696 10.1126/science.298.5595.989 Despite this number, very few of these species have detailed DNA sequence information to date; 125,426 species in GenBank, 2012 04 11 on,https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=STATISTICS&uncultured=hide&unspecified=hide NCBI Taxonomy NCBI April 11, 2012 but most (>95%) having DNA sequence for only one or two genes. "...almost none of the roughly half million plant species known to humanity has been touched by genomics at any level". The 1000 Plant Genomes Project aimed to produce a roughly a 100x increase in the number of plant species with available broad genome sequence. Evolutionary relationships There have been efforts to determine the evolutionary relationships between the known plant species, Summary of Green Plant Phylogeny and Classification 1985 Bremer Kåre Cladistics 1 369–385 4 10.1111/j.1096-0031.1985.tb00434.x 34965683 84961691 free Graham LE, Delwiche CF, Mishler BD Phylogenetic connections between the'green algae'and the'bryophytes' Advances in Bryology 1991 213–44 3 451–483 2399900 but phylogenies (or phylogenetic trees) created solely using morphological data, cellular structures, single enzymes, or on only a few sequences (like rRNA) can be prone to error; Doyle JJ Gene trees and species trees: molecular systematics as one-character taxonomy. Systematic Botany January 1992 1 1 144–63 2419070 10.2307/2419070 1992SysBo..17..144D morphological features are especially vulnerable when two species look physically similar though they are not closely related (as a result of convergent evolution for example) or homology, or when two species closely related look very different because, for example, they are able to change in response to their environment very well. These situations are very common in the plant kingdom. An alternative method for constructing evolutionary relationships is through changes in DNA sequence of many genes between the different species which is often more robust to problems of similar-appearing species. With the amount of genomic sequence produced by this project, many predicted evolutionary relationships could be better tested by sequence alignment to improve their certainty. With 383,679 nuclear gene family phylogenies and 2,306 gene age distributions with Ks plots used in the final analysis and shared in GigaDB alongside the capstone paper.Li Zheng Barker Michael S. February 1, 2020 Inferring putative ancient whole-genome duplications in the 1000 Plants (1KP) initiative: access to gene family phylogenies and age distributions GigaScience en 9 2 giaa004 10.1093/gigascience/giaa004 7011446 32043527 Biotechnology applications The list of plant genomes sequenced in the project was not random; instead plants that produce valuable chemicals or other products (secondary metabolites in many cases) were focused on in the hopes that characterizing the involved genes will allow the underlying biosynthetic processes to be used or modified. For example, there are many plants known to produce oils (like olives) and some of the oils from certain plants bear a strong chemical resemblance to petroleum products like the Oil palm and hydrocarbon-producing species. Augustus GD, Jayabalan M, Rajarathinam K, Ray AK, Seiler GJ 2002 Potential hydrocarbon producing species of Western Ghats, Tamil Nadu, India Biomass and Bioenergy 23 3 165–169 10.1016/S0961-9534(02)00045-4 2002BmBe...23..165A https://zenodo.org/record/1260178 If these plant mechanisms could be used to produce mass quantities of industrially useful oil, or modified such that they do, then they would be of great value. Here, knowing the sequence of the plant's genes involved in the metabolic pathway producing the oil is a large first step to allow such utilization. A recent example of how engineering natural biochemical pathways works is Golden rice which has involved genetically modifying its pathway, so that a precursor to vitamin A is produced in large quantities making the brown-colored rice a potential solution for vitamin A deficiency. Ye X, Al-Babili S, Klöti A, Zhang J, Lucca P, Beyer P, Potrykus I Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm Science 287 5451 303–5 January 2000 10634784 10.1126/science.287.5451.303 2000Sci...287..303Y 40258379 This is concept of engineering plants to do "work" is popularTaiz Lincoln Zeiger Eduardo Chapter 13: Secondary metabolites and plant defense Plant physiology Sinauer Associates 978-0-87893-856-8 4th 2006 and its potential would dramatically increase as a result of gene information on these 1000 plant species. Biosynthetic pathways could also be used for mass production of medicinal compounds using plants rather than manual organic chemical reactions as most are created currently. One of the most unexpected results of the project was the discovery of multiple novel light-sensitive ion-channels used extensively for optogenetic control of neurons discovered through sequencing and physiological characterization of opsins from over 100 species of alga species by the project. Klapoetke NC, Murata Y, Kim SS, Pulver SR, Birdsey-Benson A, Cho YK, Morimoto TK, Chuong AS, Carpenter EJ, Tian Z, Wang J, Xie Y, Yan Z, Zhang Y, Chow BY, Surek B, Melkonian M, Jayaraman V, Constantine-Paton M, Wong GK, Boyden ES Independent optical excitation of distinct neural populations Nature Methods 11 3 March 2014 338–346 24509633 3943671 10.1038/nmeth.2836 The characterization of these novel channelrhodopsin sequences providing resources for protein engineers who would normally have no interest in or ability to generate sequence data from these many plant species. Wong GK, Soltis DE, Leebens-Mack J, Wickett NJ, Barker MS, Van de Peer Y, Graham SW, Melkonian M Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants Annual Review of Plant Biology 71 April 2020 1 741–765 31851546 10.1146/annurev-arplant-042916-041040 209416841 free 2020AnRPB..71..741W A number of biotech companies are developing these channelrhodopsin proteins for medical purposes, with many of these optogenetic therapy candidates under clinical trials to restore vision for retinal blindness. The first published results of these treating retinitis pigmentosa coming out in July 2021. Sahel JA, Boulanger-Scemama E, Pagot C, Arleo A, Galluppi F, Martel JN, Esposti SD, Delaux A, de Saint Aubert JB, de Montleau C, Gutman E, Audo I, Duebel J, Picaud S, Dalkara D, Blouin L, Taiel M, Roska B Partial recovery of visual function in a blind patient after optogenetic therapy Nature Methods 27 7 July 2021 1223–1229 34031601 10.1038/s41591-021-01351-4 235203605 free Project approach Sequencing was initially done on the Illumina Genome Analyzer GAII next-generation DNA sequencing platform at the Beijing Genomics Institute (BGI Shenzhen, China), but later samples were run on the faster Illumina HiSeq 2000 platform. Starting with the 28 Illumina Genome Analyzer next-generation DNA sequencing machines, these were eventually upgraded to 100 HiSeq 2000 sequencers at the Beijing Genomics Institute. The initial 3Gb/run (3 billion base pairs per experiment) capacity of each of these machines enabled fast and accurate sequencing of the plant samples.http://www.genomics.cn/en/index.php Retrieved Feb. 25, 2010 March 3, 2010 https://web.archive.org/web/20100307194830/http://www.genomics.cn/en/index.php March 7, 2010 dead Species selection The selection of plant species to be sequenced was compiled through an international collaboration of the various funding agencies and researcher groups expressing their interest in certain plants. There was a focus on those plant species that are known to have useful biosynthetic capacity to facilitate the biotechnology goals of the project, and selection of other species to fill in gaps and explain some unknown evolutionary relationships of the current plant phylogeny. In addition to industrial compound biosynthetic capacity, plant species known or suspected to produce medically active chemicals (such as poppies producing opiates) were assigned a high priority to better understand the synthesis process, explore commercial production potential, and discover new pharmaceutical options. A large number of plant species with medicinal properties were selected from traditional Chinese medicine (TCM). The completed list of selected species can be publicly viewed on the website,http://www.onekp.com/samples/list.php 1kP Sample List Viewer www.onekp.com April 10, 2020 February 20, 2020 https://web.archive.org/web/20200220171335/http://www.onekp.com/samples/list.php dead and methodological details and data access details have been published in detail. Carpenter EJ, Matasci N, Ayyampalayam S, Wu S, Sun J, Yu J, Jimenez Vieira FR, Bowler C, Dorrell RG, Gitzendanner MA, Li L, Du W, K Ullrich K, Wickett NJ, Barkmann TJ, Barker MS, Leebens-Mack JH, Wong GK Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP) GigaScience 8 10 October 2019 giz126 31644802 6808545 10.1093/gigascience/giz126 Johnson Marc T. J. Carpenter Eric J. Tian Zhijian Bruskiewich Richard Burris Jason N. Carrigan Charlotte T. Chase Mark W. Clarke Neil D. Covshoff Sarah dePamphilis Claude W. Edger Patrick P. November 21, 2012 Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes PLOS ONE en 7 11 e50226 10.1371/journal.pone.0050226 1932-6203 3504007 23185583 2012PLoSO...750226J free Transcriptome vs. genome sequencing Rather than sequencing the entire genome (all DNA sequence) of the various plant species, the project sequenced only those regions of the genome that produce a protein product (coding genes); the transcriptome. This approach is justified by the focus on biochemical pathways where only the genes producing the involved proteins are required to understand the synthetic mechanism, and because these thousands of sequences would represent adequate sequence detail to construct very robust evolutionary relationships through sequence comparison. The numbers of coding genes in plant species can vary considerably, but all have tens of thousands or more making the transcriptome a large collection of information. However, non-coding sequence makes up the majority (>90%) of the genome content. Morgante M Plant genome organisation and diversity: the year of the junk! Current Opinion in Biotechnology 17 2 168–73 April 2006 16530402 10.1016/j.copbio.2006.03.001 Although this approach is similar conceptually to expressed sequence tags (ESTs), it is fundamentally different in that the entire sequence of each gene will be acquired with high coverage rather than just a small portion of the gene sequence with an EST. Morozova O, Hirst M, Marra MA 26713396 Applications of new sequencing technologies for transcriptome analysis Annual Review of Genomics and Human Genetics 10 135–51 2009 19715439 10.1146/annurev-genom-082908-145957 To distinguish the two, the non-EST method is known as "shotgun transcriptome sequencing". Transcriptome shotgun sequencing mRNA (messenger RNA) is collected from a sample, converted to cDNA by a reverse transcriptase enzyme, and then fragmented so that it can be sequenced. Other than transcriptome shotgun sequencing, this technique has been called RNA-seq and whole transcriptome shotgun sequencing (WTSS). Once the cDNA fragments are sequenced, they will be de novo assembled (without aligning to a reference genome sequence) back into the complete gene sequence by combining all of the fragments from that gene during the data analysis phase. A new a de novo transcriptome assembler designed specifically for RNA-Seq was produced for this project,Xie Yinlong Wu Gengxiong Tang Jingbo Luo Ruibang Patterson Jordan Liu Shanlin Huang Weihua He Guangzhu Gu Shengchang Li Shengkang Zhou Xin June 15, 2014 SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads https://academic.oup.com/bioinformatics/article/30/12/1660/380938 Bioinformatics en 30 12 1660–1666 10.1093/bioinformatics/btu077 24532719 1367-4803 free 1305.6760 SOAPdenovo-Trans being part of the SOAP suite of genome assembly tools from the BGI. Plant tissue sampling The samples came from around the world, with a number of particularly rare species being supplied by botanical gardens such as the Fairy Lake Botanical Garden (Shenzhen, China).January 2020 The type of tissue collected was determined by the expected location of biosynthetic activity; for example if an interesting process or chemical is known to exist primarily in the leaves, leaf sample was used. A number of RNA-sequencing protocols were adapted and tested for different tissue types, and these were openly shared via the protocols.io platform.Protocols.io T Marc J Eric Tian Zhijian Bruskiewich Richard N Jason T Charlotte W Mark D Neil Covshoff Sarah W Claude P Patrick RNA Isolation from Plant Tissue v1 (protocols.io.439gyr6) August 15, 2019 https://www.protocols.io/view/rna-isolation-from-plant-tissue-439gyr6 10.17504/protocols.io.439gyr6 free Potential limitations Since only the transcriptome was sequenced, the project did not reveal information about gene regulatory sequence, non-coding RNAs, DNA repetitive elements, or other genomic features that are not part of the coding sequence. Based on the few whole plant genomes collected so far, these non-coding regions will in fact make up the majority of the genome, Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H A draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science 296 5565 79–92 April 2002 11935017 10.1126/science.1068037 2002Sci...296...79Y 208529258 and the non-coding DNA may actually be the primary driver of trait differences seen between species. Bird CP, Stranger BE, Liu M, Thomas DJ, Ingle CE, Beazley C, Miller W, Hurles ME, Dermitzakis ET Fast-evolving noncoding sequences in the human genome Genome Biology 8 6 R118 2007 17578567 2394770 10.1186/gb-2007-8-6-r118 free Since mRNA was the starting material, the amount of sequence representation for a given gene is based on the expression level (how many mRNA molecules it produces). This means that highly expressed genes get better coverage because there is more sequence to work from. The result, then, is that some important genes may not have been reliably detected by the project if they are expressed at a low level yet still have important biochemical functions. Many plant species (especially agriculturally manipulated ones) are known to have undergone large genome-wide changes through duplication of the whole genome. The rice and the wheat genomes, for example, can have 4-6 copies of whole genomes (wheat) whereas animals typically only have 2 (diploidy). These duplicated genes may pose a problem for the de novo assembly of sequence fragments, because repeat sequences confuse the computer programs when trying to put the fragments together, and they can be difficult to track through evolution. Comparison with the 1000 Genomes Project Similarities Just as the Beijing Genomics Institute in Shenzhen, China is one of the major genomics centers involved in the 1000 Genomes Project, the institute is the site of sequencing for the 1000 Plant Genomes Project. BGI Seeks Proposals to Sequence 1,000 Plant, Animal Genomes; Pledges $100M Toward Effort https://www.genomeweb.com/sequencing/bgi-seeks-proposals-sequence-1000-plant-animal-genomes-pledges-100m-toward-effor# February 25, 2010 GenomeWeb January 12, 2010 Both projects are large-scale efforts to obtain detailed DNA sequence information to improve our understanding of the organisms, and both projects will utilize next-generation sequencing to facilitate a timely completion. Differences The goals of the two projects are significantly different. While the 1000 Genomes Project focuses on genetic variation in a single species, the 1000 Plant Genomes Project looks at the evolutionary relationships and genes of 1000 different plant species. While the 1000 Genomes Project was estimated to cost up to US$50 million, the 1000 Plant Genomes Project was not as expensive; the difference in cost coming from the target sequence in the genomes. Since the 1000 Plant Genomes Project only sequenced the transcriptome, whereas the human project sequenced as much of the genome as is decided feasible, there is a much lower amount of sequencing effort needed in this more specific approach. While this means that there was less overall sequence output relative to the 1000 Genomes Project, the non-coding portions of the genomes excluded in the 1000 Plant Genomes Project were not as important to its goals like they are to the human project. So then the more focused approach of the 1000 Plant Genomes Project minimized cost while still achieving its goals. Funding The project was funded by Alberta Innovates - Technology Futures (merger of iCORE ), Genome Alberta, the University of Alberta, the Beijing Genomics Institute (BGI), and Musea Ventures (a USA-based private investment firm).http://alberta.ca/home/NewsFrame.cfm?ReleaseID=/acn/200811/2475592E5F382-B4A5-7B90-D0E37ED2E1ACCB0C.html Alberta iCORE researcher leads international genome project Government of Alberta November 13, 2008 August 21, 2018 https://web.archive.org/web/20120925211520/http://alberta.ca/home/NewsFrame.cfm?ReleaseID=%2Facn%2F200811%2F2475592E5F382-B4A5-7B90-D0E37ED2E1ACCB0C.html September 25, 2012 live To date, the project received $1.5 million CAD from the Alberta Government and another $0.5 million from Musea Ventures. In January 2010, BGI announced that it would be contributing $100 million to large-scale sequencing projects of plants and animals (including the 1000 Plant Genomes Project, and then following on to the 10,000 Plant Genome Project). Related projects The 1000 Genomes Project – A Deep Catalog of Human Genetic Variation The 1001 Genomes Project – Sequencing the whole genome of 1,001 Arabidopsis strains Weigel D, Mott R The 1001 genomes project for Arabidopsis thaliana Genome Biology 10 5 107 2009 19519932 2718507 10.1186/gb-2009-10-5-107 free Genome 10K – Whole genome sequence of 10,000 vertebrate species Genome 10K Community of Scientists Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species The Journal of Heredity 100 6 659–74 2009 19892720 2877544 10.1093/jhered/esp086 See also Biology 1000 Genomes Project International HapMap Project explicit Human Genome Project 100,000 Genomes Project List of biological databases References 30em External links http://www.onekp.com Category:Genome projects