1000 Plant Genomes Project


The 1000 Plant Genomes Project was an international research effort to establish the most detailed catalogue of genetic variation in plants. It was announced in 2008, shortly after the human 1000 Genomes Project, and was a similar large-scale genomics project using the high speed and efficiency of next-generation DNA sequencing. Headed by Dr. Gane Ka-Shu Wong and Dr. Michael Deyholos of the University of Alberta, the project successfully sequenced the transcriptomes of 1000 different plant species by 2014. With the final products including a capstone publication finally published in 2019.
1KP was one of the large-scale sequencing projects designed to take advantage of the wider availability of high-throughput DNA sequencing technologies. The similar 1000 Genomes Project, for example, obtained high-coverage genome sequences of 1000 individual people between 2008 and 2015, to better understand human genetic variation. This project providing a template for further planetary-scale genome projects including the 10KP Project sequencing the whole genomes of 10,000 Plants, and the Earth BioGenome Project, aiming to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity.

Goals

, the number of classified green plant species was estimated to be around 370,000, however, there are probably many thousands more yet unclassified. Despite this number, very few of these species have detailed DNA sequence information to date; 125,426 species in GenBank,, but most 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, but phylogenies created solely using morphological data, cellular structures, single enzymes, or on only a few sequences can be prone to error; morphological features are especially vulnerable when two species look physically similar though they are not closely related 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.

Biotechnology applications

The list of plant genomes sequenced in the project was not random; instead plants that produce valuable chemicals or other products 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 and some of the oils from certain plants bear a strong chemical resemblance to petroleum products like the Oil palm and hydrocarbon-producing species. 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. This is concept of engineering plants to do "work" is popular 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.

Project approach

Sequencing was initially done on the Illumina Genome Analyzer GAII next-generation DNA sequencing platform at the Beijing Genomics Institute, 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 capacity of each of these machines enabled fast and accurate sequencing of the plant samples.

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 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. The completed list of selected species can be publicly viewed on the website, and methodological details and data access details have been published in detail.

Transcriptome vs. genome sequencing

Rather than sequencing the entire genome of the various plant species, the project sequenced only those regions of the genome that produce a protein product ; 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 of the genome content. Although this approach is similar conceptually to expressed sequence tags, 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. To distinguish the two, the non-EST method is known as “shotgun transcriptome sequencing”.

Transcriptome shotgun sequencing

mRNA 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. Once the cDNA fragments are sequenced, they will be de novo assembled 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, 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. 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.

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, and the non-coding DNA may actually be the primary driver of trait differences seen between species.
Since mRNA was the starting material, the amount of sequence representation for a given gene is based on the expression level. 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 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 whereas animals typically only have 2. 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. 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 $50 million USD, 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, , the , the , and . To date, the project initially received $1.5 million CAD from the Alberta Government and another $0.5 million from Musea Ventures. An additional $2.5 million CAD was then contributed by the Alberta Government. In January 2010, BGI announced that it would be contributing $100 million to large-scale sequencing projects of plants and animals.

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