A plant genome assembly represents the complete genomic sequence of a plant species, which is assembled into chromosomes and other organelles by using DNA (deoxyribonucleic acid) fragments that are obtained from different types of sequencing technology.
Structure
The genome of plants can vary in their structure and complexity from small genomes like green algae (15 Mbp). to very large and complex genomes that have typically much higher ploidy, higher rates of heterozygosity and repetitive elements than species from other kingdoms. One of the most complex plant genome assemblies available is that of loblolly pine (22 Gbp). Due to their complexity, the plants’ genome sequences can't be assembled back into chromosomes using only short reads provided by next-generation- sequencing technologies (NGS), and therefore most plant genome assemblies available that used NGS alone are highly fragmented, contain large numbers of contigs, and genome regions are not finished. Highly repetitive sequences, often larger than 10kbp, are the main challenge in plants. Most of the chromosomal sequences are produced by the activity of mobile genetic elements (MGEs) in the plant genomes. MGEs are divided into two classes: class I or retrotransposons, and class II or DNA transposons. In plants, long- terminal repeat (LTR) retrotransposons are predominant and constitute from 15% to 90% of the genome. Polyploidy is another challenge in assembling a plant genome, and it is estimated that ~80% of plants are polyploids.
Assemblies
The first complete plant genome assembly, that of Arabidopsis thaliana, was finished in 2000, being the third multicellular eukaryotic genome published after C. elegans and D. melanogaster. Arabidopsis, unlike other plants’ genomes (e.g. Malus) has convenient traits, such as a small nuclear genome (135Mbp) and a short generation time (8 weeks from seed to seed). The genome has five chromosomes reflecting approximately 4% of the human genome size. The genome was sequenced and annotated by the Arabidopsis Genome Initiative (AGI).
The initiative for sequencing the genome of rice (Oryza sativa), began in September 1997, when scientists from many nations agreed to an international collaboration to sequence the rice genome, forming “The International Rice Genome Sequencing Project” (IRGSP). At an estimated size between 400-430 Mb, approximatively four times larger in dimensions than A. thaliana, rice has the smallest of the major cereal crop genomes.
Between 2000 and 2008 in total 10 plant genomes were published while in 2012 alone, 13 plant genomes were published. Since then the number was constantly increasing, and now more than 400 plant genomes are available in the NCBI genome database, of which 72 were re-annotated [NCBI].
Databases
EnsemblPlants is part of EnsemblGenome database and contains resources for a reduced number of sequenced plant species (45, Oct. 2017). It mainly provides genome sequences, gene models, functional annotations and polymorphic loci. For some of the plant species, additional information is provided including population structure, individual genotypes, linkage, and phenotype data.
Gramene is an online web database resource for plant comparative genomics and pathway analysis based on Ensembl technology.
Plant Genome DataBase Japan (PGDBj) is a website that contains information related to genomes of model and crop plants from databases. It has three main components: ortholog db, DNA marker and linkage map db, and plant resource db, where multiple plant resources accumulated by different institutes are integrated. The aim is “to provide a platform, enabling comparative searches of different resources” (pgdbj.jp).
PlantsDB is a resource for analysing and storing genetic and genomic information from various plants, and offers tools to query these data and to perform comparative analysis with the help of in-house tools.
PLAZA is another online resource for comparative genomics that integrates plant sequence data and comparative genomic methods, and performs evolutionary analysis within the green plant lineage (Viridiplantae).
The Arabidopsis Information Resource (TAIR) maintains a web database of the “model higher plant Arabidopsis Thaliana “.
Assembly strategies
In general, for sequencing and assembling large and complex genomes like plants, different strategies are used, based on the technologies available at that time when the project started.