The draft genome sequence of a desert tr ee populus pruinosa wenlu yang 1, kun wang 1, jian zhang 2, jianchao ma 2, jianquan liu 1,2, tao ma 1 1 moe key laboratory for bioresources and eco. Bac ends were sequenced to assist longrange assembly of whole genome shotgun sequence scaffolds and more. The complete chloroplast genome sequence of populus mexicana. Over 45,000 putative proteincoding genes were identified. The whole genome sequence data reported in this paper have been deposited in the genome warehouse in national genomics data center 1, beijing institute of genomics china national center for bioinformation, chinese academy of sciences, under accession number gwhxxxx00000000 that is publicly accessible at. This genome wide association study gwas dataset includes more than 28 million single nucleotide polymorphisms, or snps that have been derived from 17 trillion bases of sequence data generated from 882 undomesticated populus genotypes. To use the download service, run a search in assembly, use facets to refine the set of genome assemblies of interest, open the download assemblies menu, choose the source database genbank or refseq. Sep 21, 2004 the genus populus is the internationally accepted model for molecular tree biology. A total of 60 gb of clean reads from whole genome sequencing.
Kersten b, faivre rampant p, mader m, le paslier mc, bounon r, berard a, vettori c, schroeder h, leple jc, fladung m. A complete genome sequence was obtained for a severe acute respiratory syndrome coronavirus 2 sarscov2 strain isolated from an oropharyngeal swab specimen of a nepalese patient with. Thus, in addition to examining gene and genome evolution in populus, the genomes of these species provide an excellent model for studying how evolutionary processes affect patterns of genetic variation across genomes. We employed pacbio singlemolecular realtime sequencing and hic technology to generate a reference sequence of the poplar 84k populus alba x populus tremula var. First genome of populus populus trichocarpa was published in 2006, as a model tree. The subclade highlighted in yellow includes genes indicated by asterisks that have been shown to maintain the indeterminate inflorescence or vegetative phases, whereas the. The genome of black cottonwood, populus trichocarpa torr. Its rapid growth and compact genome size 500 mb, n18 has lead to its use as a model organism for tree species. The genome sequences were assembled into the chromosome levels, with a contig n50 size of 1. The complete mitochondrial genome sequence of populus. Populus trichocarpa poplar is distinguished from its herbaceous counterparts arabidopsis and rice by its woody structure, perennial life cycle, and dioecious, twowhorled flowers. Revisiting the sequencing of the first tree genome. Transcriptome sequencing of transgenic poplar populus. Populus trichocarpa, the black cottonwood, western balsampoplar or california poplar, is a deciduous broadleaf tree species native to western north america.
Analysis of the assembled genome revealed a whole genome. In july 2015, there were 81 different pseudomonas species that had at least one genome sequence deposited in genbank, along with another 125 genomes that were designated pseudomonas species, followed by a strain name. The complete chloroplast genome sequence of populus deltoides. The total chloroplast genome sequence lengths for the five plastomes were 156,789, 156,523, 156,512, 156,5, and 156,465 bp, respectively. Nov 21, 20 little is known about the genes that confer salt tolerance in trees. Madsbox genes are known to be involved in many important processes during plant development. When the poplar genome sequence, generated by the doe joint genome institute, was published in the september 15, 2006 issue of the journal science, we planted a commemorative sapling on our front lawn that was clonally propagated from the poplar or black cottonwood tree, populus trichocarpa, whose dna. We report the draft genome of the black cottonwood tree, populus trichocarpa. Poplar was chosen as the first tree dna sequence decoded because of its relatively compact genetic complement, some 50 times smaller than the genome. Analysis of the assembled genome revealed a whole genome duplication event, with approximately 8,000 pairs of duplicated genes from that event. Microsatellite dna markers in populus tremuloides genome. Jan 15, 2020 populus trichocarpa was chosen as the first tree to be sequenced because of the relatively small size of its genome. This is the second improved version of poplar v3 assembly and includes 81 mb of finished clone sequence combined with a new, high density poplar map. A total of 60 gb of clean reads from whole genome sequencing of a p.
Willow is a widely used dioecious woody plant of salicaceae family in china. Populus alba is widely distributed and cultivated in europe and asia. The complete chloroplast genome sequence of desert poplar populus euphratica. A physical map of the highly heterozygous populus genome. Genome sequence and genetic transformation of a widely. Analysis of the assembled genome revealed a whole genome duplication event. As a representative dicot, the genomic sequences of populus poplar. Pdf the complete chloroplast genome sequence of populus.
In this study, we assembled the complete mitochondrial mt genome sequence of s. Sep 01, 2006 we report the draft genome of the black cottonwood tree, populus trichocarpa. Pdf the genome of black cottonwood, populus trichocarpa. The complete chloroplast genome of populus wilsonii was reconstructed by referencebased assembly using whole genome sequencing data. Although this species has ecologically and economically important values, its genome sequence is currently not available, hindering the development of new varieties with wider adaptive and commercial traits. Issues wit h agestructured modeling and the inability to adjust values, have been resolved. The draft genome sequence of a desert tree populus pruinosa. Populus trichocarpa poplar is a deciduous broadleaf tree that is native to western north america. In this study, the whole chloroplast cp genome sequence of siyang2 was assembled and characterized by highthroughput sequencing data.
Plantgdb download portal plantgdb resources for plant. Comparative analysis of the complete chloroplast genomes. This is the second improved version of poplar v3 assembly and includes 81 mb of finished clone sequence. Tools sequence analysis tools accessed from the genome. Its rapid growth and compact genome size 500 mb, n18 has lead to its use as a model organism for tree species taxonomy id 3694. Tools sequence analysis tools accessed from the genome context view menu use the current genomic region as input. To test this, we compared the shrinkage and expansion of gene families within each genome. Markers for eight new microsatellite dna or simple sequence repeat ssr loci were developed and characterized in trembling aspen populus tremuloides from a partial genomic library. We also provide 4,000 assembled full clone sequences to serve as a basis for the upcoming annotation of the populus genome sequence.
Our results showed that positive and negative selection broadly affects patterns of genomic variation, but to varying degrees across coding and noncoding regions. This landmark decision was the culmination of work by the forest science community to develop populus. Ten years ago, it was announced that the joint genome institute with funds provided by the department of energy, office of science, biological and environmental research would sequence the black cottonwood populus trichocarpa torr. We performed this analysis using tissue from the populus trichocarpa clone nisqually1. The organization of the chloroplast genomes of both populus. Jun 03, 2002 we report molecular genetic linkage maps for an interspecific hybrid population of populus, a model system in foresttree biology. A total of genes were identified in each genome, including 85 proteincoding genes, 37 trna genes and eight rrna genes. Please cite the accession number gwhxxxx00000000 like this. The reorganized genomes ftp site supports download needs such as. Retroposition, as an important copy mechanism for generating new genes, was believed to play a negligible role in plants. Simple sequence repeats with primers developed from low coverage dna sequencing. Due to rapid development of sequencing and genome assembly technologies, the cost for whole genome sequencing has been dropped a lot reaching that 1,000 dollars per 1 gbp.
Populus simonii is an important tree in the genus populus, widely distributed in the northern hemisphere and having a long cultivation history. Genomewide identification and expression analysis of heat. A populus est resource for plant functional genomics pnas. This genomic information will enable comparative studies of tree root endophytes and the mechanisms of microbeplant associations.
A final draft sequence will be released in early 2005. We report molecular genetic linkage maps for an interspecific hybrid population of populus, a model system in foresttree biology. It is used for timber, and is notable as a model organism in plant biology. Forest service for its rapid growth under field conditions coyle et al. In july 2015, there were 81 different pseudomonas species that had at least one genome sequence. The populus trichocarpa genome has a haploid chromosome number of 19, and with over 400 mb is nearly four times larger than the genome of arabidopsis. Genome sequences of populus tremula chloroplast and. Integration of shotgun sequence assembly with genetic mapping enabled chromosomescale reconstruction of the genome. The genome download service in the assembly resource makes it easy to download data for multiple genomes without having to write scripts.
To identify heatresponsive mirnas at the genome wide level in populus, solexa sequencing was employed to sequence two libraries from populus tomentosa, treated and untreated by heat stress. The willow genome and divergent evolution from poplar. The chloroplast genomes of the five populus species are very similar. The sequencing was performed at the joint genome institute using the shotgun method. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones p. Copied from jgi phytozome wv94 is a populus deltoides marsh. Cytogenetic analysis of populus trichocarpa ribosomal dna, telomere repeat sequence, and markerselected bacs. Characterization of the complete chloroplast genomes of.
Extensive structural renovation of retrogenes in the. Efficient crisprcas9mediated targeted mutagenesis in. A second, older duplication event is indistinguishably coincident with the divergence of the populus and arabidopsis lineages from jgi the joint genome insitute and tuskan, et. We identified 106 retrogenes and found the majority 89% of them are associated with functional signatures in sequence evolution. We have established a github project site for source code management.
Complete genome sequence of a 2019 novel coronavirus sars. The complete chloroplast genome sequence of populus wilsonii and its phylogenetic analysis. Plantgdb download portal resources for plant comparative. Cytogenetic analysis of populus trichocarpa ribosomal. Genomic insights into salt adaptation in a desert poplar. Pdf the draft genome sequence of a desert tree populus pruinosa. Complete populus genome sequences are available for the nucleus p.
Jul 20, 2015 since the whole genome sequence of populus trichocarpa was released in 2006 16, extensive genomic resources are now available for functional genomics studies in this species, which has been used. The populus trichocarpa genome has a haploid chromosome number of 19, and with over 400 mb is nearly four times larger than the genome. Select plantgdb or any xgdb for genome browser data from the menu at left. Characterization of the complete chloroplast genomes of five. Retrieve the unmasked or softmasked genome sequence for a specific genome. Populus trichocarpa provide an opportunity to investigate this issue. Sep 15, 2016 when the poplar genome sequence, generated by the doe joint genome institute, was published in the september 15, 2006 issue of the journal science, we planted a commemorative sapling on our front lawn that was clonally propagated from the poplar or black cottonwood tree, populus trichocarpa, whose dna was used for the study. Through a process of hybrid genome assembly, a total of 464 m of the genome. Access to the dataset of these populus genome sequences. The poplar genome at 10 doe joint genome institute. With a genome of just over 500 million letters of genetic code, populus trichocarpa was sequenced eight times over to attain the highest quality standards. Functional and evolutionary genomic inferences in populus. Genotypingbysequencing for populus population genomics. The complete chloroplast genome sequence of populus davidiana dode.
To further advance evolutionary and functional genomic analyses in populus, we produced genome. More than 45,000 putative proteincoding genes were identified. The complete chloroplast genome sequence of populus mexicana was characterized from illumina pairend sequencing. The complete cp genome was 156,957 bp in length, containing a large singlecopy region lsc of 85,096 bp, and a small singlecopy region ssc of 16,563 bp, which were separated by a pair of 27,649 bp. The updated genomes ftp provides more uniformity across species. Populus trichocarpa was chosen as the first tree to be sequenced because of the relatively small size of its genome. Since the whole genome sequence of populus trichocarpa was released in 2006 16, extensive genomic resources are now available for functional genomics studies in this species, which. Comparative analysis of the complete chloroplast genomes of.
All six arabidopsis family members, populus trichocarpa members present in genbank or identified in the genome sequence, and selected genes from other species are included. Populus pruinosa is a large tree that grows in deserts and shows distinct differences in both morphology and adaptation compared to its sister species, p. The hardwood genomics project hosts genomes, transcriptomes, and annotations for forest trees and other angiosperm woody plant species. Linkage analysis from 93 of the 450 backcross progeny grown in the field for 15 years. Due to their high biomass yields, willows are promising sources for bioenergy crops.
Although this species has ecologically and economically important values, its genome sequence. Here, we report the draft genome sequence of larkinella sp. A second possibility is that populus retained more gene copies than salix following genome duplication. The processed sequences were mapped to reference genome sequences of populus trichocarpa. The populus genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily populus trichocarpa torr. Sequence analysis identified 4 conserved mirnas belonging to 30 mirna families, and 16 novel mirnas belonging to 14 families. Molecular linkage maps of the populus genome genome. One of korean populus species, called as hyunsasinamu mi populus alba x populus tremula var. Diversity of pseudomonas genomes, including populus. We have analyzed 102,019 populus ests that clustered into 11,885 clusters and 12,759 singletons.