Tim langdon at aberystwyth university we are sequencing the a. Lactuca serriola is the wild progenitor of cultivated lettuce lactuca sativa, and can be affected by lettuce downy mildew, one of the most serious diseases of lettuce. The nucleotide sequence of this genome was deposited into ncbi genbank under the accession cp017580. Lettuce lactuca sativa l overview lettuce lactuca sativa l. Complete chloroplast genome sequences have been very useful for understanding phylogenetic relationships in angiosperms at the family level and above, but there are currently large gaps in coverage. Agrobacteriummediated transformation of lettuce lactuca. The oat genome project avena sativa, avena eriantha, and. Transcriptomic analysis reveals the roles of gibberellin. Identification, genetic localization, and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce and wild relatives lactuca spp. Megablast is intended for comparing a query to closely related sequences and works best if the target percent identity is 95% or more but is very fast. The purpose of this study is to report the characterization of complete cp genome of g.
The genome assembly described in this paper is available for download and blast on coge, organism id36218, lactuca sativa lettuce and from ncbi under bioproject prjna173551 as soon as it is approved. Here we present a reference assembly for the species and family. Us20200029523a1 lactuca sativa with bremia lactucae. The complete genome sequence of the lactuca sativa lettuce. Discontiguous megablast uses an initial seed that ignores some bases allowing mismatches and is intended for crossspecies comparisons. Component of the parthenolide biosynthetic pathway.
Application of the trap technique to lettuce lactuca sativa l. Lettucerelated ncbi datasets taxonomical classification asteraceae cichorioideae lactucinae lactuca lactuca sativa ncbi lactuca sativa nucleotie sequences dataset ncbi lactuca sativa est sequences dataset ncbi lactuca sativa genes dataset ncbi lactuca sativa protein dataset. The lactuca sativa whole genome shotgun wgs project has the project accession afsa00000000. A set of 61 simple sequence repeat ssr markers was developed from the 19 523 lactuca sativa and lactuca serriola unigenes. It will also soon be available as part of the phytozome genome collection. The complete chloroplast genome sequence of helwingia. Members of the lettuce genome sequencing consortium. Here we describe the development of a plastid transformation system for lettuce, lactuca sativa l. Nov 25, 2015 elucidating the genetic basis of antioxidant status in lettuce lactuca. Application of the trap technique to lettuce lactuca sativa. Doublestranded rnas purified from cultivated lactuca sativa or wild l. The analysis of f 2 progeny and derived f 3 families of lactuca sativa segregating for resistance to corky root rot caused by rhizomonas suberifaciens permitted the identification of restriction fragment length polymorphism rflp and single nucleotide polymorphism snp markers linked to the recessive resistance gene cor.
Ncbi lactuca sativa nucleotie sequences dataset ncbi lactuca sativa est sequences dataset ncbi lactuca sativa genes dataset. Lactuca sativa seeds exhibit thermoinhibition, or failure to complete germination when imbibed at warm temperatures. Cyp71bl2 costunolide synthase lactuca sativa garden. The complete genome sequence of the lactuca sativa lettuce chloroplast conference paper in plant and cell physiology january 2004 with 246 reads how we measure reads. Genome assembly with in vitro proximity ligation data and wholegenome. Development of estssr markers for the study of population. Seven genomic libraries were prepared from dark grown seedlings of lactuca sativa cv. Microsatellite retrieval in lettuce lactuca sativa l. By using enriched genomic libraries, microsatellitecontaining sequences were isolated from lettuce lactuca sativa with high efficiency. The genome size has been estimated by flow cytometry to be 2. Hydroxylates germacrene a acid to 6alphahydroxygermacrne a acid, a precursor of sesquiterpene lactones that spontaneously.
A whole genome shotgun strategy was used to sequence and assemble the genome of l. We report the chloroplast genome for helwingia himalaica, the first in the distinctive family helwingiaceae and only the second genus to be sequenced in the order aquifoliales. Crop improvement and protection research unit, 1636 east alisal street, salinas, ca 93905, usa 2the genome center and department of plant sciences, university of california, 451. Complete chloroplast genome sequences of mongolia medicine. The complete chloroplast genome sequence of gentiana. The highpotency medical marijuana strain purple kush was used for sequencing. Chromosomal pseudomolecules of lactuca sativa var salinas constructed using v7 dovetail superscaffolds and genetic information from am interspecific ril mapping population. Over the past decades, there have been many controversies about the phylogeny of lactuca species due to their complex and diverse morphological charactersand insuf. The chloroplast dna was extracted with ctab and randomly cloned for dna sequencing. The frequency of codon usage was calculated from exon sequences of all proteincoding genes in the artemisia frigida genome. In order to further enhance lettucebreeding efforts, the team at keygene performed whole genome sequencing of two lettuce lines using the highyield, highthroughput promethion platform 1. Transgenic plastids offer unique advantages in plant biotechnology, including highlevel foreign protein expression. Compositae genome project database lactuca sativa homepage lettuce genechip project website.
Xxvii international horticultural congress ihc2006. Plantgdb download portal resources for plant comparative. Details oryza sativa indica group ensembl genomes 46. In addition to its agronomic importance, rice is an important model species for monocot plants and cereals such as maize, wheat, barley and sorghum. The nucleotide sequence of this genome was deposited into ncbi genbank under the accession cp017674. Genome assembly with in vitro proximity ligation data and whole genome triplication in lettuce. Draft genome sequence of salmonella enterica subsp. However, broad application of plastid genome engineering in biotechnology has been largely hampered by the lack of plastid transformation systems for major crops. This version of the project 01 has the accession number afsa0000, and consists of sequences afsa0001afsa01876110. Availability of dna sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Rapid identification of lettuce seed germination mutants by bulked segregant analysis and whole genome sequencing. It is the grain with the second highest worldwide production after zea mays.
Lettuce lactuca sativa is a major crop and a member of the large, highly successful compositae family of flowering plants. Search or download speciesparsed, public plant sequence data genbank and uniprot, or use our ftp server for batch download. This project is focused on generating a high quality draft whole genome sequence of lactuca sativa that is an economically important, representative species of the compositae family. The genus gentiana contains 362 species, but there are only two valuable complete cp genomes. Sequence determination and gene identification of lactuca sativa chloroplast genome in the inversion regions four cloned cpdna fragments 7. Us20200029523a1 lactuca sativa with bremia lactucae downy. The nucleotide sequence of this genome was deposited. Vick1 1usdaars, northern crop science laboratory, 7 north 18th street, fargo, nd 58105, usa. Two chloroplast dna inversions originated simultaneously. About the assembly from this site you can browse and download the whole genome sequence, predicted gene models, functional annotations, comparative alignments and more from the shulaev et al. Rapid identification of lettuce seed germination mutants. Its availability will aid the development of therapeutic marijuana strains with tailored cannabinoid profiles and provide a basis for the breeding of hemp with improved agronomic characteristics.
A dna construct containing the immunoglobulin gbinding protein a gene of staphylococcus aureus proa genetically fused to a nucleotide sequence encoding proinsulin pins was. For both samples, blast annotation revealed contigs with homology to betaflexiviridae family members. These activities involve complicated preparatory procedures like chloroplast dna isolation or. Elucidating the genetic basis of antioxidant status in. Request pdf on jan 1, 2004, h kanamoto and others published the complete genome sequence of the lactuca sativa lettuce chloroplast find, read and. Lettuce lactuca sativa is an important crop, with 74 billion harvested globally every year. Application of the trap technique to lettuce lactuca. The nucleotide sequence of this genome was deposited into. The tip of the iceberg sequencing the lettuce genome.
This project provides the assembled draft genome and transcriptome of cannabis sativa. Download one protein sequence per gene fasta proteome id i up000235145. Genus name comes from the latin word lac meaning milk in obvious reference to the milky plant sap. Development of molecular markers for markerassisted. Involved in the biosynthesis of germacrenederived sesquiterpene lactones pubmed. The current invention also relates to seed and other plant material obtainable from this plant as well as to a method for. Cultivar salinas and its derivatives are some of the most widely grown genotypes worldwide. Snpbased codominant markers for a recessive gene conferring. A total of 4,560 coding genes, 16 rrnas, 78 trnas, and 15 noncoding rnas were predicted. Genome assembly with in vitro proximity ligation data and. Here, we present the 3,795,952 bp complete genome sequence of the biofilmforming curtobacterium sp.
The file may contain a single sequence or a list of sequences. We have employed the method of enriched microsatellite libraries to develop 97 genomic ssr markers. All plantgdb sequences and associated data are available for search or download. With this approach, a sizeable fraction up to 55% of the clones contained a microsatellite. Select plantgdb or any xgdb for genome browser data from the menu at left. The genome of indica is very similar to that of japonica, which is generally restricted to temperate climes such as japan. The sequencing has been completed and the draft genome assembled into 15,471 scaffolds comprising 2. We report here the genome sequence of salmonella enterica subsp. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. Salinas reference genome author links open overlay panel bart verwaaijen a b daniel wibberg a johanna nelkner a miriam gordin a oliver rupp c anika winkler a andreas bremges a jochen blom c rita grosch. Genome assembly with in vitro proximity ligation data and whole.
Oryza sativa japonica rice is the staple food for 2. Here, we report the 3,508,491 bp complete genome sequence of microbacterium sp. The current invention concerns a lactuca sativa plant resistant to bremia lactucae, characterized in that the bremia resistance locus is linked to a genetic determinant and obtainable from the genome of a wild lactuca plant, preferably from the genome of lactuca serriola. Complete genome sequence of lettuce chordovirus 1 isolated. The data may be either a list of database accession numbers, ncbi gi numbers, or sequences in fasta format. From this site you can browse and download the whole genome sequence, predicted gene models, functional annotations, comparative alignments and more from the shulaev et al. The full genome sequence of the isolate from cultivated lettuce jg1 was completed 8,536 nucleotides nt, excluding. Efficient and stable transformation of lactuca sativa l. These data will aid in the anchoring of the hexaploid aaddcc a. We collaborated with bgi, shenzhen to sequence the lettuce genome l. However only a very limited number of microsattelitebased markers are publicly available.
Salinas with funding from an international consortium of ten breeding companies. Inthis study we provide the most extensive molecular. Lettucerelated ncbi datasets taxonomical classification. Oryza sativa indica is one of the two most commonly cultivated subspecies of rice along with o.
An ftp server is also available for batch download of either public sequence or put assembly data. Lettuce lactuca sativa is a valuable crop in the united states and worldwide. A breeding program to improve the nutritional quality of lettuce lactuca sativa l. Background the chloroplast cp genome is useful in plant systematics, genetic diversity analysis, molecular identification and divergence dating. Garden lettuce, or lactuca sativa, is the plant species that includes a salad bars worth of lettuce types, ranging from iceberg to romaine. Select a link in the resources box for further details. The complete nucleotide sequence of the chloroplast genome of lactuca sativa lettuce has been determined. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. The draft genome and transcriptome of cannabis sativa. Lactuca sativa lactuca sativa although the exact origins of the lettuce are unknown it was certainly known to the greeks and romans, and has been grown in britain since at least the middle of the sixteenth century.
Genomic libraries were prepared from total genomic dna. Sequence data are refreshed every 4 months, coinciding with oddnumbered genbank bimonthly version releases. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or bac clones. This is in addition to the popseq based work done at aberystwyth university. The chloroplast was isolated from 1monthold seedlings by two stepwise percoll density gradient centrifugation. Development of molecular markers for markerassisted selection of dieback disease resistance in lettuce lactuca sativa i. The complete genome sequence of the lactuca sativa. Use the browse button to upload a file from your local disk. High temperatures induce a transition from vegetative to reproductive growth, and an extended period at high temperatures causes premature bolting, which seriously affects the quality and economic value of the product. Ncbi, or phytozome to download the complete genome sequence as below. Plantgdbs version update is named after the corresponding genbank release, e. The previous chapters were limited to phenetic analyses ofl. The availability of the cannabis sativa genome enables the study of a multifunctional plant that occupies a unique role in human culture.
118 831 934 138 689 965 1163 22 323 1018 352 1657 258 1591 1621 1310 1269 552 1482 1305 1236 1168 1236 1216 723 632 1124 548 966 1313 1516 51 346 390 568 1421 877 1271 902 825 247 931 551 973