Expression Atlas update: from tissues to single cells

Nucleic Acids Research, Год журнала: 2019, Номер unknown

Опубликована: Окт. 16, 2019

Abstract Expression Atlas is EMBL-EBI’s resource for gene and protein expression. It sources compiles data on the abundance localisation of RNA proteins in various biological systems contexts provides open access to this research community. With increased availability single cell RNA-Seq datasets public archives, we have now extended with a new added-value service display expression cells. Single Cell was launched 2018 currently includes 123 studies from 12 species. The website can be searched by genes within or across species reveal experiments, tissues types where expressed under which conditions it marker gene. Within each study, cells visualized using pre-calculated t-SNE plot coloured different features clusters based experiment, there are links downloadable files, such as quantification matrices, clustering results, reports protocols associated metadata, assigned types.

Язык: Английский

---

Mass-spectrometry-based draft of the Arabidopsis proteome

Nature, Год журнала: 2020, Номер 579(7799), С. 409 - 414

Опубликована: Март 11, 2020

Язык: Английский

---

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

eLife, Год журнала: 2020, Номер 9

Опубликована: Янв. 14, 2020

Understanding genome organization and gene regulation requires insight into RNA transcription, processing modification. We adapted nanopore direct sequencing to examine from a wild-type accession of the model plant Arabidopsis thaliana mutant defective in mRNA methylation (m6A). Here we show that m6A can be mapped full-length mRNAs transcriptome-wide reveal combinatorial diversity cap-associated transcription start sites, splicing events, poly(A) site choice tail length. Loss 3’ untranslated regions is associated with decreased relative transcript abundance 3′ end formation. A functional consequence disrupted lengthening circadian period. conclude complexity modification single molecule reads. These findings refine annotation. Further, applying this approach less well-studied species could transform our understanding what their genomes encode.

Язык: Английский

---

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana

Cell, Год журнала: 2019, Номер 178(5), С. 1260 - 1272.e14

Опубликована: Авг. 1, 2019

Infectious disease is both a major force of selection in nature and prime cause yield loss agriculture. In plants, resistance often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins their effects on the host. Consistent with extensive balancing positive selection, NLRs are encoded one most variable gene families but true extent intraspecific NLR diversity has been unclear. Here, we define nearly complete species-wide pan-NLRome Arabidopsis thaliana based sequence enrichment long-read sequencing. The largely saturates approximately 40 well-chosen wild strains, half being present accessions. We chart architectural diversity, identify new architectures, quantify selective forces act specific domains. Our study provides blueprint for defining pan-NLRomes.

Язык: Английский

---

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

Nature Communications, Год журнала: 2018, Номер 9(1)

Опубликована: Фев. 1, 2018

Abstract The handheld Oxford Nanopore MinION sequencer generates ultra-long reads with minimal cost and time requirements, which makes sequencing genomes at the bench feasible. Here, we sequence gold standard Arabidopsis thaliana genome (KBS-Mac-74 accession) on sequencer, assemble using typical consumer computing hardware (4 Cores, 16 Gb RAM) into chromosome arms (62 contigs an N50 length of 12.3 Mb). We validate contiguity quality assembly two independent single-molecule technologies, Bionano optical maps Pacific Biosciences Sequel sequencing. new A. KBS-Mac-74 enables resolution a quantitative trait locus that had previously been recalcitrant to Sanger-based BAC approach. In summary, demonstrate even when purpose is understand complex structural variation single region genome, complete becoming simplest way achieve this goal.

Язык: Английский

---

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

Nucleic Acids Research, Год журнала: 2017, Номер 45(9), С. 5061 - 5073

Опубликована: Апрель 5, 2017

Alternative splicing generates multiple transcript and protein isoforms from the same gene thus is important in expression regulation. To date, RNA-sequencing (RNA-seq) standard method for quantifying changes alternative on a genome-wide scale. Understanding current limitations of RNA-seq crucial reliable analysis lack high quality, comprehensive transcriptomes most species, including model organisms such as Arabidopsis, major constraint accurate quantification isoforms. address this, we designed novel pipeline with stringent filters assembled Reference Transcript Dataset Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts 34 212 genes. Extensive experimental validation showed that AtRTD2 its modified version, AtRTD2-QUASI, use Quantification Alternatively Spliced Isoforms, outperform other available analysis. This strategy can be implemented species to build transcript-level analyses.

Язык: Английский

---

Genome evolution and diversity of wild and cultivated potatoes

Nature, Год журнала: 2022, Номер 606(7914), С. 535 - 541

Опубликована: Июнь 8, 2022

Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have potential to revolutionize future potato production1-4. So far, relatively few studies examined genome evolution diversity wild cultivated landrace potatoes, which limits application their breeding. Here we assemble 44 high-quality genomes from 24 20 accessions that representative Solanum section Petota, tuber-bearing clade, as well 2 neighbouring section, Etuberosum. Extensive discordance phylogenomic relationships suggests complexity evolution. We find substantially expanded its repertoire disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative effect tuber-based propagation strategies genome. discover a transcription factor determines tuber identity interacts mobile tuberization inductive signal SP6A. also identify 561,433 high-confidence structural variants construct map large inversions, provides insights for improving inbred lines precluding linkage drag, exemplified by 5.8-Mb inversion associated carotenoid content tubers. This study will accelerate enrich our understanding biology global staple crop.

Язык: Английский

---

An m⁶A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis

The Plant Cell, Год журнала: 2018, Номер 30(5), С. 952 - 967

Опубликована: Апрель 11, 2018

Methylation of N6-adenosine (m6A) in mRNA is an important posttranscriptional gene regulatory mechanism eukaryotes. m6A provides a binding site for effector proteins ("readers") that influence pre-mRNA splicing, degradation, or translational efficiency. YT521-B homology (YTH) domain are readers with established functions animals. Plants contain more YTH than other eukaryotes, but their biological importance remains unknown. Here, we show the cytoplasmic Arabidopsis thaliana EVOLUTIONARILY CONSERVED C-TERMINAL REGION2/3 (ECT2/3) required correct timing leaf formation and normal morphology. These depend fully on intact sites ECT2 ECT3, indicating they function as readers. Mutation close homolog, ECT4, enhances delayed emergence morphology defects ect2/ect3 mutants, all three ECT expressed at shoot apex young seedlings division zone developing leaves. ECT3 also highly early stages trichome development morphology, previously reported itself. Overall, our study establishes relevance m6A-YTH module execution plant organogenesis.

Язык: Английский

---

The Chinese pine genome and methylome unveil key features of conifer evolution

Cell, Год журнала: 2021, Номер 185(1), С. 204 - 217.e14

Опубликована: Дек. 28, 2021

Conifers dominate the world's forest ecosystems and are most widely planted tree species. Their giant complex genomes present great challenges for assembling a complete reference genome evolutionary genomic studies. We 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) revealed that its size is mostly attributable to huge intergenic regions long introns with high transposable element (TE) content. Large genes exhibited higher expressions levels. Despite lack recent whole-genome duplication, 91.2% were duplicated through dispersed expanded gene families mainly related stress responses, which may underpin conifers' adaptation, particularly in cold and/or arid conditions. The reproductive regulation network distinct compared angiosperms. Slow removal TEs high-level methylation have contributed expansion. This study provides insights into conifer evolution resources advancing research on adaptation development.

Язык: Английский

---

An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2019, Номер unknown

Опубликована: Сен. 14, 2019

Abstract The original Heinz 1706 reference genome was produced by a large team of scientists from across the globe variety input sources that included 454 sequences in addition to full-length BACs, BAC and fosmid ends sequenced with Sanger technology. We present here latest tomato (SL4.0) assembled de novo PacBio long reads scaffolded using Hi-C contact maps. assembly validated Bionano optical maps 10X linked-read sequences. This is highly contiguous fewer gaps compared previous builds almost all scaffolds have been anchored oriented 12 chromosomes. found more repeats versions one largest repeat classes identified are LTR retrotransposons. also describe updates annotation since last publication. corresponding ITAG4.0 has 4,794 novel genes along 29,281 preserved ITAG2.4. Most updated extensions 5’ 3’ UTRs resulting doubling annotated per gene. can be accessed SGN through BLAST database, Pathway database (SolCyc), Apollo, JBrowse browser FTP available at https://solgenomics.net .

Язык: Английский

---