156 research outputs found
Potential of platinum standard reference genomes to exploit natural variation in the wild relatives of rice
No full textAs the world’s population expands from 7.6 billion to 10 billion over the next 30 years, scientists and farmers across the globe must explore every angle necessary to provide a safe, stable and sustainable food supply for generations to come. Rice, and its wild relatives in the genus Oryza, will play a significant role in helping to solve this 10 billion people question due to its place as a staple food for billions. The genus Oryza is composed of 27 species that span 15 million years of evolutionary diversification and have been shown to contain a plethora of untapped adaptive traits, e.g., biotic and abiotic resistances, which can be used to improve cultivated rice. Such traits can be introduced into cultivated rice, in some cases by conventional crossing, and others via genetic transformation and gene editing methods. In cases where traits are too complex to easily transfer to cultivated rice [e.g., quantitative trait loci (QTL)], an alternative strategy is to domesticate the wild relative that already contains the desired adaptive traits – i.e., “neodomestication”. To utilize the Oryza genus for crop improvement and neodomestication, we first need a set of genomic resources that can be used to efficiently identify, capture, and guide molecular crop improvement. Here, we introduce the concept of platinum standard reference genome sequences (PSRefSeq) – a new standard by which contiguous near-gap free reference genomes can now be produced. By having a set of PSRefSeqs for every Oryza species we set a new bar for how crop wild relatives can be integrated into crop improvement programs
Scoping and targeted reviews to support development of SPIRIT and CONSORT extensions for randomised controlled trials with surrogate primary endpoints: protocol
No full textIntroduction: Using a surrogate endpoint as a substitute for a primary patient-relevant outcome enables randomised controlled trials (RCTs) to be conducted more efficiently, that is, with shorter time, smaller sample size and lower cost. However, there is currently no consensus-driven guideline for the reporting of RCTs using a surrogate endpoint as a primary outcome; therefore, we seek to develop SPIRIT (Standard Protocol Items: Recommendations for Interventional Trials) and CONSORT (Consolidated Standards of Reporting Trials) extensions to improve the design and reporting of these trials. As an initial step, scoping and targeted reviews will identify potential items for inclusion in the extensions and participants to contribute to a Delphi consensus process.
Methods and analysis: The scoping review will search and include literature reporting on the current understanding, limitations and guidance on using surrogate endpoints in trials. Relevant literature will be identified through: (1) bibliographic databases; (2) grey literature; (3) handsearching of reference lists and (4) solicitation from experts. Data from eligible records will be thematically analysed into potential items for inclusion in extensions. The targeted review will search for RCT reports and protocols published from 2017 to 2021 in six high impact general medical journals. Trial corresponding author contacts will be listed as potential participants for the Delphi exercise.
Ethics and dissemination: Ethical approval is not required. The reviews will support the development of SPIRIT and CONSORT extensions for reporting surrogate primary endpoints (surrogate endpoint as the primary outcome). The findings will be published in open-access publications
Deciphering UBP1C Function: Phase Separation, RNA Binding, and Its Role in Plant Stress Responses
No full textPlants, due to their sessile nature, are equipped with intricate molecular mechanisms to respond to environmental stresses, including the formation of stress granules (SGs), membrane-less organelles that sequester translationally repressed mRNAs and proteins during stress. Assembly of SGs is through a phenomenon known as liquid-liquid phase separation (LLPS), mediated by multivalent protein and RNA interactions. Although the predominance of SGs as a survival mechanism has been established in plants, understanding the general composition and its molecular drive remains poorly understood. Our research focuses on unraveling the molecular intricacies of plant SGs, with a particular emphasis on the Oligouridylate binding protein 1c (UBP1C), a known SG-associated protein. UBP1C, characterized by its tri-RNA-Recognition Motifs , has previously been identified as a key player in hypoxia-induced SGs formation, yet its precise role and molecular characteristics remain elusive. Using a multi-faceted approach, we explore the contributions of UBP1C RRM domains to SG recruitment, dynamics, and interactome profile under heat stress. Deletion constructs targeting UBP1C’s RRMs revealed the indispensability of these domains for localization to SGs under heat stress. Our findings further highlight how UBP1C’s modular domains mediate both RNA binding and LLPs, hypothesizing the facilitation of UBP1C to recruit specific mRNAs to SGs, thereby influencing SG RNA composition and functionality. Ongoing work aims to characterize RNA and protein composition of SGs in UBP1C mutants and explore how UBP1C-mediated RNA sequestration influences mRNA stability and translational control during stress
De novo assembly of the Tamarindus indica genome as part of the Kingdom of Saudi Arabia Native Genome Project
No full textThe Kingdom of Saudi Arabia Native Genome project aims to generate genomic resources for all the plants, animals, and associated microbiome species in the Kingdom. Tamarindus indica was pointed out by the MEWA as an endangered native species in the KSA and forms part of the first 15 plant species to be studied in the NGP. A voucher tree was identified in the Rijal Almaa region, from which leaf samples were collected. HMW DNA was extracted from this tissue and sequenced using CCS with the Pac-Bio Sequel II platform. The raw data obtained from the sequencing was assembled using HIFIASM, contaminant contigs were removed, and the 15 largest contigs were selected as the primary T. indica assembly. The genome sequence of Sindora glabra was used as reference guide for primary scaffolding, and T. indica optical maps were used for super-scaffolding. Secondary scaffolding utilized Hi-C data to produce a chromosome level assembly of the T. indica genome. Transposable element analysis and a preliminary annotation were performed on the final assembly. This project represents the first step in studying T. indica for the NGP. The final assembly can be used as a foundation for more genetic studies on this species, as a possible reference for other legume species from the Detarioideae family, and for Neo-domestication and reforestation. The pipeline developed for this project can also be used as a template for sequencing and assembling the remaining species in the NGP
Discovering candidate gene loci for grain traits using Rice (Oryza sativa) pan-genomic approaches
No full textRice is the staple food for half the world’s population, necessitating the production of at least 100M metric tons annually by 2050 to meet rising demand. Breeding rice varieties with high yield, better quality, and stress resistance is essential for food security. Genomic studies, such as the 3K-RGP, significantly contributed to understanding adaptation, genetic conservation, and gene mapping using the IRGSP RefSeq. However, a single reference cannot capture the extensive genetic diversity of the 3K-RGP, highlighting the need for a pan-genome approach. In this study, I detected SNPs and conducted GWAS using 16 PSRefSeqs, representing the genetic diversity of the 3K- RGP. Comparative genome analysis showed that ~36.5Mb of sequence is absent in a single genome but present in at least one of the other 15 PSRefSeqs. To fully discover the genetic variants of the 3K-RGP, the whole dataset was aligned against the 16 PSRefSeqs and identified 438.4M SNPs, averaging 27.3M variants per genome. Among these, 1.3M SNPs were novel and absent in IRGSP. GWAS was conducted for grain length, width, and weight using the LD pruned dataset and each PSRefSeq as reference. IRGSP identified 5, 10, and 12 associations, while the other 15 PSRefSeqs identified an additional 19, 5, and 7 associations for grain length, weight, and width, respectively. This highlights the importance of using subpopulation-aware references for comprehensive genetic mapping. Lastly, to validate the candidate peaks, I conducted candidate region-based GWAS using an unpruned dataset. A total of 16, 4, and 5 out of 19, 5, and 7 peaks revealed more associations without pruning in grain length, weight, and width, respectively. For example, a unique association was identified for grain length on Chr12:10784520 (1 SNP) using cAus1:N22 after LD pruning, whereas analysis without pruning identified seven associations on Chr12:10,818,211-11,636,314. Comparative gene analysis in this region revealed that ten genomes from the PSRefSeq panel have unique genes present, but the association was only observed in cAus1:N22, where a single unique gene, OsN22_12G009891, was found. The function of this gene was identified as hypothetical and requires functional validation. This study demonstrates the advantage of detecting natural variants and conducting GWAS using a pan-genome over a single reference genome (GJ-temp:IRGSP)
Draft Assembly and Baseline Annotation of the Ziziphus spina-christi Genome
No full textThird generation sequencing has revolutionized our understanding of genomics, and enabled the in-depth discovery of complex plant genomes. In this project I aimed to assemble and annotate the genome of Z. spina-christi, a native plant to Saudi Arabia, as part of the the Kingdom of Saudi Arabia Native Genome Project established at the Center for Desert Agriculture at KAUST. Initially, a voucher plant was selected from the Al Lith region of Western Saudi Arabia. Fresh leaf tissue was collected for high-molecular weight (HMW) DNA extraction, as well as seed for greenhouse propagation. After HMW DNA extraction, library construction and PacBio HiFi sequencing, I generated a de novo assembly of the Z. spina-christi genome using the Hifiasm assembler, which yielded a 1.9 Gbp long assembly with high levels of duplication. The assembled contigs were scaffolded using an in-house script based on the software RagTag, that yielded a 406 Mbp long scaffold with 331 gaps (85.45% of estimated genome size). A preliminary analysis of the assembly for transposable elements revealed a TE content of 32.36%, with Long Terminal Repeats retrotransposons (LTR-RTs) being the major contributor to the total TE content. Basline annotation was completed using Omicsbox revealing 18,330 functional genes. This work describes the first genomic resource for the desert plant Z. spina-christi. To improve the assembly, I suggest the use of scaffolding using optical mapping, long Nanopore reads and Hi-C data to capture the spatial organization of the genome. Further experimental, genetic and TEs analysis is needed to explore the plant’s resilience to abiotic stresses in extreme environments
Assembly of Two CCDD Rice Genomes, Oryza grandiglumis and Oryza latifolia, and the Study of Their Evolutionary Changes
No full textEvery day more than half of the world consumes rice as a primary dietary resource. Thus, rice is one of the most important food crops in the world. Rice and its wild relatives are part of the genus Oryza. Studying the genome structure, function, and evolution of Oryza species in a comparative genomics framework is a useful approach to provide a wealth of knowledge that can significantly improve valuable agronomic traits. The Oryza genus includes 27 species, with 11 different genome types as identified by genetic and cytogenetic analyses. Six genome types, including that of domesticated rice - O. sativa and O. glaberrima, are diploid, and the remaining 5 are tetraploids. Three of the tetraploid species contain the CCDD genome types (O. grandiglumis, O. latifolia, and O. alta), which arose less than 2 million years ago. Polyploidization is one of the major contributors to evolutionary divergence and can thereby lead to adaptation to new environmental niches. An important first step in the characterization of the polyploid Oryza species is the generation of a high-quality reference genome sequence. Unfortunately, up until recently, the generation of such an important and fundamental resource from polyploid species has been challenging, primarily due to their genome complexity and repetitive sequence content. In this project, I assembled two high-quality genomes assemblies for O. grandiglumis and O. latifolia using PacBio long-read sequencing technology and an assembly pipeline that employed 3 genome assemblers (i.e., Canu/2.0, Mecat2, and Flye/2.5) and multiple rounds of sequence polishing with both Arrow and Pilon/1.23. After the primary assembly, sequence contigs were arranged into pseudomolecules, and homeologous chromosomes were assigned to their respective genome types (i.e., CC or DD). Finally, the assemblies were extensively edited manually to close as many gaps as possible. Both assemblies were then analyzed for transposable element and structural variant content between species and homoeologous chromosomes. This enabled us to study the evolutionary divergence of those two genomes, and to explore the possibility of neo-domesticating either species in future research for my PhD dissertation
De novo assembly of the Haloxylon persicum genome as a part of the KSA Native Genome Project
No full textHaloxylon persicum is a xerophytic desert tree that grows mostly in deserts
in West and Central Asia. This tree is very tolerant to the harsh conditions
of deserts, mainly drought and heat. As a part of the Kingdom of Saudi Arabia
Native Genome Project, a voucher specimen was identified, and the genome of this
plant was sequenced, assembled, and annotated. The chromosome level assembly
was performed using the integration of PacBio Hifi reads and Bionano optical
maps, resulting in 9 chromosome-sized molecules that only exhibit 3 gaps located
in highly repetitive regions. The annotation of the transposable elements in
the genome shows that more than 55% of the genome consists of transposable
elements. Moreover, genes were predicted using Iso-seq and RNA-seq and annotated
using publicly available protein databases, resulting in the identification of more
than 45,000 predicted genes, of which ≈ 10,000 have RNA evidence. The genome
assembly and annotation of Haloxylon persicum will: provide valuable insight
on the evolutionary history of desert plants, aid in discovering the mechanisms
developed by this species to cope with the extreme desert conditions and unveil
the possibilities and opportunities of neo-domesticating this plant. Furthermore,
this assembly can serve as a reference for assembling other plant species in the
KSA Native genome project or any other project worldwide
10,000 Rice Genome Project
No full textThe 10K-RGP samples were sequenced using 150 bp paired-end reads on an Illumina NovaSeq 6000 platform. This yielded approximately 30 TB of raw data, comprising 541 billion paired-end reads and totaling 81,256 gigabases.
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Genetic interaction between BIRD proteins and JA signaling pathway in tomato
No full textJasmonic acid (JA) signaling is important for regulating plant defense responses and developmental processes. However, the specific interactions between tomato BIRD/IDD transcription factors and JA signaling pathways remain poorly understood. Using CRISPR/Cas9 genome editing, my study generated tomato mutant lines targeting key JA signaling genes—Coronatine Insensitive 1 (COI1), and MYC transcription factors (MYC1, MYC2; basic helix-loop-helix transcription factors)—in wild-type (WT) and sljkd1 mutant backgrounds. JACKDAW (JKD), encoded by sljkd1, is a member of the BIRD transcription factor family involved in developmental regulation. Phenotypic analysis confirmed previously described developmental alterations, such as prolonged flowering and reduced fruit set, associated with coi1 mutations. Transcriptional studies using histochemical GUS staining and promoter-driven luciferase assays demonstrated that tomato BIRD proteins selectively regulate key genes involved in hormone signaling (JA, SA) and developmental processes. These findings provide novel insights into how BIRD proteins modulate hormone-dependent growth-defense trade-offs. Future research will focus on generating homozygous, Cas9-free mutant lines to further clarify the mechanisms underpinning these regulatory interactions
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