Biology subjects

Iqbal, S.

Publications and source records attributed to Iqbal, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Transient transcriptomic rejuvenation during intestinal and liver regeneration in mice

Aging and regeneration are fundamental biological processes, but the relationship between them is poorly understood. During intestinal regeneration, adult epithelial cells reactivate developmental programs that support repair. To investigate if this plasticity alters tissue biological age, we developed and validated intestinal tissue and epithelium-specific transcriptomic aging clocks. Across various regeneration models, epithelial states were predicted by these clocks to be younger than controls. Their expression changes were also negatively associated with intestinal aging signatures. The resulting younger state was characterized by YAP-associated regeneration and reduced mature enterocyte identity. In a separate irradiation model, the predicted epithelial age first increased, then fell at the peak of regeneration and later increased again during recovery. The pace of this response differed with host age. In a chemotherapy-induced injury model, epithelium in young animals also entered this younger state earlier and then returned to its preinjury state during recovery. Old epithelium responded later, but also reversibly transitioned through a rejuvenated state. Further spatial transcriptomic analyses linked lower epithelial age with regeneration in selected injured and tumor-associated regions. In addition, liver regeneration after partial hepatectomy in old animals also led to a decreased transcriptomic age, accompanied by pathway changes negatively associated with aging signatures. Overall, these findings suggest that mammalian regeneration is associated with a transient reduction in biological age, whose timing and persistence depend on tissue, host age and the course of repair.

cell biology↗

bioRxiv2026

Systemic control and inter-organ communication of ovarian aging

Whether ovarian aging is intrinsic and unidirectional or dynamically regulated by systemic context remains an open question for fertility and women's healthspan. To address it, we developed a mouse ovarian transcriptomic aging clock (OvaAge) and applied it, together with published transcriptomic, epigenetic and pathway-resolved DNA methylation (PathAge) clocks, multi-omic analyses and reproductive outcomes, to new reciprocal heterochronic ovary transplantation and parabiosis experiments. Ovarian molecular age shifted in both directions: aged ovaries became younger in young hosts and young ovaries became older in aged hosts, and in each case the shift was partial across transcriptomic, epigenetic and pathway-resolved measures. Ovaries from 13-month-old C57BL/6J donors supported full-term pregnancies and live births at 17-18 months of age when transplanted into young hosts, but not when transplanted into old hosts, and young ovaries supported live births in 17-18-month-old recipients. Donor ovary age altered the transcriptomic age of the uterus in both directions, while young ovaries also lowered the transcriptomic age of aged liver and brain, identifying the ovary as an active node within an inter-organ aging network. Across unilateral and bilateral transplantation and parabiosis, an older environment increased inflammatory gene expression in the ovary, whereas a younger environment reduced it and increased mitochondrial and biosynthetic programs. Integration of methylation, expression and cell-type markers linked these changes to declining oocyte-associated programs and an expanding stromal compartment enriched for multinucleated giant cells (MNGCs). MNGC-rich regions formed a reversibly remodeled, focally aged niche with distinct spatial metabolic features, and a related macrophage expression signature was detected in human ovaries. Together, these findings identify ovarian aging as a modular, bidirectionally plastic process that is regulated by the systemic environment and point to tractable intervention points.

systems biology↗

bioRxiv2026

First detected incursions of avian influenza H5N1 clade 2.3.4.4b into mainland Australia from the Southern Ocean

High pathogenicity avian influenza H5N1 clade 2.3.4.4b has caused a panzootic of devastating impact to poultry and wildlife globally. The Australian continent and broader Oceania until recently remained the last major region without confirmed detections. Here we report the first H5N1 clade 2.3.4.4b detections from two live seabirds - a brown skua and a southern giant petrel - found on the south coast of Western Australia in June 2026. Virus genome sequencing showed that both viruses were most closely related to H5N1 viruses detected recently on sub-Antarctic islands in the Southern Indian Ocean. In time-calibrated phylogeographic analyses, both viruses sampled in Western Australia clustered with viruses from Heard Island, a sub-Antarctic external territory of Australia. Ancestral location reconstruction also identified Heard Island as the most probable source location, although unsampled intermediate locations cannot be excluded. The two Western Australian detections were estimated to be independent incursions from Heard Island, rather than local transmission on mainland Australia. There was no evidence of reassortment with endemic avian influenza viruses in Australia, and both virus sequences retained key avian-like genetic markers and lacked known substitutions for reduced antiviral susceptibility. These detections revealed a Southern Ocean pathway of recurrent H5N1 incursions into Australia, highlighting the risk of potential establishment on the mainland and the need for heightened surveillance and rapid, nationally-coordinated, virus genomic characterisation.

microbiology↗

bioRxiv2026

Causally measuring aging and rejuvenation through transcriptomic damage

Aging is caused, fully in large part, by the progressive accumulation of damage, yet quantifying age-related damage across tissues and conditions remains a challenge. Here, we present a computational framework to quantify damage from standard RNA-sequencing data. It captures four classes of aberrant transcript structures, including premature termination upon intron retention, domain-disrupting splice variants, repeat elements, and gene fusion events, each reflecting distinct forms of RNA integrity loss. Using this method, we revealed a robust age-associated increase in transcriptomic damage across tissues. To integrate these measurements into a unified biomarker, we constructed a transcriptomic damage-based aging (tDamAge) clock using machine learning models trained across mouse tissues or human peripheral blood. It could predict age and detect transcriptomic shifts under both pro-aging and anti-aging conditions. Progeroid models exhibited accelerated tDamAge, whereas interventions such as caloric restriction, rapamycin, and methionine restriction lowered tDamAge. Cross-dataset analysis showed that diverse anti-aging interventions converge on shared transcriptomic signatures, particularly RNA processing and chromatin organization pathways, and these age-associated patterns could be reversed by interventions. We further identified elevated damage age acceleration in Alzheimers disease and observed rejuvenation-like reductions during embryonic development. Together, our findings establish transcriptomic damage as a causal, quantifiable and biologically interpretable feature of aging and demonstrate that tDamAge could detect age progression, acceleration, deceleration, and reversal.

bioinformatics↗

bioRxiv2026

Coherent Structured Illumination Microscopy with Enhanced Optical Sectioning

Coherent structured illumination microscopy (c-SIM) is a synthetic aperture optical technique for sub-diffraction limit imaging that extends the utility of traditional SIM to non-fluorescent samples. Here, we present a complementary 5-beam implementation of c-SIM that provides enhanced optical sectioning compared to conventional quadrupolar illumination. Since our approach detects intensity images due to coherent light scattering, it avoids the complications associated with detecting complex fields. Through comparative measurements on calibration samples and live microalgae, we show that 5-beam c-SIM effectively suppresses coherent defocus effects, improving image quality while simultaneously providing a 2-fold lateral resolution improvement.

bioengineering↗

bioRxiv2026

Human Proteome-wide Mechanistic Interpretation of Missense Variants through Protein Feature Enrichment Score

Missense variant interpretation remains a central challenge in clinical and medical genetics, with most observed variants being variants of uncertain significance (VUS). Computational variant effect predictors can achieve high pathogenicity classification performance, but without revealing the underlying mechanism and a translatable interpretation. Here we present the Protein Feature Enrichment Score (PFES), which quantifies the molecular context of missense variants through statistical enrichment of 103 protein structural, functional, and physicochemical features across 85,321 pathogenic and 130,719 control variants spanning 20 protein functional classes. We show that the protein feature (PF) enrichment patterns of variants are conserved within functional classes and vary substantially across classes, both in magnitude and directions depending on functional context. PFES not only partitions variants into PF-Enriched (pathogenic-like), PF-Neutral, and PF-Depleted (benign-like) categories but also provides a mechanistic interpretation by decomposing the score into subscores from biologically interpretable protein feature attributes. We demonstrate that PFES shows a high concordance with VUS reclassification and prioritization: across 596 genes, pathogenicity-leaning VUS-high variants were seven-fold enriched in PF-Enriched variants. PFES decomposition further revealed that loss-of-function and gain-of-function variants are distinguished by disproportionate enrichment of protein-protein interaction features in the latter. We computed PFES across 223 million possible missense variants (17.7% PF-Enriched) and built a publicly available resource that addresses not just whether a variant is pathogenic, but which protein characteristics are disrupted. Proteome-wide application across 20,153 genes prioritizes established rare disease genes and nominates therapeutically amenable targets whose pathogenic variation is driven by interpretable structural and functional protein feature disruption. One Sentence SummaryPFES is a proteome-wide resource to quantify the protein context of missense variants, enabling mechanistically transparent variant interpretation.

bioinformatics↗

bioRxiv2026

Do drugs with biliary toxicity cause cholangiocarcinoma?

AO_SCPLOWBSTRACTC_SCPLOWMany commonly used therapeutic drugs cause biliary toxicity, but it is unclear if they are directly responsible for the increasing incidence of cholangiocarcinoma (CCA). We tested experimentally and analyzed through a cohort approach whether drugs, such as the commonly used antibiotic Augmentin, which is a poster-child of biliary toxicity, are causally linked to CCA development. Using sophisticated analytical tools in cholangiocytes, including single extracellular vesicle (EV) analysis, we found no evidence that Augmentin increases the cholangiocyte malignancy marker YAP1 or phospho-YAP1. Furthermore, we analyzed the CCA incidence in our healthcare system and determined it to be 0.0932% (Augmentin group) and 0.0799% (amoxicillin control group). Although the Augmentin group showed a numerically higher CCA incidence, the association did not reach statistical significance (RR = 1.1669, 95% CI 0.6200-2.1961; Fishers exact test, P = 0.7493). Similarly, we found no evidence for cholangiocarcinoma development with other commonly used drugs, including chlorpromazine, floxuridine, 5-fluorouracil, flucloxacillin and terbinafine. We conclude that there is no direct causal relationship between clinical Augmentin doses and CCA development.

cancer biology↗

bioRxiv2025

Adenylyl cyclase 9: fundamental change of regulation in vertebrates and gene sub-functionalization after teleost-specific whole-genome duplication

Adenosine 3:5 monophosphate (cAMP) is a ubiquitous signalling molecule generated by the adenylyl cyclase family of proteins which is encoded by ten genes. The biological significance of this diversity is not well understood. In mammals, transmembrane adenylyl cyclase 9 (AC9) is resistant to regulation by heterotrimeric G proteins. A major facet of this resistance is auto-inhibition -- in the presence of activated Gs, AC9 is inhibited by its C-terminal domain. Here, we examined the natural evolution of this seemingly paradoxical control mechanism. At the primary sequence level, the hallmarks of auto-inhibition are apparent in all vertebrates, none are found in invertebrates. Teleost-specific genome duplication (TGD) resulted in adcy9 ohnologs, one of which lacked the hallmarks of auto-inhibition. This was confirmed in functional assays upon cloning and heterologous expression of the requisite cDNAs. The tissue distributions of the adcy9 ohnologs in teleost species also pointed to their sub-functionalization. Above all, auto-inhibited adcy9 was largely restricted to the brain indicating a fundamental role in brain development or function. Our findings document a quantum leap of the regulation of the enzymatic activity of AC9 in vertebrates and the potency of TGD to meet an adaptational challenge through functionally diversified ohnologs.

evolutionary biology↗

bioRxiv2025

Reduced CSF1R expression in myeloid cells has limited impact on chronic lymphocytic leukemia progression

Targeting the colony-stimulating factor 1 receptor (CSF1R) to remove tumor-associated macrophages is being explored as cancer therapy. This strategy may be relevant for chronic lymphocytic leukemia (CLL), which strongly depends on support from myeloid cells. However, it is unclear how CSF1R expression affects the CLL microenvironment and leukemic progression. To examine this question, we created CLL mice with Csf1r haploinsufficiency to investigate changes in myeloid cells, Csf1r expression, and leukemia progression. Reducing Csf1r expression on circulating monocytes did not change the overall numbers of monocytes or macrophages in blood and lymphoid tissues. Mice with lower Csf1r levels had less leukemia during early disease, but this effect faded with disease progression, and their overall survival was similar to controls. Furthermore, reduced Csf1r expression on macrophages did not affect the survival or migration of patient-derived CLL cells. In summary, our results show that while the CSF1R pathway is important for maintaining the myeloid cells that support CLL, simply reducing CSF1R expression has only a limited effect on disease progression. Attempts to target the CSF1R for leukemic therapy might benefit from a stronger depletion of macrophages or the combination with other agents.

cancer biology↗

bioRxiv2025

Alanine catabolism of Paneth cells maintains intestinal stem cell function during dietary restriction

Background and aimsPaneth cell niche promotes the function of intestinal stem cells (ISCs) during reduced food intake, but how ISC activity can be boosted when availability of resources is simultaneously reduced remains unknown. MethodsMice were subjected to dietary restriction (DR) and ad libitum (AL) dietary regime. FACS-sorted DR and AL Paneth cells and Lgr5+ stem cells were co-cultured, and organoid formation supportive capacity of Paneth cells was assessed. The role of Gpt2 - a Paneth cell specific mitochondrial alanine transaminase, was investigated by targeting pharmacologically and genetically in the intestinal organoids. By using U-13C labelled Alanine, an intercellular metabolic exchange assay was developed - and a conversion and transport of lactate from Paneth cells to stem cells, was followed by metabolomics. The in vivo role of Gpt2 was investigated in a conditional knock out mouse model. ResultsWe discovered that an increase in ISC function upon dietary restriction (DR) or DR mimicking condition, is dependent on Gpt2 in Paneth cells. Metabolic tracing of alanine directly showed DR boosts Paneth cell alanine catabolism, increasing lactate production via gluconeogenesis. Alanine derived lactate is shuttled from Paneth cells to neighboring stem cells, promoting TCA cycle and enhancing the ISC function during DR. Correspondingly, pharmacologic inhibition in vitro and genetic targeting of Gpt2 in vivo abolished the DR induced capacity of Paneth cells to support ISC function. ConclusionsOur results unravel dynamic intercellular metabolic cooperation in tissue adaptation, where Paneth cells upregulated Gpt2 catabolize increased amount of alanine to generate lactate as a transferable energy source, and to augment stem cell functions under DR.

cell biology↗

bioRxiv2024

Exercise and disease state influence the beneficial effects of Fn14-depletion on survival and muscle pathology in the SOD1G93A amyotrophic lateral sclerosis (ALS) mouse model

BackgroundAmyotrophic lateral sclerosis (ALS) is a devastating and incurable neurodegenerative disease. Accumulating evidence strongly suggests that intrinsic muscle defects exist and contribute to disease progression, including imbalances in whole-body metabolic homeostasis. We have previously reported that tumour necrosis factor (TNF)-like weak inducer of apoptosis (TWEAK) and fibroblast growth factor inducible 14 (Fn14) are significantly upregulated in skeletal muscle of the SOD1G93A ALS mouse model. While antagonising TWEAK did not impact survival, we did observe positive effects in skeletal muscle. Given that Fn14 has been proposed as the main effector of the TWEAK/Fn14 activity and that Fn14 can act independently from TWEAK in muscle, we suggest that manipulating Fn14 instead of TWEAK in the SOD1G93A ALS mice could lead to differential and potentially improved benefits. MethodsWe thus investigated the contribution of Fn14 to disease phenotypes in the SOD1G93A ALS mice. To do so, Fn14 knockout mice (Fn14-/-) were crossed onto the SOD1G93A background to generate SOD1G93A;Fn14-/- mice. Investigations were performed on both unexercised and exercised (rotarod and/or grid test) animals (wild type (WT), Fn14-/-, SOD1G93A and SOD1G93A;Fn14-/-). ResultsHere, we firstly confirm that the TWEAK/Fn14 pathway is dysregulated in skeletal muscle of SOD1G93A mice. We then show that Fn14-depleted SOD1G93A mice display an increased lifespan and decreased muscle pathology, without an impact on motor function, and that this is dependent on exposure to exercise. Indeed, we observe that endurance (rotarod) and resistance (grid test) exercises influence the positive effects of Fn14 deletion on survival and muscle phenotypes in SOD1G93A mice, which may be further influenced by genotype and disease state. ConclusionsOur study provides further insights on the different roles of the TWEAK/Fn14 pathway in pathological skeletal muscle and how they can be influenced by age, disease and metabolic state. This is particularly relevant in the ALS field, where combinatorial therapies that include exercise regimens are currently being explored. As such, a better understanding and consideration of the interactions between treatments, muscle metabolism and exercise will be of importance in future studies.

pathology↗

bioRxiv2024

ema-tool: a Python Library for the Comparative Analysis of Embeddings from Biomedical Foundation Models

Foundation models, which encode patterns in large, high-dimensional data as embeddings, show promise in many machine learning related applications in molecular biology. Embeddings learned by the models provide informative features for downstream prediction tasks, however, the information captured by the model is often not interpretable. One approach to understanding the captured information is through the analysis of their learned embeddings, which in molecular biology so far has mainly focused on visualizing individual embedding spaces. This study introduces a quantitative framework for cross-space comparison, enabling intuitive exploration and comparison of embedding spaces in molecular biology. The framework emphasizes analyzing the distribution of known biological information within embedding space neighborhoods and provides insights into relationships between multiple embedding spaces. Comparison techniques include global pairwise distance measurements as well as local nearest neighbor analyses. By applying our framework to embeddings from protein language models, we demonstrate how embedding space analysis can serve as a valuable pre-filtering step for task-specific supervised machine learning applications and for the recognition of differential patterns in data encoded within and across different embedding spaces. To support a wide usability, we provide a Python library that implements all analysis methods, available at https://github.com/broadinstitute/EmmaEmb.

bioinformatics↗

bioRxiv2024

Multi-tissue network analysis reveals the effect of JNK inhibition on dietary sucrose-induced metabolic dysfunction in rats

Excessive consumption of sucrose, in the form of sugar-sweetened beverages, has been implicated in the pathogenesis of metabolic dysfunctionLassociated fatty liver disease (MAFLD) and other related metabolic syndromes. The c-Jun N-terminal kinase (JNK) pathway plays a crucial role in response to dietary stressors, and it was demonstrated that the inhibition of the JNK pathway could potentially be used in the treatment of MAFLD. However, the intricate mechanisms underlying these interventions remain incompletely understood given their multifaceted effects across multiple tissues. In this study, we challenged rats with sucrose-sweetened water and investigated the potential effects of JNK inhibition by employing network analysis based on the transcriptome profiling obtained from hepatic and extrahepatic tissues, including visceral white adipose tissue, skeletal muscle, and brain. Our data demonstrate that JNK inhibition by JNK-IN-5A effectively reduces the circulating triglyceride accumulation and inflammation in rats subjected to sucrose consumption. Coexpression analysis and genome-scale metabolic modelling reveal that sucrose overconsumption primarily induces transcriptional dysfunction related to fatty acid and oxidative metabolism in the liver and adipose tissues, which are largely rectified after JNK inhibition at a clinically relevant dose. Skeletal muscle exhibited minimal transcriptional changes to sucrose overconsumption but underwent substantial metabolic adaptation following the JNK inhibition. Overall, our data provides novel insights into the molecular basis by which JNK inhibition exerts its metabolic effect in the metabolically active tissues. Furthermore, our findings underpin the critical role of extrahepatic metabolism in the development of diet-induced steatosis, offering valuable guidance for future studies focused on JNK-targeting for effective treatment of MAFLD.

bioinformatics↗

bioRxiv2024

Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures

Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics technologies have enabled the detection and generation of variants at an unprecedented scale. However, efficient tools and resources are needed to link these two disparate data types - to "map" variants onto protein structures, to better understand how the variation causes disease and thereby design therapeutics. Here we present the Genomics 2 Proteins Portal (G2P; g2p.broadinstitute.org/): a human proteome-wide resource that maps 19,996,443 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the G2P portal generalizes the capability of linking genomics to proteins beyond databases by allowing users to interactively upload protein residue-wise annotations (variants, scores, etc.) as well as the protein structure to establish the connection. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotype.

bioinformatics↗

bioRxiv2023

Functional Analysis of Human GRIN2A Mutations Associated with Schizophrenia and Neurodevelopmental Disorders Reveals Distinct Pathological Mechanism

Human genetic studies have revealed rare missense and protein-truncating variants in GRIN2A, encoding for the GluN2A subunit of the NMDA receptors, that confer significant risk for schizophrenia (SCZ). Mutations in GRIN2A are also associated with epilepsy and developmental delay/intellectual disability (DD/ID). However, it remains enigmatic how alterations to the same protein can result in diverse clinical phenotypes. Here, we performed functional characterization of human GluN1/GluN2A heteromeric NMDA receptors that contain SCZ-linked GluN2A variants, and compared them to NMDA receptors with GluN2A variants associated with epilepsy or DD/ID. Our findings demonstrate that SCZ-associated GRIN2A variants were predominantly loss-of-function (LoF), whereas epilepsy and DD/ID-associated variants resulted in both gain- and loss-of-function phenotypes. We additionally show that M653I and S809R, LoF GRIN2A variants associated with DD/ID, exert a dominant-negative effect when co-expressed with a wild-type GluN2A, whereas E58Ter and Y698C, SCZ-linked LoF variants, and A727T, an epilepsy-linked LoF variant, do not. These data offer a potential mechanism by which SCZ/epilepsy and DD/ID-linked variants can cause different effects on receptor function and therefore result in divergent pathological outcomes.

neuroscience↗

bioRxiv2023

Mapping MAVE data for use in human genomics applications

The large-scale experimental measures of variant functional assays submitted to MaveDB have the potential to provide key information for resolving variants of uncertain significance, but the reporting of results relative to assayed sequence hinders their downstream utility. The Atlas of Variant Effects Alliance mapped multiplexed assays of variant effect data to human reference sequences, creating a robust set of machine-readable homology mappings. This method processed approximately 2.5 million protein and genomic variants in MaveDB, successfully mapping 98.61% of examined variants and disseminating data to resources such as the UCSC Genome Browser and Ensembl Variant Effect Predictor.

bioinformatics↗

bioRxiv2022

Deep learning-based Drug discovery of Mac domain of SARS-CoV-2 (WT) Spike inhibitors: using experimental ACE2 Inhibition TR-FRET Assay Screening and Molecular Dynamic Simulations.

SARS-CoV-2 exploits the homotrimer transmembrane Spike glycoproteins (S protein) during host cell invasion. Omicron, delta, and prototype SARS-CoV-2 receptor-binding domain show similar binding strength to hACE2 (Angiotensin-Converting Enzyme 2). Here we utilized multi-ligand virtual screening to identify small molecule inhibitors for their efficacy against SARS-CoV-2 virus using quantum Docking, pseudovirus ACE2 Inhibition TR-FRET Assay Screening, and Molecular Dynamic simulations (MDS). 350-thousand compounds were screened against the macrodomain of non-structural protein 3 of SARS-CoV-2. Using TR-FRET Assay, we filtered out two of 10 compounds that had no reported activity in in-vitro screen against Spike S1: ACE2 binding assay. Percentage Inhibition at 30 {micro}M was found to be 79% for "Compound F1877-0839" and 69% for "Compound F0470-0003". This first of its kind study identified "FILLY" pocket in macrodomains. Our 200 ns MDS revealed stable binding poses of both leads. They can be used for further development of preclinical candidates. Abstract Image O_FIG O_LINKSMALLFIG WIDTH=178 HEIGHT=200 SRC="FIGDIR/small/512637v1_ufig1.gif" ALT="Figure 1"> View larger version (83K): org.highwire.dtl.DTLVardef@a8be27org.highwire.dtl.DTLVardef@5bff16org.highwire.dtl.DTLVardef@1c835f4org.highwire.dtl.DTLVardef@14e5438_HPS_FORMAT_FIGEXP M_FIG C_FIG In BriefIqbal et al., described a deep learning guided drug discovery, efficacy against SARS-CoV-2 Spike inhibitors: using experimental pseudovirus ACE2 Inhibition TR-FRET Assay. Our molecular dynamic simulation results were next validated a posteriori against the corresponding experimental data of identified leads with 80 percent inhibition. Moreover, this study is first of kind to identify "FILLY" pocket in macrodomains. HighlightsO_LIExperimental pseudovirus ACE2 Inhibition TR-FRET Assay and HTS lead to identification of two potential clinical leads. C_LIO_LIConformational Dynamics analysis reveal the structural stability of complexes throughout 200 ns molecular dynamic simulations. C_LIO_LIUnveiling of the impact surface charge on the Variant of Concerns C_LIO_LIDetection of conformational changes within ACE2/RBD complex C_LIO_LIWe identified the FILLY pocket in the SARS viruses. C_LI

bioinformatics↗

bioRxiv2022

A near complete genome assembly of chia assists in identification of key fatty acid desaturases in developing seeds

Chia is an annual crop whose seeds have the highest content of -linolenic acid (ALA) of any plant species. We generated a high-quality assembly of the chia genome using circular consensus sequencing of PacBio. The assembled six chromosomes are composed of 21 contigs and have a total length of 361.7 Mb. Genome annotation revealed a 53.5% repeat content and 35,850 protein-coding genes. Chia shared a common ancestor with Salvia splendens ~6.1 million years ago. Utilizing the reference genome and two transcriptome datasets, we identified candidate fatty acid desaturases responsible for ALA biosynthesis during chia seed development. Because the seed of S. splendens contains significantly lower proportion of ALA but similar total contents of unsaturated fatty acids, we suggest that strong expression of two ShFAD3 genes are critical for the high ALA content of chia seeds. This genome assembly will serve as a valuable resource for breeding, comparative genomics, and functional genomics studies of chia.

genomics↗