Biology subjects

Blilou, I.

Publications and source records attributed to Blilou, I..

9 recordsLinked to original sources

bioRxiv2025

Foundational genomic resources for date palm: A gap-free, telomere-to-telomere phased assembly of Ajwa and 19 high-quality genome assemblies of Phoenix dactylifera.

Phoenix dactylifera L. is an economically, nutritionally, and culturally important fruit crop in the arid and semi-arid regions of the Middle East and North Africa. Here, we present a gap-free, telomere-to-telomere reference genome of the variety Ajwa, along with 19 additional high-quality assemblies (18 female and 1 male). These assemblies reveal novel chromosomal structures validated through cytogenetics, Hi-C, optical mapping, and synteny analyses with other palm genomes. Chromosome names were revised based on average lengths across all sequenced genomes. The Sex Determination Region (SDR) on chromosome 14 was confirmed through male-specific k-mer analysis, spanning approximately 14.7 Mb. Nucleolar organizing regions (NORs) were localized on chromosome 10, where a large 45S rDNA locus displayed unique repeat spacer motifs containing transposon-like sequences. In some accessions, a second NOR was identified on the female sex chromosome. This collection of date palm assemblies, anchored by the Ajwa reference genome, provides a critical resource for advancing breeding strategies aimed at enhancing the genetic resilience and productivity of date palm.

genomics↗

bioRxiv2023

Zaxinone Synthase overexpression modulates rice physiology and metabolism, improving growth and productivity under normal and low phosphate supply

The rice Zaxinone Synthase (ZAS) gene encodes a carotenoid cleavage dioxygenase (CCD) that forms the apocarotenoid growth regulator zaxinone. Here, we generated and characterized constitutive ZAS-overexpressing rice lines, to better understand ZAS role in determining zaxinone content and regulating growth and architecture. ZAS overexpression enhanced endogenous zaxinone level, promoted root growth and meristem size, and increased the number of productive tillers, leading to an up to 30% higher grain yield per plant. Hormone analysis revealed a decrease in strigolactone (SL) content, which we confirmed by rescuing the high-tillering phenotype through application of a SL analog. Metabolomics analysis revealed that ZAS overexpressing plants accumulate higher amounts of monosaccharide sugars, in line with transcriptome analysis. Moreover, transgenic plants showed higher carbon (C) assimilation rate and elevated root phosphate, nitrate and sulfate level, enhancing the tolerance towards low phosphate (Pi) and indicating a generally better nutrient uptake. Our study shows that ZAS regulates hormone homeostasis and a combination of physiological processes to promote growth and grain yield, which makes this gene an excellent candidate for sustainable crop improvement. TeaserZaxinone Synthase overexpression modulates rice metabolism and physiology and improves growth and phosphate uptake.

plant biology↗

bioRxiv2023

Disruption of the rice 4-DEOXYOROBANCHOL HYDROXYLASE unravels specific functions of canonical strigolactones

Strigolactones (SLs) regulate many developmental processes, including shoot-branching/tillering, and mediate rhizospheric interactions. SLs are structurally diverse, divided into a canonical and a non-canonical sub-family. To better understand the biological function of particular SLs, we generated CRISPR/Cas9 mutants disrupted in OsMAX1-1400 or OsMAX1-1900, which encode cytochrome P450 enzymes (CYP711A clade) contributing to SL diversity. The disruption of OsMAX1-1900 did neither affect the SL pattern nor plant architecture, indicating a functional redundancy. In contrast, disruption of OsMAX1-1400 activity, a 4-deoxyorobanchol hydroxylase, led to a complete lack of orobanchol and an accumulation of its precursor 4-deoxyorobanchol (4DO), both of which are a canonical SLs common in different plant species, accompanied by higher levels of the non-canonical methyl 4-oxo-carlactonoate (4-oxo-MeCLA). Os1400 mutants showed also shorter plant height, panicle and panicle base length, but did not exhibit a tillering phenotype. Hormone quantification and transcriptome analysis revealed elevated auxin levels and changes in the expression of auxin-related, as well as of SL biosynthetic genes. Interestingly, the Os900/1400 double mutant lacking both orobanchol and 4DO did not show the observed Os1400 architectural phenotypes, indicating that they are a result of 4DO accumulation. A comparison of the mycorrhization and Striga seed germinating activity of Os900, Os900/1400, and Os1400 loss-of-function mutants demonstrates that the germination activity positively correlates with 4DO content while disrupting OsMAX1-1400 negatively impact mycorrhizal symbiosis. Taken together, our paper deciphers the biological function of canonical SLs in rice and depicts their particular contributions to establishing architecture and rhizospheric communications.

plant biology↗

bioRxiv2022

The Arabidopsis SHORTROOT network coordinates shoot apical meristem development with auxin dependent lateral organ initiation

Unlike animals, plants have the capacity to produce new organs post-embryonically throughout their entire life cycle. This is due to stem cells present in the shoot and the root apical meristems (SAM and RAM, respectively). In the SAM, stem cells are located in the central zone (CZ) where they divide slowly. Stem cell daughters are displaced laterally and enter the peripheral zone (PZ). Here, their mitotic activity increases, and lateral organ primordia (LOP) are formed. How the spatial arrangement of these different domains is initiated and controlled during SAM growth and development, and how sites of LOP are determined in the PZ is not yet completely understood. In the RAM, the GRAS family transcription factor SHORTROOT (SHR) acts as a master regulator of signalling pathways that maintain the root stem cell niche and control formation of ground tissue layers. We hypothesized that SHR could perform a similar role in the SAM, and found that SHR, together with its target transcription factors SCARECROW (SCR), SCARECROW-LIKE23 (SCL23) and JACKDAW (JKD), controls shoot meristem size by regulating cell division rates, and promotes formation of lateral organs. SHR, SCR, SCL23 and JKD are expressed in very distinct patterns in the SAM. Where these expression domains overlap, they can physically interact to activate expression of the key cell cycle regulator CYCLIND6;1 (CYCD6;1) and thereby promote the formation of new cell layers. In the PZ, upregulation of SHR expression at sites of organ initiation depends on the phytohormone auxin, acting through the auxin response factor MONOPTEROS (MP) and auxin response elements in the SHR promoter. In the CZ, the SHR-target SCL23 physically interacts with WUS, a key regulator of stem cell maintenance, and both SCL23 and WUS expression are subject to negative feedback regulation from stem cells through the CLAVATA signalling pathway. Together, our findings illustrate how SHR-dependent transcription factor complexes act in different domains of the shoot meristem to mediate cell division and auxin dependent organ initiation in the PZ, and coordinate this activity with stem cell maintenance in the CZ of the SAM.

plant biology↗

bioRxiv2022

ZAXINONE SYNTHASE 2 regulates growth and arbuscular mycorrhizal symbiosis in rice

Carotenoid cleavage, catalyzed by CAROTENOID CLEAVAGE DIOXYGENASES (CCDs), provides signaling molecules and precursors of plant hormones. Recently, we showed that zaxinone, a novel apocarotenoid metabolite formed by the CCD Zaxinone Synthase (ZAS), is a growth regulator required for normal rice growth and development. The rice genome encodes three OsZAS homologs, called here OsZAS1b, OsZAS1c, and OsZAS2, with unknown functions. Here, we investigated the enzymatic activity, expression pattern, and subcellular localization of OsZAS2, and generated and characterized loss-of-function CRISPR/Cas9-Oszas2 mutants. We show that OsZAS2 formed zaxinone in vitro. OsZAS2 is a plastid-localized enzyme mainly expressed in the root cortex under phosphate starvation. Moreover, OsZAS2 expression increased during mycorrhization, specifically in arbuscule-containing cells. Oszas2 mutants contained lower zaxinone content in roots and exhibited reduced root and shoot biomass, less productive tiller, and higher strigolactone (SL) levels. Exogenous zaxinone application repressed SL biosynthesis and partially rescued the growth retardation of Oszas2 mutant. Consistent with the OsZAS2 expression pattern, Oszas2 mutants displayed a lower frequency of AM colonization. In conclusion, OsZAS2 encodes a further zaxinone-forming enzyme that determines rice growth and architecture and strigolactone content and is required for optimal mycorrhization.

plant biology↗

bioRxiv2022

The Arabidopsis D27like1 is a novel Isomerase that Contributes to SL Biosynthesis and Negatively Impacts ABA Level

The enzyme DWARF27 (D27) catalyzes the reversible isomerization of all-trans- into 9-cis-{beta}-carotene, initiating strigolactone (SL) biosynthesis. Genomes of higher plants encode two D27-homologs, D27-like1 and -like2, with unknown functions. Here, we investigated the enzymatic activity and biological function of the Arabidopsis D27-like1. In vitro enzymatic assays and Expression in Synechocystis sp. PCC6803 revealed a yet not reported 13-cis/15-cis/9-cis- and a 9-cis/all-trans-{beta}-carotene isomerization. Although disruption of AtD27-like1 did not cause SL deficiency phenotypes, overexpression of AtD27-like1 in the Atd27 mutant restored the more-branching phenotype, indicating a contribution of AtD27-like1 to SL biosynthesis. Accordingly, generated Atd27 Atd27like1 double mutants showed more pronounced branching phenotype, compared to Atd27. The contribution of AtD27-like1 to SL biosynthesis is likely due to its formation of 9-cis-{beta}-carotene that was present at higher levels in AtD27-like1 overexpressing lines. In contrast, AtD27-like1 expression correlated negatively with the content of 9-cis-violaxanthin, a precursor of abscisic acid (ABA), in shoots. Consistently, ABA levels were higher in shoots and also in dry seeds of the Atd27like1 and Atd27 Atd27like1 mutants. Transgenic lines expressing {beta}-glucuronidase (GUS) driven by the AtD27LIKE1 promoter and transcript analysis performed with hormone-treated Arabidopsis seedlings unraveled that AtD27LIKE1 is expressed in different tissues and regulated ABA and auxin. Taken together, our work revealed a cis/cis-{beta}-carotene isomerase activity that affects the content of both cis-carotenoid derived plant hormones ABA and SLs.

plant biology↗

bioRxiv2022

RETINOBLASTOMA RELATED (RBR) interaction with key factors of the RNA-directed DNA methylation (RdDM) pathway

O_LITransposable elements and other repetitive elements are silenced by the RNA-directed DNA methylation pathway (RdDM). In RdDM, POLIV-derived transcripts are converted into double stranded RNA (dsRNA) by the activity of RDR2 and subsequently processed into 24 nucleotide short interfering RNAs (24 -nt siRNAs) by DCL3. 24-nt siRNAs are recruited by AGO4 and serve as guides to direct AGO4 - siRNA complexes to chromatin bound POLV-derived transcripts generated from the template/target DNA. The interaction between POLV, AGO4, DMS3, DRD1, RDM1 and DRM2 promotes DRM2-mediated de novo DNA methylation. C_LIO_LIThe Arabidopsis Retinoblastoma protein homolog is a master regulator of cell cycle, stem cell maintenance and development. In silico exploration of RBR protein partners revealed that several members of the RdDM pathway contain a motif that confers high affinity binding to RBR, including the largest subunits of POLIV and POLV (NRPD1 and NRPE1), the shared second largest subunit of POLIV and POLV (NRPD/E2), RDR1, RDR2, DCL3, DRM2 and SUVR2. We demonstrate that RBR binds to DRM2, DRD1 and SUVR2. We also report that seedlings from loss -of-function mutants in RdDM and in RBR show similar phenotypes in the root apical meristem. Furthermore, we show that RdDM and SUVR2 targets are up-regulated in the 35S::AmiGO-RBR background. C_LIO_LIOur results suggest a novel mechanism for RBR function in transcriptional gene silencing based on the interaction with key players of the RdDM pathway and opens several new hypotheses, including the convergence of RBR-DRM2 on the transcriptional control of TEs and several cell/tissue and stage -specific target genes. C_LI

developmental biology↗

bioRxiv2021

The PLETHORA/PIN-FORMED/AUXIN network mediates terminal prehaustorium formation in the parasitic plant Striga hermonthica

The parasitic plant Striga hermonthica invades the host root through the formation of a haustorium and has detrimental impacts on cereal crops. The haustorium is derived directly from the differentiation of the Striga radicle. Currently, how Striga root cell lineages are patterned and the molecular mechanisms leading to radicle differentiation shortly after germination remain unclear. In this study, we determined the developmental-morphodynamic programs that regulate terminal haustorium formation in S. hermonthica at spatiotemporal and cellular resolutions. We showed that in S. hermonthica roots, meristematic cells first undergo multiplanar divisions, which decrease during growth and correlate with reduced expression of the stem cell regulator PLETHORA1. We also found that PIN-FORMED (PIN) proteins undergo a shift in polarity. Using the layout of the root structure and the polarity of outer-membrane PIN proteins, we constructed a mathematical model of auxin transport that explains the auxin distribution patterns observed during S. hermonthica root growth. Our results reveal a fundamental molecular and cellular framework governing the switch of S. hermonthica roots from the vegetative to the invasive state by inducing meristem differentiation through auxin excretion to the environment and explain how asymmetric PIN polarity controls auxin distribution to maintain meristem activity and sustain root growth.

plant biology↗

bioRxiv2020

Development and cell cycle dynamics of the root apical meristem in the fern Ceratopteris richardii

Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne root of Ceratopteris. We followed early stages and emergence of the root meristem in sporelings. While assessing root growth, the first shoot-borne root ceases its elongation between the emergence of the fifth and sixth roots, suggesting Ceratopteris roots follow a determinate developmental program. We report cell division frequencies in the stem cell niche after detecting labeled nuclei in the root apical cell (RAC) and derivatives after 8 hours of exposure. These results demonstrate the RAC has a continuous mitotic activity during root development. Detection of cell cycle activity in the RAC at early times suggests this cell acts as a non-quiescent organizing center. Overall, our results provide a framework to study root function and development in ferns and to better understand the evolutionary history of this organ. Summary StatementIn the Ceratopteris root, the apical cell and its derivatives have a high division frequency, suggesting the apical cell acts as a non-quiescent organizing center in the stem cell niche.

developmental biology↗