Expression of coffee florigen CaFT1 reveals a sustained floral induction window associated with asynchronous flowering in tropical perennials

Cardon, Carlos Henrique; Oliveira, Raphael Ricon de; Lesy, Victoria; Ribeiro, Thales Henrique Cherubino; Fust, Catherine; Pereira, Luísa Peloso; Colasanti, Joseph; Chalfun-Júnior, Antônio

doi:10.1016/j.plantsci.2022.111479

Cited by 11 publications

(5 citation statements)

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“…After exploring the C. arabica sub-genome organization, we performed a regulatory network analysis to understand its transcriptional activation and regulatory modules related to leaf metabolism. To do so, we used 24 RNAseq libraries previously published from fully expanded leaves collected during the morning and under a heterogeneous set of environmental conditions (Cardon et al 2022).…”

Section: Resultsmentioning

confidence: 99%

“…Supplemental Table S1 shows details of each Bioproject, from which approximately 174 billion nucleic bases in 81 RNAseq libraries are publicly available through SRA. Multiple coffee tissues such as beans (Cheng et al 2020; Cheng et al 2018), leaves (de Oliveira et al 2020; Cardon et al 2022), seeds (Stavrinides et al 2020) and roots (dos Santos et al 2019) were used to find exons and predict genes in this study.…”

Section: Methodsmentioning

confidence: 99%

“…To infer co-expression modules (clusters) of expressed PCG in fully expanded leaves of C. arabica we applied procedures from the Weighted Gene Co-expression Network Analysis (WGNA) R-package (Langfelder and Horvath 2008). The libraries from the bioproject ID PRJNA851465 were selected because they represent leaves under a heterogeneous set of environmental conditions which are expected to trigger multiple regulatory networks to cope with the field variability (Cardon et al 2022). The BioSamples covered two cities (Pirapora and Varginha) during two harvest times (April and October) and with two C. arabica cultivars (Acauã and Catuaí).…”

Section: Methodsmentioning

confidence: 99%

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Differential universal ortholog composition ofCoffea arabicaL. sub-genomes and its contribution to regulatory networks governing essential biological processes

Ribeiro

Oliveira

Chalfun-Júnior

2023

Preprint

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The polyploidy of Coffea arabica is an important trait affecting the evolution of this species. Genetic variability is scarce due to its recent origin as an interspecific hybrid from a single successful crossing event between Coffea canephora and Coffea eugenioides relatives. To further investigate the genomic composition of an allotetraploid we coupled high-throughput methodologies of co-expression analysis and full-length protein coding genes inference. Many of the expected orthologs were found to be missing from one of the two homoeologous chromosomes. The gene expression machinery is mainly represented by single-copy essential orthologs located in the Coffea eugenioides sub-genome. This result suggests a preference of the transcriptional and RNA processing machinery to be regulated by one parental sub-genome. To understand the operational modules of the sub-genomes transcription, we performed co-expression analysis that revealed 23 co-regulated modules. This system-wide approach clarified how biological processes (i.e., photosynthesis, cell wall biogenesis, translation, transcription, catabolism and biosynthesis) are running in synchrony and reinforces that there is an ongoing selective pressure in C. arabica that constrains the number of copies of some universal orthologues. Thus, this work contributes to our understanding of genome evolution in recent polyploids and supports crop breeding programs.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Differential universal ortholog composition ofCoffea arabicaL. sub-genomes and its contribution to regulatory networks governing essential biological processes

Ribeiro

Oliveira

Chalfun-Júnior

2023

Preprint

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“…To search for putative conserved miRNAs and their precursors, we applied an adapted algorithm previously described by De Souza Gomes et al (2011) to the genome and transcriptome databases of C. canephora (Denoeud et al, 2014). The second prediction of conserved and novel miRNAs was made from RNA‐seq libraries of C. arabica (Cardon et al, 2022; de Oliveira et al, 2020), in which mapped small RNA (sRNA) reads were used as input to two different computational pipelines for the discovery of miRNAs – a stringent pipeline for de novo identification and a relaxed pipeline for identification of conserved “known” miRNAs (Jeong et al, 2013). Steps in both pipelines involved processing using Perl scripts as described earlier (Jeong et al, 2011), with a modified version of miREAP (https://sourceforge.net/projects/mireap/) and CentroidFold (Sato et al, 2009).…”

Section: Methodsmentioning

confidence: 99%

Microsporogenesis and the biosynthesis of floral small interfering RNAs in coffee have a unique pattern among eudicots, suggesting a sensitivity to climate changes

de Oliveira,

de Campos Rume

et al. 2024

Plant Direct

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Recently, the siRNAs pathways, and especially reproductive phasiRNAs, have attracted attention in eudicots since their biological roles are still unknown and their biogenesis took different evolutionary pathways compared to monocots. In this work, we used Coffea arabica L., a recent allotetraploid formed from the hybridization of Coffea canephora and C. eugenioides unreduced gametes, to explore microsporogenesis and small RNAs‐related pathways in a eudicot crop. First, we identified the microsporogenesis stages during anther development revealing that pre‐meiosis occurs in anthers of 1.5 mm inside floral buds (FBs), whereas meiosis between 1.5 and 4.2 mm FBs, and post‐meiosis in FBs larger than 4.2 mm. These stages coincide with the Brazilian winter, a period of FBs reduced growth which suggests temperature sensitivity. Next, we identified and quantified the expression of reproductive 21‐ and 24‐nt phasiRNAs during coffee anther development together with their canonical and novel miRNA triggers, and characterized the DCL and AGO families. Our results showed that the pattern of reproductive phasiRNA abundance in C. arabica is unique among described eudicots and the canonical trigger car‐miR2275 is involved in the processing of both 21‐ and 24‐nt phasiRNAs. Fourteen DCL genes were identified, but DCL5, related to phasiRNA biosynthesis in monocots, was not, according to its specificity for monocots. Thus, our work explored the knowledge gap about microsporogenesis and related siRNAs pathways in coffee, contributing to the control of reproductive development and the improvement of fertility in eudicots.

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“…Orthologs of FT have been identified in several species such as rice (Tamaki et al, 2007), coffee (Cardon et al, 2022) and many others (Pin and Nilsson, 2012). FT belongs to the PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN (PEBP) family, which is conserved in plants and animals (Jin et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Unveiling the phenology and associated floral regulatory pathways ofHumulus lupulusL. in subtropical conditions

Gutiérrez,

de Oliveira,

Ribeiro

et al. 2023

Preprint

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TheHumulus lupulusL. (hops) is traditionally produced in temperate regions, historically attributed to the belief that vernalization was necessary for reproductive transition. Nevertheless, recent studies have revealed the potential for hop plants to flower in tropical and subtropical climates, thereby reshaping cultivation prospects once the developmental disparities are understood and adapted for optimized production. Here, we delved into the hop phenological cycle and the underlying floral regulatory pathways ultimately, seeking to devise strategies to modulate development and enhance production in regions with low latitudes. In contrast to cultivation in temperate regions, hops grown in the subtropical climate of Minas Gerais, Brazil, flower multiple times throughout the year, independently of the season. Hop is a short-day plant, and in Brazil, the photoperiod is consistently inductive due to daylight hours always being below the described threshold (16,5 h of light critical point). We observed that the reproductive transition of hop initiates after a specific number of nodes, 25 to 28, leading us to hypothesize that this process is primarily controlled by endogenous factors. To explore this issue, we first identified in the hop genome families of miRNAs related to reproductive transition, such as the families MIR156 and MIR172, and the PEBP family which includes the FLOWERING LOCUS T (FT). The expression of miR156 decreased along development inversely to miR172 and in synchrony with the upregulation ofHlFT3andHlFT5. These findings strongly support that the reproductive transition in hops under inductive photoperiodic conditions is primarily regulated by endogenous factors related to development and aging throughout the miRNA and FT-associated pathways. Thus, our study shedded light on the intricate molecular mechanisms that underlie hop floral development paving the way for potential advancements in hop production on a global scale.

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Expression of coffee florigen CaFT1 reveals a sustained floral induction window associated with asynchronous flowering in tropical perennials

Cited by 11 publications

References 104 publications

Differential universal ortholog composition ofCoffea arabicaL. sub-genomes and its contribution to regulatory networks governing essential biological processes

Differential universal ortholog composition ofCoffea arabicaL. sub-genomes and its contribution to regulatory networks governing essential biological processes

Microsporogenesis and the biosynthesis of floral small interfering RNAs in coffee have a unique pattern among eudicots, suggesting a sensitivity to climate changes

Unveiling the phenology and associated floral regulatory pathways ofHumulus lupulusL. in subtropical conditions

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