Full-length transcriptome analysis of <i>Adiantum flabellulatum</i> gametophyte

Cai, Zeping; Xie, Zhenyu; Huang, Luyao; Wang, Zixuan; Pan, Min; Yu, Xudong; Xu, Shitao; Luo, Jiajia

doi:10.7717/peerj.13079

Cited by 5 publications

(6 citation statements)

References 53 publications

(53 reference statements)

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“…In this study, we specifically examine the transcriptome of the gametophyte, noting its ease of cultivation in a laboratory setting, which allows for the collection of sufficient material to conduct molecular analyses. According to a previous study (Wyder et al, 2020), a collection of 436,707 transcripts was obtained after assembled the RNA-seq reads, a higher number than in other species of ferns, such as Adiantum flabellulatum , with 354,228 transcripts (Cai et al, 2022); or Vandenboschia speciosa , with 36,430 (Bakkali et al, 2021), or 43,139 (Martín-Blazquez et al, 2023). All these studies contribute to enhancing our genomic understanding of unsequenced fern species, which have remained elusive until recently.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic analyses in the gametophyte of Dryopteris affinis: apomixis and more

Ojosnegros,

Alvarez,

Gagliardini

et al. 2024

Preprint

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The gametophyte of the fern Dryopteris affinis ssp. affinis represents a good model to explore the molecular basis of vegetative and reproductive development, as well as stress responses. Specifically, this fern reproduces asexually by apogamy, a peculiar case of apomixis whereby a sporophyte forms directly from a gametophytic cell without fertilization. Using an RNA-sequencing approach, we have previously annotated more than six thousand transcripts. Here, we selected one hundred of the inferred proteins that seemed particularly interesting for a detailed study of their potential functions, protein-protein interactions, and molecular phylogenies. As expected, a plethora of proteins associated with gametogenesis and embryogenesis in angiosperms, such as FERONIA (FER) and CHROMATING REMODELING 11 (CHR11) were identified, and more than a dozen candidates potentially involved in apomixis, such as ARGONAUTE4 (AGO4), AGO9, and AGO10, BABY BOOM (BBM), FASCIATED STEM4 (FAS4), FERTILIZATION-INDEPENDENT ENDOSPERM (FIE), and MATERNAL EFFECT EMBRYO ARREST29 (MEE29). In addition, proteins involved in the response to biotic and abiotic stresses were widely represented, as shown by the enrichment of heat-shock proteins. Using the String platform, studying interactomes revealed that most of the protein-protein interactions were predicted based on experimental, database, and text mining datasets, with MULTICOPY SUPPRESSOR OF IRA4 (MSI4) showing the highest number of 16 interactions. Lastly, some proteins were studied from a phylogenetic point of view, comparing the alignments with respect to more distantly or closely related plant groups, identifying AGO1 as the evolutionarily most similar to that other ferns and the most distant to the predicted common ancestor. This work sets the stage for future functional characterizations in relation to gametophyte development including apomictic reproduction.

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Section: Discussionmentioning

confidence: 99%

Transcriptomic analyses in the gametophyte of Dryopteris affinis: apomixis and more

Ojosnegros,

Alvarez,

Gagliardini

et al. 2024

Preprint

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“…The clean reads were aligned to the full-length transcripts (PRJNA733457) of A. flabellulatum gametophytes by Bowtie2 (v2.2.5, Baltimore, MD, USA) [ 30 , 31 ], and then a sequencing saturation analysis was performed. The expression levels of genes (calculated in fragments per kilobase of transcript per million mapped reads, FPKM) in each sample were counted by RSEM software (v1.2.8, Madison, WI, USA) [ 32 ].…”

Section: Methodsmentioning

confidence: 99%

“…After removing the isoforms with average FPKMs < 0.5 in both treatments, the differentially expressed genes (DEGs) were screened under the conditions of |log 2 FoldChange| ≥ 1 and Q -Values < 0.001. According to the methods of Cai et al [ 30 ], all DEGs were annotated and classified by GO ( (accessed on 24 April 2022)) and KEGG ( (accessed on 24 April 2022)) analysis [ 30 ]. After that, enrichment of the analysis was performed by using the Phyper package in R software (Auckland, New Zealand).…”

Section: Methodsmentioning

confidence: 99%

Excavation of Genes Responsive to Brassinosteroids by Transcriptome Sequencing in Adiantum flabellulatum Gametophytes

Cai

Xie

Wang

et al. 2022

Genes

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Brassinosteroids (BRs) are a class of polyhydroxysteroid plant hormones; they play important roles in the development and stress resistance of plants. The research on BRs has mainly been carried out in angiosperms, but in ferns—research is still limited to the physiological level and is not in-depth. In this study, Adiantum flabellulatum gametophytes were used as materials and treated with 10−6 M brassinolide (BL). The differentially expressed genes (DEGs) responsive to BRs were identified by transcriptome sequencing, GO, KEGG analysis, as well as a quantitative real-time polymerase chain reaction. From this, a total of 8394 DEGs were screened. We found that the expressions of photosynthetic genes were widely inhibited by high concentrations of BL in A. flabellulatum gametophytes. Moreover, we detected many BR synthase genes, except BR6ox2, which may be why castasterone (CS) rather than BL was detected in ferns. Additionally, we identified (for the first time) that the expressions of BR synthase genes (CYP90B1, CYP90C1, CYP90D1, CPD, and BR6ox1) were negatively regulated by BL in fern gametophytes, which indicated that ferns, including gametophytes, also needed the regulatory mechanism for maintaining BR homeostasis. Based on transcriptome sequencing, this study can provide a large number of gene expression data for BRs regulating the development of fern gametophytes.

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“…For example, in the transcriptomes of ferns Huperzia serrata and Monachosorum maximowiczii , the proportion of transcription factors/transcriptional regulators is only 1.87% and 1.11%, respectively ( Liu et al., 2016 ; Yang et al., 2017 ). In the transcriptome of the gametophyte of Adiantum flabellulatum that we previously reported, the proportion of transcription factors/transcriptional regulators is 2.25% ( Cai et al., 2022a ). The genome of Salvinia cucullata , the smallest known genome among ferns, has only 983 transcription factors/transcriptional regulators, accounting for 4.94% of all genes, which is also lower than that in gymnosperms or angiosperms ( Li et al., 2018 ).…”

Section: Introductionmentioning

confidence: 94%

Light response of gametophyte in Adiantum flabellulatum: transcriptome analysis and identification of key genes and pathways

Cai,

Wang,

Xie

et al. 2023

Front. Plant Sci.

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Light serves not only as a signaling cue perceived by plant photoreceptors but also as an essential energy source captured by chloroplasts. However, excessive light can impose stress on plants. Fern gametophytes possess the unique ability to survive independently and play a critical role in the alternation of generations. Due to their predominantly shaded distribution under canopies, light availability becomes a limiting factor for gametophyte survival, making it imperative to investigate their response to light. Previous research on fern gametophytes’ light response has been limited to the physiological level. In this study, we examined the light response of Adiantum flabellulatum gametophytes under different photosynthetic photon flux density (PPFD) levels and identified their high sensitivity to low light. We thereby determined optimal and stress-inducing light conditions. By employing transcriptome sequencing, weighted gene co-expression network analysis, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, we identified 10,995 differentially expressed genes (DEGs). Notably, 3 PHYBs and 5 Type 1 CRYs (CRY1s) were significantly down-regulated at low PPFD (0.1 μmol m-2 s-1). Furthermore, we annotated 927 DEGs to pathways related to photosynthesis and 210 to the flavonoid biosynthesis pathway involved in photoprotection. Additionally, we predicted 34 transcription factor families and identified a close correlation between mTERFs and photosynthesis, as well as a strong co-expression relationship between MYBs and bHLHs and genes encoding flavonoid synthesis enzymes. This comprehensive analysis enhances our understanding of the light response of fern gametophytes and provides novel insights into the mechanisms governing their responses to light.

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Full-length transcriptome analysis of Adiantum flabellulatum gametophyte

Cited by 5 publications

References 53 publications

Transcriptomic analyses in the gametophyte of Dryopteris affinis: apomixis and more

Transcriptomic analyses in the gametophyte of Dryopteris affinis: apomixis and more

Excavation of Genes Responsive to Brassinosteroids by Transcriptome Sequencing in Adiantum flabellulatum Gametophytes

Light response of gametophyte in Adiantum flabellulatum: transcriptome analysis and identification of key genes and pathways

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