Comprehensive tissue-specific transcriptome profiling of pineapple (<i>Ananas comosus</i>) and building an eFP-browser for further study

Mao, Qi; Chen, Chengjie; Xie, Tongxin; Luan, Aiping; Liu, Chaoyang; He, Yehua

doi:10.7717/peerj.6028

Cited by 16 publications

(23 citation statements)

References 30 publications

(37 reference statements)

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“…The RT-qPCR results were consistent highly with our RNA-seq results (Fig. 8 A) and another published dataset of pineapple tissue-specific transcriptome 34 (Fig. 8 B), which provided solid proofs for the subsequent propose of ABCDE gene model (Fig.…”

Section: Resultssupporting

confidence: 90%

“…The expression level of each gene was quantified as fragments per kilobase of exon model per million reads mapped (FPKM) values by featureCounts 65 . The third dataset from previous published study provided available expression matrix including different floral organs in transcripts per kilobase million (TPM) by Stringtie 34 , 66 . Two heat expression maps were generated by the Pheatmap package in R software using pre-treated FPKM values by log 2 transformation.…”

Section: Methodsmentioning

confidence: 99%

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The pineapple MADS-box gene family and the evolution of early monocot flower

Chang

Zhang

et al. 2021

Sci Rep

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Unlike the flower of the model monocot rice, which has diverged greatly from the ancestral monocot flower, the pineapple (Ananas comosus) flower is more typical of monocot flowers. Here, we identified 43 pineapple genes containing MADS-box domains, including 11 type I and 32 type II genes. RNA-seq expression data generated from five pineapple floral organs (sepals, petals, stamens, pistils, and ovules) and quantitative real-time PCR revealed tissue-specific expression patterns for some genes. We found that AcAGL6 and AcFUL1 were mainly expressed in sepals and petals, suggesting their involvement in the regulation of these floral organs. A pineapple ‘ABCDE’ model was proposed based on the phylogenetic analysis and expression patterns of MADS-box genes. Unlike rice and orchid with frequent species-specific gene duplication and subsequent expression divergence, the composition and expression of the ABCDE genes were conserved in pineapple. We also found that AcSEP1/3, AcAG, AcAGL11a/b/c, and AcFUL1 were highly expressed at different stages of fruit development and have similar expression profiles, implicating these genes’ role in fruit development and ripening processes. We propose that the pineapple flower can be used as a model for studying the ancestral form of monocot flowers to investigate their development and evolutionary history.

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Section: Resultssupporting

confidence: 90%

Section: Methodsmentioning

confidence: 99%

The pineapple MADS-box gene family and the evolution of early monocot flower

Chang

Zhang

et al. 2021

Sci Rep

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“…S4). In pineapple, genes co-expressed in bracts participate in plant-pathogen interactions and these genes may paly roles in plant defence [43]. Therefore, we can infer that the bract and shoot apex may function in plant defence.…”

Section: Discussionmentioning

confidence: 99%

“…Researchers have found that the divergence of tissue-speci c gene expression patterns modulates ion maintenance in tissues and improves salinity tolerance in Populus euphratica [42]. In pineapple (Ananas comosus), researchers detected 273 tissue-speci c genes, which provided a basis for the study of the genetic mechanisms that regulate fruit phenotypes [43]. Although studies of L. chinense tissues (leaves and petals) have been reported, tissue-speci c genes in L. chinense remain unknown, and this lack of knowledge impedes our understanding of tissue traits of this species [5,6].…”

Section: Introductionmentioning

confidence: 99%

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Tu¹,

Shen²,

Wen³

et al. 2020

Preprint

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Background Liriodendron chinense (Hemsl.) Sarg. is an economically and ecologically important deciduous tree species that has been studied for many years. Although the complete L. chinense genome has been sequenced, the gene co-expression modules and tissue-specific genes of L. chinense remain unknown. Results Here, we used the bracts, petals, sepals, stamens, pistils, leaves, and the shoot apex of L. chinense as materials and analysed their gene co-expression modules and tissue-specific genes via hybrid sequencing. We identified 3,032 DEGs between the floral and vegetative tissues and 2,126 tissue-specific genes. By using WGCNA analysis, we identified 13 gene co-expression modules, and KEGG pathway enrichment analysis revealed that tissue-specific genes and genes from different modules were enriched in different pathways. Genes associated with plant defence were highly expressed in the bracts, genes participating in plant hormone signal transduction were highly expressed in the shoot apex, and genes participating in photosynthesis were highly expressed in the leaves, petals and sepals. Moreover, we identified 10 MIKC-type MADS-box genes that were classified as member of the AP3/PI, SVP, SEP, AG/SHP/STK, AGL12, SOC1 and TM8 subfamily. Phylogenetic analysis showed that the expression profiles of these ten genes were consistent with those reported in Arabidopsis and Populus , indicating that these genes are highly conserved evolutionarily and related to floral and vegetative tissue development. The small number of MIKC-type MADS-box genes in L. chinense was probably owing to its incomplete genome annotation. Conclusions In this work, we provided a reference transcriptome for L. chinense research by using hybrid sequencing. We identified 2,126 tissue-specific genes and 3,032 DEGs that contributed greatly to the functional differences between vegetative organs and floral organs. By using WGCNA analysis, 13 gene co-expression modules and 52 hub genes from six co-expression modules of interest were identified. Moreover, we identified 10 MIKC-type MADS-box genes that might be related to the development and growth regulation of floral and vegetative organs. These findings will improve our understanding of gene co-expression, tissue specific genes and flower development model of L. chinense .

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“…This combined with other genomics tools, such as Electronic Fluorescent Pictograph (eFP) browsers [1] to help visualise where a gene is expressed, allows faster identi cation of gene function in different species. To date, eFP browsers have been successfully developed in plants such as Arabidopsis [1], tomato [2], strawberry [3], and pineapple [4].…”

Section: Introductionmentioning

confidence: 99%

An Actinidia chinensis (kiwifruit) eFP browser and network analysis of transcription factors

Brian¹,

Warren²,

McAtee³

et al. 2020

Preprint

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BackgroundTranscriptomic studies combined with a well annotated genome have laid the foundations for new understanding of molecular processes. Tools which visualise gene expression patterns have further added to these resources. The manual annotation of the Actinidia chinensis (kiwifruit) genome has resulted in a high quality set of 33,044 genes. Here we investigate gene expression patterns in diverse tissues, visualised in an Electronic Fluorescent Pictograph (eFP) browser, to study the relationship of transcription factor (TF) expression using network analysis. ResultsSixty-one samples covering diverse tissues at different developmental time points were selected for RNAseq analysis and an eFP browser was generated to visualise this dataset. 2,839 TFs representing 57 different classes were identified and named. Network analysis of the TF expression patterns separated TFs into 14 different modules. Two modules consisting of 237 TFs were correlated with floral bud and flower development, a further two modules containing 160 TFs were associated with fruit development and maturation. A single module of 480 TFs was associated with ethylene-induced fruit ripening. Three “hub” genes correlated with flower and fruit development consisted of a HAF-like gene central to gynoecium development, an ERF and a DOF gene. Maturing and ripening hub genes included a KNOX gene that was associated with seed maturation, and a GRAS-like TF.ConclusionsThis study provides an insight into the complexity of the transcriptional control of flower and fruit development, as well as providing a new resource to the plant community. The eFP browser is provided in an accessible format that allows researchers to download and work internally.

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Comprehensive tissue-specific transcriptome profiling of pineapple (Ananas comosus) and building an eFP-browser for further study

Cited by 16 publications

References 30 publications

The pineapple MADS-box gene family and the evolution of early monocot flower

The pineapple MADS-box gene family and the evolution of early monocot flower

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

An Actinidia chinensis (kiwifruit) eFP browser and network analysis of transcription factors

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