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

Plant material preparation and RNA sequencing

All plants of pineapple cultivar “Shenwan” used for this study were cultivated in Shenwan Town, Zhongshan City, Guangdong, China. Three distinct plant stages were defined according to fruit development. Stage 1 begins when flower buds begin to bloom and the collective fruit begins to expand in size. Stage 2 begins when flowering ceases, and the collective fruit expands at its fastest rate. Stage 3 corresponds to the time when collective fruit stops expanding and begins to ripen. In total, 11 tissues were manually separated from pineapple. These included bract, core, flower disk, leaf, ovary wall, ovule, petal, placenta, receptacle, sepal, stamen, and style tissues. All samples were collected and stored immediately in liquid nitrogen before RNA extraction. We extracted total RNA from all samples using TRIzol (Invitrogen, Carlsbad, CA, USA) and determined RNA quality of samples using Agilent 2100. RNA samples with RIN numbers lower than eight were re-extracted. All RNA samples were then forwarded to a sequencing provider for RNA sequencing.

Expression profiling

Pre-filtered data received from the sequencing provider was manually checked by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). All sequencing adapters and low quality reads were filtered using Trimmomatic (Bolger, Lohse & Usadel, 2014). Only paired reads were kept for downstream analysis. STAR aligner was employed to map all clean reads onto the published pineapple genome (Dobin et al., 2013). The resulting BAM files were then processed using StringTie for estimation of expression levels (Pertea et al., 2015), in which the transcripts per kilo base million (TPM) normalized method was employed. The TAU method proposed by Yanai et al. (2005) was applied on the expression matrix to detect genes that were constitutively expressed or expressed in specific tissues (Kryuchkova & Robinson-Rechavi, 2015). Genes with TAU scores lower than 0.2 were defined as constitutively expressed genes while those with TAU scores higher than 0.99 were defined as tissue-specific genes.

WGCNA analysis and KEGG pathway enrichment analysis

To construct a gene co-expression network for pineapple fruit, we employed the WGCNA package (Langfelder & Horvath, 2008). Genes that were not expressed or were expressed at very low levels (TPM lower than 0.1) in all samples were filtered out. The filtered TPM matrix was then imported into WGCNA for analysis. All parameters were kept as default except the following: networkType was set to signed, softPower to 10, minModuleSize to 100, deepSplit to 2.0, and MEDissThres to 0.1. A software package made in-house, TBtools, was used for the Gene Ontology Term and the KEGG pathway enrichment analysis and visualization (Chen et al., 2018).

eFP browser database construction

We used a docker container to construct a pineapple fruit eFP browser that could be used over the long term. The CentOS 7 image was pulled from docker.io, and dependent software packages for the eFP browser were installed according to the manual. The eFP browser installation package was downloaded from http://www.bar.utoronto.ca/efp/development/ and some scripts in the package were adapted for RNAseq data. To facilitate the data importing process, we wrote two python scripts to convert tab-delimited files into SQL command records. After the browser was set up locally, we made a docker image and uploaded it to our VPS (http://www.tbtools.xyz/efp/cgi-bin/efpWeb.cgi) to provide service for all users.

Pineapple fruit detaching and sampling

Pineapple forms a collective fruit that is developed from approximately 100 individual florets. This fruit formation is similar to some berries (Figs. 1A and 1B). Pineapple fruit development accompanies its flower development. In this study we focused on fruit development and defined the time when the first round/batch of flowers started to open as the first fruit developmental stage. The stage when flowering ceases was defined as the second stage. Finally, the third stage was defined as when florets reached mature status and stopped expanding (Fig. 1A).

Pineapple fruits contain several main tissue types: bracts, sepals, flower disks, receptacles, ovaries walls, placentas, ovules, and cores (Fig. 1B). In addition, we also examined flower tissues such as petals, styles, and stamens, as well as vegetative tissues such as leaves, roots, and stems. The berry floret is enlarged as it expands. Petals are colored pale purple. Importantly, the rate of enlargement of the bract and receptacle are faster than the rates of the flower disk and placenta, which results in the formation of pineapple fruit eyes.

The global landscape of the pineapple fruit developmental transcriptome

To characterize expression dynamics throughout pineapple fruit development, RNAseq libraries were constructed and sequenced for 14 different tissues collected at three major developmental stages (Table S1; Fig. S1). Using the Illumina sequencing platform, ∼1.19 billion 125 bp paired-end reads (149 GB) were generated, corresponding to an average of 33 million reads per tissue sample (Table S1). Most reads were mapped onto exon regions, indicating that the RNAseq data was clean and could be used in further analyses (Fig. S1).

The pineapple genome was expected to contain 27,024 genes (Ming et al., 2015). We found that 23,789 (88.02% of the total) annotated genes were expressed in at least one of the 14 tissue types (Figs. 2A and 2B). The detection of expression of such a high proportion of genes may be attributed to the diversity of tissues included in the study as well as high sequencing depth and coverage. The expression of 3,235 gene models (11.98% of the total) were either not detected in any of the tissues or were detected below background levels (TPM lower than 0.1). These gene models may represent pseudogenes or they may be expressed only under specific biotic or abiotic stress conditions. Expression pattern correlation analysis showed that expression profiles of vegetative tissues were more distinct than profiles of reproductive tissues (highlighted in purple and red rectangles in Fig. 2C).

Tissue-specific and constitutive expression dynamics

Genes can be expressed constitutively or preferentially according to their different roles in plant development. To study the mechanisms underlying the development of pineapple collective fruit, we utilized TAU methods to detect housekeeping (TAU scores lower than 0.2) and tissue-specific (TAU scores higher than 0.99) genes. In total, 273 genes were found to be expressed constitutively with varying expression levels (Fig. 3A; Tables S2–S3). In contrast, we found 1,051 tissue-specific genes (Fig. 3B; Tables S4 and S5). Of these, most were expressed preferentially in stamen (286 genes), root (170 genes), and leaf (147 genes) (Fig. 3B; Table 1). Among these genes, most were also stage-specific, and were preferentially expressed in the same tissue at a given development stage (Fig. S2).

Co-expression network analysis

Using the sequencing data generated earlier, we used WGCNA to detect gene co-expression during pineapple fruit development. In total, 18 gene modules were classified, with the number of genes involved ranging from 155 (light green module) to 4,522 (turquoise module) (Fig. 4A; Table S6). Among these modules, several showed spatial and temporal expression patterns (Fig. S3). Genes of the red module were preferentially expressed in bracts and sepals. KEGG pathway enrichment analysis indicated that the functions of the genes of the red module were associated with plant defense, including plant-pathogen interactions and MAPK signaling (Figs. 4B; Fig. S4). In reproductive tissues, such as receptacles, stamens, and styles, genes of the salmon-colored module were highly expressed at the beginning of fruit expansion and faded afterward. These genes were generally not expressed in vegetative tissues such as leaves and roots. According to pathway enrichment analysis, these genes were involved in endocytosis, transport and catabolism, and cutin suberine and wax biosynthesis (Figs. 4C; Fig. S5). Genes belonging to the light cyan module were also expressed at lower levels in vegetative tissues, however, in reproductive tissues, they showed expression patterns similar to those of the genes in the salmon-colored group. As indicated by gene set enrichment analysis, genes involved in terpenoids and polyketides metabolism were over-represented in this group (Fig. 4D; Fig. S6).

The Pineapple eFP browser for fruit development analysis

Electronic fluorescent pictograph browsers can accelerate routine gene expression analysis, especially in developmental biology. To facilitate visual exploration of gene expression during pineapple fruit development, we leveraged docker technology to build a pineapple eFP browser (http://www.tbtools.xyz/efp/cgi-bin/efpWeb.cgi). The browser provides a user-friendly web-based interface. Users can enter a specific pineapple gene id and obtain information on its expression in a short time. To ensure that the pineapple eFP browser was working correctly, we manually checked the gene expression pattern graphs of three different genes. Three genes (Aco031614, Aco023419, and Aco004566) were used for this test. Figure 5B uses darker colors to denote higher expression levels of the query gene in specific tissues. This figure shows that a randomly picked gene (Aco031614) is expressed at the highest levels in bracts, followed by sepals, petals, core, and others (Fig. 5B). A stamen-specific gene (Aco023419) was shown in an image in which only stamens were colored red; all other tissues were colored bright yellow (Fig. 5C). In contrast, all tissues were colored red when testing a constitutively expressed gene (Aco004566) (Fig. 5D).

We obtained a comprehensive and high-quality fruit transcriptome for pineapple fruit

Although extensive RNA sequencing data for pineapple exists on public repositories such as NCBI SRA, only a few of these were produced from fruit (Ong, Voo & Kumar, 2012; Ma et al., 2015; Ming et al., 2015; Chen et al., 2016; Liu & Fan, 2016; Redwan, Saidin & Vijay Kumar, 2016). No data is available for the different tissues present in the pineapple collective fruit, and this fact hinders studies of pineapple fruit development. Here, we present 36 libraries of pineapple, covering all distinct tissues of its fruit at three developmental stages. Almost 90% of the genes were detected in the current analysis based on gene strucutre annotation from the reference pineapple genome. The difference in the number of genes detected in each tissue indicated that many genes are expressed preferentially in some tissues and not at all in others. In order to generate a transcriptional landscape of pineapple for further study, no replicate has been set. To ensure the data is trusted, we have applied qRT-PCR to validate expression of two pineapple gene families in our previous work (Liu et al., 2017; Xie et al., 2018).

Detection of constitutively expressed and tissue-specific genes provide the basis for further study of pineapple fruit development

Tissue-specific genes play fundamental roles in tissue differentiation and maintenance (Pattison et al., 2015). Detection of tissue-specific genes in pineapple fruit tissues can provide the basis for further study of genetic mechanisms responsible for fruit phenotypes, and may also provide a basis for genetic manipulation. For instance, in collaboration with a developed pineapple genetic-transformation system (Soneji & Nageswara, 2009), we can express a gene of interest in a specific tissue with the promoter sequence of a tissue-specific gene. In this study, we identified ∼1,000 tissue-specific genes. Among these, stamens possessed the most tissue-specific genes; this may be expected since many pollen-specific genes have already been characterized. In addition, leaf and root tissues both possessed more than 100 tissue-specific genes; this is almost twice the number of genes in fruit tissues. This may be due to that these genes are involved in nutrient uptake.

In contrast, only a few genes were preferentially expressed in tissues of the pineapple fruit. a total of 29 genes were core-specific genes. Among them, Aco002250 coding a copper ion binding protein possessed the highest expression level. Its homology, LOC_Os01g32790, in rice is preferentially expressed in inflorescence according to the records in the MSU Rice database (Kawahara et al., 2013). A Chalcone synthase (CHS) gene, Aco008872, was also found to be core-specific. In maize, silencing CHS increases Lignin Content (Eloy et al., 2017). The pineapple fruit core is the extension of the stem, which is rich in lignin. As the fruit develops, the CHS gene specifically expressed in the core might take part in reducing the lignin content, making the core more edible. In total, we detected 31 genes preferentially expressed in flower-disk. Most of them were annotated as “hypothetical protein.” One auxin response factor might be useful for further study, whose homology, AT1G30330, in Arabidopsis is preferentially expressed carpel according to eFP browser on TAIR (www.arabidopsis.org). Pineapple flower-disk decides the depth of the fruit-eye. Controlling expression pattern of pineapple ARF6 might be a possible way to breeding pineapples for shallow fruit-eyes. A total of 34 genes were found to be ovary-wall specific genes. It is interesting that, out of them, two shikimate kinase gene, Aco004125 and Aco029719, possessed the highest expression levels. Shikimate kinase is the key component of the shikimate pathway, from where a vast number of aromatic compounds originated (Bentley & Haslam, 1990). Pineapple is famous for its special fragrance. The high expression level and the preferential expression pattern of these two shikimate kinase genes in ovary-wall indicate that pineapple fragrance may be generated from ovary-wall and these two genes are involved in fragrance production of pineapple. In total, 47 genes are preferentially expressed in pineapple placenta. Among them, we found Aco006346 coding a homology of sugar transporter SWEET17. In Arabidopsis, SWEET17 mediates fructose transport across the tonoplast (Guo et al., 2014). Pineapple SWEET17 might also play a similar role during fruit development. Apart from this, we also identified 273 constitutively expressed genes, and these may serve as useful reference genes for qRT-PCR experiments of pineapple fruit.

Gene module classification can facilitate further study of pineapple fruit

Genes function as networks in all biological processes. To uncover the mechanisms underlying different traits, network-level analyses are required. Here, we classified all expressed pineapple genes into 18 gene modules. Among these, genes of the red module were preferentially expressed in bracts and sepals. According to the KEGG pathway enrichment result, most members were associated with plant defense, including plant-pathogen interactions and MAPK signaling. As the pineapple fruit develops, it faces various kinds of bio-stress like pest binding. Thus, it is possible that these resistance-associated genes are expressed with higher levels in the outer part of pineapple fruit to defense the adversity. Genes of salmon module might have similar functions but function in a different way. These genes, functionally related to cutin, suberine, and wax biosynthesis, are only highly expressed at the beginning of fruit expansion. They may be important for all reproductive tissues of pineapple but only functions at the specific stage. In contrast, genes in the light cyan module seems to be linked to fruit quality. Most members of this group are involved in terpenoid and polyketide metabolism. It is likely that this module contains key genes related to pineapple ripening and fragrance biogenesis. In addition, other modules also seem to have distinct expression profiles and apparent functions. Together, these modules can be used for gene screening and further experimentation.

The eFP browser is an important tool for pineapple fruit study

Studies of fruit are important for fruit tree breeding and research, since different crops form different fruit types. Tomato, the most famous fruit study model species (Kimura & Sinha, 2008), bears simple fruit developed from ovaries. Strawberry, another model fruit species (Li et al., 2011), possesses aggregate accessory fruit developed from receptacles (Hollender et al., 2012). Both species have eFP browsers, which provide researchers with a simple method to explore gene expression data. In the present study, we built a pineapple eFP browser in which distinct pineapple tissues are colour-coded. Compared to traditional gene expression databases, which visualized gene expression matrices as tile plots (Nussbaumer et al., 2014), users can explore specific genes in a cartoon image and see how expression levels differ among pineapple tissues. Moreover, the browser leverages docker technology; with docker images, users can also re-build their own pineapple fruit eFP browsers locally relatively easily in multiple operating systems. In this way, the pineapple eFP browser can be accessible without a network connection.