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Genome‐wide transcriptome signatures of ant‐farmed Squamellaria epiphytes reveal key functions in a unique symbiosis

Abstract Farming of fungi by ants, termites, or beetles has led to ecologically successful societies fueled by industrial‐scale food production. Another type of obligate insect agriculture in Fiji involves the symbiosis between the ant Philidris nagasau and epiphytes in the genus Squamellaria (Rubiaceae) that the ants fertilize, defend, harvest, and depend on for nesting. All farmed Squamellaria form tubers (domatia) with preformed entrance holes and complex cavity networks occupied by P. nagasau. The inner surface of the domatia consists of smooth‐surfaced walls where the ants nest and rear their brood, and warty‐surfaced walls where they fertilize their crop by defecation. Here, we use RNA sequencing to identify gene expression patterns associated with the smooth versus warty wall types. Since wall differentiation occurred in the most recent common ancestor of all farmed species of Squamellaria, our study also identifies genetic pathways co‐opted following the emergence of agriculture. Warty‐surfaced walls show many upregulated genes linked to auxin transport, root development, and nitrogen transport consistent with their root‐like function; their defense‐related genes are also upregulated, probably to protect these permeable areas from pathogen entry. In smooth‐surfaced walls, genes functioning in suberin and wax biosynthesis are upregulated, contributing to the formation of an impermeable ant‐nesting area in the domatium. This study throws light on a number of functional characteristics of plant farming by ants and illustrates the power of genomic studies of symbiosis.

Genomic approaches to insect agriculture have revealed reciprocal biochemical and genetic adaptations. For example, in leaf-cutting ants, genes in the ants' arginine biosynthetic pathway have been lost because arginine is supplied by the ants' fungal crop. Conversely, the fungal crops show changes in chitin synthesis and loss of enzymes to degrade lignin (Nygaard et al., 2011(Nygaard et al., , 2016. And in Termitomyces fungi cultivated by Macrotermes termites, the degradation of complex plant carbohydrates occurs via the cooperation of both the fungus and the termites, as well as their bacterial gut microbiomes (Poulsen et al., 2014). In ant/plant symbioses, genome sequencing of Pseudomyrmex ant species that independently evolved obligate nesting in mutualistic plants revealed positive selection of many genes involved in nervous system functioning, associated with their aggressive behavior toward herbivorous insects (Rubin & Moreau, 2016). However, to our knowledge, no genomic study has focused on the plant partners involved in these symbioses, likely because of the difficulty of working with large plant genomes without reference.
In the present study, we apply transcriptomics to the plant partner in an obligate insect agriculture system discovered in Fiji.
This system involves the symbiosis between the ant Philidris nagasau (Dolichoderinae) and epiphytes in the genus Squamellaria (Rubiaceae) that the ants fertilize, defend, harvest, and depend on for nesting (Chomicki et al., , 2020Chomicki & Renner, 2016a, 2016b. Fiji harbors nine species of Squamellaria of which six are obligately ant farmed, while three form facultative mutualisms with a wide range of ants, with the obligate ant-farmed species forming a clade, the others a grade (Chomicki & Renner, 2016a, 2016b. All Squamellaria species, like other species in the Hydnophytinae clade of the Rubiaceae, form a large tuber with self-formed entrance holes and complex cavity networks in which ants nest (Chomicki & Renner, 2017. Ant-farmed Squamellaria also offer food rewards to their ant partners, and in return, the ants fertilize their hosts (their "crop") by defecation, disperse their seeds, protect the seeds from predators, and defend the plant against herbivores (Chomicki et al., 2016(Chomicki et al., , 2020Chomicki & Renner, 2016a. The single ant species involved in the Squamellaria farming symbiosis, P. nagasau, besides displaying numerous of specialized behaviors, also evolved the ability to evaluate and optimize the yield of its crop (in terms of food rewards) by cultivating its crop in high-light conditions (Chomicki et al., 2020).
An important trait of all farmed Squamellaria species is the differentiation of the inner domatium walls .
Nonfarmed Squamellaria exhibit an intermixing of warty-surfaced and smooth-surfaced sections in their domatia, with low nitrogen uptake efficiency. In contrast, the inner cavity surface of farmed Squamellaria is differentiated into smooth areas that are impermeable to water or solutes and hyperabsorptive warty areas that are specialized for nitrogen uptake ; Figure 1). This led us to hypothesize that genes involved in suberin or wax production might be upregulated in the smooth tissues, while genes involved in nitrogen uptake might be upregulated in the warty tissues on which the ants defecate. To test these hypotheses, we here use genome-wide transcriptomes of the inner domatium walls of an obligately farmed Squamellaria species (S. imberbis, Figure 1a).
Using de novo RNA sequencing (RNA-seq), we aimed to answer the following questions: (i) What classes of genes are upregulated in warty-surfaced versus smooth-surfaced domatium walls? (ii) Are genes encoding for biosynthesis or regulation of wax or suberin compounds upregulated in smooth walls? And because warts are functionally analogous to roots (iii) are root development genes upregulated in warty walls?

| Study site and samples preparation
Samples of three S. imberbis individuals were collected on Vanua Levu island in Fiji, along the Cross Island road before the bifurcation to Nabouwalu and Labasa in July 2018. Samples were immediately placed in RNAlater (Sigma-Aldrich) until their extraction <72 h later. Plants were identified by the senior author (G.C.), following the taxonomy of Chomicki and Renner (2016b)

| Sequencing and dataset preparation
For each RNA sample, a strand-specific cDNA library (library type: RF, the first read of a fragment pair is from the opposite strand) with mRNA selection using poly-A tail enrichment was constructed and sequenced using the Illumina HiSeq 2500 Genome Sequencer (Illumina, San Diego). Libraries were sequenced to a depth of at least 37 million pairs of reads of 150-bp length. Library preparation and sequencing was performed by the company Eurofins Genomics (Konstanz, Germany).
Raw reads were preprocessed by performing adapter and base trimming, using a quality Phred score of 30 as implemented in the software Trim Galore! v0.6.4 (Krueger, 2015). FastQC v0.11.9 (Andrews, 2010) was used to assess the quality of trimmed reads, with the per-base sequence quality scores of all sequences higher than 34. The raw sequence datasets are available in the Short Read Archive of the NCBI repository (https://www.ncbi.nlm.nih.gov/sra) under the BioProject accession number PRJNA734727.

| De novo assembly and quantitation
De novo assembly of all the trimmed RNA-seq data was conducted using Trinity v2.8.5 (Grabherr et al., 2011). All sequences of the three tissue types were combined to obtain a single complete assembly. Then the abundance of each sample transcript was independently estimated on both isoform and gene level, using the alignment-free method implemented in the software Salmon v0.14.1 (Patro et al., 2017). When estimating gene counts, trimmed mean of M values (TMM) were used for normalization, and the scaled Transcripts-per-million (TPM) method in tximport (Soneson et al., 2015) was used to exclude effects of differential transcript usage caused by differences in isoform lengths. All estimates of the nine samples (three tissue types from three plant individuals) were used to construct matrices of raw counts, TPM expression values (not cross-sample normalized), and TMM-normalized expression values. correlation coefficient did not show that the replicates are more correlated within samples, PCA indicated that each type of tissue clustered together using the first two principal components ( Figure S1).

| Differential expression analyses
Among the three types of samples (warty surfaces, smooth surfaces, tuber tissue), differential pairwise expression analyses were  Table S1.

| Functional annotation
Coding region prediction for all DE Trinity gene assemblies was Finally, gene ontology annotation data of A. thaliana were acquired from PANTHER v14.0 (Thomas et al., 2003) and further annotated to the orthologous genes of S. imberbis. The annotation of all DE transcripts is reported in Table S2.

| Gene set enrichment analysis
To build a customized annotation database of S. imberbis, we annotated the complete transcriptomic assembly as described in section

and then used Gene Ontology terms in Biological Processes
(GOBP) of the Arabidopsis orthologs to annotate the corresponding S. imberbis genes. Next, GeneSCF v1.1 (Subhash & Kanduri, 2016) was used for GOBP enrichment analysis of each group of differentially expressed genes in each of the three tissue types. All significantly enriched GO terms are marked in Table S2, and detailed enrichment statistics are given in Table S3.

| Most differentially expressed genes are upregulated in warty inner domatium tissues
Sequencing statistics are summarized in Table 1. Among the 737,226 assembled transcripts, 962 genes were found differentially expressed in at least one comparison between two tissue types (false discovery rate [FDR] <0.001, see Table S1 for statistics of DE analysis of all annotated genes in this study). Comparing warty-surface tissue and tuber tissue (the control) revealed that 859 genes were significantly more expressed in warts and 44 genes were significantly more expressed in tubers. Comparing warty tissue and smooth tissue showed that 78 genes were significantly more expressed in warty-surface tissue and 9 were significantly more expressed in smooth-surface tissue. Comparison of smooth tissue and tuber tissue indicated that 97 genes were significantly more expressed in the former and 5 more in the latter. Among all 3 tissue types, 66 genes were most expressed in warty tissue, 3 in smooth tissue, and 4 in tuber tissue. In addition, 57 genes were least expressed in tuber tissue. No genes were least Note: "Warty" refers to warty-walled inner domatium tissue; "smooth" refers to smooth-walled inner domatium tissue; "tuber" refers to nondifferentiated domatium tissue, which served as a control. Each sample comes from a different plant individual.
TA B L E 1 Summary of RNA-sequencing quality expressed in warty or smooth tissue compared to the control. Of the 962 differentially expressed genes, 153 could be annotated successfully to genes of A. thaliana (Figure 2).

| Genes functioning in wax and suberin biosynthesis are upregulated in smooth inner domatium tissues
Of the 97 orthologues significantly more expressed in smooth tissues, 2 were annotated to Arabidopsis KCS6 and the MYB94 and MYB96 genes, which function in wax biosynthesis (Figure 3; Lee et al., 2014;Millar et al., 1999;Seo et al., 2011) and 2 to the ATP-Binding Cassette genes ABCG6 and ABCG20, which function in suberin biosynthesis (Figure 3; Yadav et al., 2014). The Gene Ontology term suberin biosynthetic process (GO: 0010345) was significantly enriched with a p-value of 4.78E-05 and FDR of 6.21E-04. Besides, a series of GO biological processes related to wax/suberin biosynthesis (GO:0006869~lipid transport, GO:0019915~lipid storage, GO:0042761 ~ very long-chain fatty acid biosynthetic process, and GO:0010208 ~ pollen wall assembly) were also significantly enriched in smooth surfaces (p < .02, FDR < 0.03).

F I G U R E 2
Heatmap of the expression level of 153 Trinity genes that are expressed differentially in at least one kind of tissue, predicted to be coding sequences and annotated successfully to genes of Arabidopsis thaliana. Gene names are composed of a prefix of "Si"

| Genes functioning in root development are upregulated in warty domatium tissues
Some of the auxin-related genes upregulated in warty tissues are also involved in root development, that is, ABCG37, ACT7, and the NAC Domain Transcription Factors FEZ (Růžička et al., 2010;Willemsen et al., 2008). Other genes related to root development that were significantly more expressed in warts included Ammonium Transporter 1;1 (AMT1;1), Sucrose Nonfermenting 1-Related Protein Kinase 2.4 (SnRK2.4) and more members of the Actin gene family (ACT1, ACT2, and ACT8) (Lima et al., 2010;McLoughlin et al., 2012).
In total, five Trinity genes related to root development were significantly more expressed in warty tissue. Genes significantly more expressed in regular tuber tissue were annotated to the Lateral Organ Boundaries-Domain 16 and 29 (LBD16 and LBD29) ( Figure 5).
However, no GOBP related to root development was significantly enriched among DE genes.

| Genes functioning in biotic and abiotic stress responses are upregulated in warty inner domatium tissues
A total of 54 Trinity genes that are orthologous to Arabidopsis genes involved in defense and response to external stimuli were significantly more expressed in warty surfaces ( Figure 6).

| Genes functioning in nitrogen uptake and transport are upregulated in warty inner domatium tissues
Two Trinity genes that are orthologues of A. thaliana genes related to nitrogen metabolism and transport were significantly more expressed in warty tissues (Figure 7), namely Ammonium Transporter 1;1 (AMT1;1), AMT1;2 and Glutamate dehydrogenase 1 (GDH1), which function in ammonia assimilation and ammonium transport (Mayer & Ludewig, 2006;Meng et al., 2016). We also identified the significant enrichment of three GOBP related to ammonium transport (GO: 0015843~methylammonium transport, GO: 0015696~ammonium transport, and GO: 0072488~ammonium transmembrane transport).

| Upregulation of wax and suberin genes is associated with the formation of clean and sturdy nesting sites inside domatia
This transcriptome analysis revealed that genes upregulated in the inner walls of ant-housing plant tubers (domatia) function in the biosynthesis of wax and suberin (Figures 3 and 8) field have shown that these surfaces do not absorb water or solutes, which suggested an impermeable coating . Both suberin and waxes are hydrophobic impermeable materials. For suberin, a group of ABCG half-transporters (ABCG1,6,16,20) has been shown to control water and solute movement, typically in roots and seed coats (Yadav et al., 2014). For wax, the KCS6 gene (also known as CUT1) is involved in the production of cuticular wax, which makes up all stem wax components in Arabidopsis (Millar et al., 1999). The upregulation of these genes in a certain section of the domatium cavities allows the formation of a sturdy nesting site for Philidris nagasau ants.
Besides forming hydrophobic barriers, wax also functions as a defense against bacterial and fungal pathogens (Jenks et al., 1994;Wang et al., 2020;Zhang et al., 2019) and insect herbivores (Eigenbrode & Espelie, 1995), and suberin is also thought to play an important role in limiting pathogen access (Pollard et al., 2008;Thomas et al., 2007). Thus, the coating of smooth walls with wax and suberin likely reduces bacterial and fungal pathogen growth (Zhang et al., 2019). Another potential role of the wax/suberin coating is the protection of wall tissue against damage from the claws of the ants' tarsae; the constant high concentration of workers in these cavities might otherwise incur a high mechanical cost to the domatium tissue. Thick cuticles inside a domatium are also seen in unrelated species, for instance in the leaf domatia of Hirtella physophora (Leroy et al., 2008). Further work is needed to test these potential roles in defense against pathogens and mechanical stress.

| Warts are functionally analogous to adventitious roots
Auxin plays many roles related to plant growth and body formation, from root development to shoot apical dominance and branching regulation, flowering, wound response, and fruit growth (Woodward & Bartel, 2005). It also controls adventitious root development in response to environmental signals (Gonin et al., 2019). In this study, many of the genes upregulated in warty inner domatium tissues relate to auxin transport and have orthologues expressed in A. thaliana roots (Figures 4, 5 and 8). For example, ABCG37 is expressed in the lateral root cap and epidermis (Růžička et al., 2010); and the NAC Domain Transcription Factors FEZ is expressed in root cap stem cells, promoting periclinal root cap-forming cell division (Willemsen et al., 2008). That warts inside domatium cavities may be analogous to roots was originally hypothesized by Beccari (1884-86) at the end of the 19th century, while he investigated the closely related genus Myrmecodia, and field experiments on nutrient uptake in two Squamellaria species have demonstrated the warts' hyperabsorptive function . The transcriptomic data obtained here now support this function. Warts, thus, appear to be functionally analogous to adventitious roots.
Besides auxin-related processes that are active during root development (Overvoorde et al., 2010), other genes involved in root development were also upregulated in warty surfaces compared to smooth surfaces and undifferentiated tuber tissues. Among them, multiple isovariants of the Actin gene family regulate different aspects of root development. Mutants of ACT2 and ACT8 genes exhibit root hair defects, while a mutant of the ACT7 gene exhibits root elongation defects (Kandasamy et al., 2009) SiLBD20  (McLoughlin et al., 2012) and AMT1;1, which increases lateral root initiation and higher order lateral root branching when stimulated by local ammonium supply (Lima et al., 2010).

| Defense-and stress-related genes are upregulated to protect permeable warty inner domatium surfaces
Fifty-four genes upregulated in the warty inner domatium surfaces function in defense and in response to a variety of external stimuli ( Figure 6). For example, the SSL gene family plays key roles in bacteria-, fungus-and wounding-induced plant defense mechanisms (Sohani et al., 2009); pectin methylesterases (PMEs) function mainly in immunity against gram-negative bacteria such as Pseudomonas syringae (Bethke et al., 2014); and the induction of Terpene Synthase 12 (TPS21) results in increased emission of sesquiterpenes, which is among the herbivore-induced plant volatiles that attract natural enemies of attacking insects and that warn neighboring plants (Hong et al., 2012;War et al., 2011 highly expressed in warty surfaces suggests that the plant upregulates chemical defenses to counteract the surface permeability required for nutrient and water absorption. Two genes upregulated in warts that appear to be particularly important are Galactinol synthase (GolS) 1 and 2, which function in response to abiotic stresses such as osmotic and oxidative stress, heat, chilling, and water deprivation. GolS1 is a heat shock target gene, which is responsible for heat stress-dependent synthesis of raffinose (Panikulangara et al., 2004), and GolS2 leads to increased drought resistance (Taji et al., 2002) and oxidative stress (Nishizawa et al., 2008). In Squamellaria domatia, the concentrated defecation of ants on the warty surfaces may create a hypertonic environment, and tolerance of oxidative or hypertonic stress may be crucial.

| CON CLUS ION
The obligate mutualism between Squamellaria and Philidris ants has led to the differentiation of the plant's inner domatium walls into warty surfaces for defecation and smooth surfaces for nesting. This transcriptome analysis revealed genes functioning in nutrient uptake and defense against pathogens upregulated in the warty surfaces, contributing to the plant's ability to use nutrients from the ants' targeted defecation while minimizing pathogen entry (Figure 8). It also identified genes functioning in wax and suberin biosynthesis upregulated in the smooth surfaces, contributing to the formation of clean nesting sites. This work paves the way for comparative genomic studies of symbiosis-related genes across the Hydnophytinae clade, the most species-rich clade of ant-plants worldwide.

ACK N OWLED G M ENTS
We thank Brian Haas for advice with TRINITY and replicate checks. Orchid Foundation. We thank Veronika Mayer, an anonymous reviewer, and the editor Chris R. Smith for comments that helped improve the manuscript.

CO N FLI C T O F I NTE R E S T
The authors declare no competing interest.

DATA AVAILABILITY STATEMENT
RNA-seq sequences are available in GenBank (https://www.ncbi. nlm.nih.gov/genba nk/) at the accession number SRA (BioProject F I G U R E 8 Model showing the main functions underlying the genes expressed in warty versus smooth walls in Squamellaria imberbis domatia. In warty walls, our transcriptome analysis revealed that putative genes are involved in wart development and possibly spacing (root transcriptional regulators, cell elongation factors and genes involved in auxin transport and response); genes are involved in the response to biotic and abiotic stresses (including defense against fungal and bacterial pathogens); and finally, genes that likely play a role in the uptake of ant-derived nitrogen. In smooth walls, upregulation of wax and suberin genes likely acts in concert to generate the impermeable coating on these walls for ant nesting