Conservation and divergence of small RNA pathways and microRNAs in land plants
- Chenjiang You†1, 2, 3,
- Jie Cui†1, 2,
- Hui Wang4,
- Xinping Qi5,
- Li-Yaung Kuo6,
- Hong Ma5,
- Lei Gao1,
- Beixin Mo1Email author and
- Xuemei Chen1, 3, 7Email authorView ORCID ID profile
© The Author(s). 2017
Received: 1 February 2017
Accepted: 31 July 2017
Published: 23 August 2017
As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. However, both small RNAs themselves and small RNA pathways are not well characterized in other land plants such as lycophytes and ferns, preventing a comprehensive evolutionary perspective on small RNAs in land plants.
Using 25 representatives from major lineages of lycophytes and ferns, most of which lack sequenced genomes, we characterized small RNAs and small RNA pathways in these plants. We identified homologs of DICER-LIKE (DCL), ARGONAUTE (AGO), and other genes involved in small RNA pathways, predicted over 2600 conserved microRNA (miRNA) candidates, and performed phylogenetic analyses on small RNA pathways as well as miRNAs. Pathways underlying miRNA biogenesis, degradation, and activity were established in the common ancestor of land plants, but the 24-nucleotide siRNA pathway that guides DNA methylation is incomplete in sister species of seed plants, especially lycophytes. We show that the functional diversification of key gene families such as DCL and AGO as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered a conserved AGO subfamily absent in angiosperms.
Our phylogenetic analyses of miRNAs in bryophytes, lycophytes, ferns, and angiosperms refine the time-of-origin for conserved miRNA families as well as small RNA machinery in land plants.
RNAs are some of the most important components of life. They not only serve as mediators between genes and proteins as depicted in the central dogma , but also act as direct regulators of life processes, such as in the form of ribozymes and regulatory RNAs [2, 3]. Two major classes of small regulatory RNAs, microRNAs (miRNAs) and small interfering RNAs (siRNAs), impact a multitude of biological processes in almost all eukaryotic lineages. In plants, small RNAs repress gene expression either at the transcriptional level by DNA methylation or at the posttranscriptional level via mRNA cleavage and/or translational inhibition .
Plant miRNAs largely act at the posttranscriptional level—they recognize target mRNAs through sequence complementarity and lead to mRNA cleavage or translational repression . The basic frameworks of miRNA biogenesis, function, and turnover have been established from studies in model angiosperms . A miRNA gene is transcribed by RNA polymerase II (Pol II). The primary transcript is processed by DICER-LIKE 1 (DCL1) into a miRNA/miRNA* duplex with a length of approximately 21 nucleotides (nt) . The RNA binding protein HYPONASTIC LEAVES 1 (HYL1) and the zinc-finger protein SERRATE (SE) aid DCL1 in precursor processing [7–10]. The duplex is methylated by the methyltransferase HUA ENHANCER 1 (HEN1) . Afterwards, one strand of the duplex associates with ARGONAUTE1 (AGO1) to form the RNA-induced silencing complex (RISC) , which recognizes and represses target mRNAs [12, 13]. AGO1 is a major miRNA effector, as its endonuclease activity is responsible for target mRNA cleavage [14, 15]. HEN1 SUPPRESSOR1 (HESO1) and RNA URIDYLYLTRANSFERASE1 (URT1) are nucleotidyl transferases that act cooperatively to 3′ oligouridylate unmethylated miRNAs, thereby triggering miRNA decay . SMALL RNA DEGRADING NUCLEASE (SDN) is a family of 3′-5′ exonucleases that also participate in miRNA degradation .
One main function of endogenous siRNAs in plants is RNA-directed DNA methylation (RdDM), which silences transposable elements and repeat sequences to maintain genome stability [4, 18]. In Arabidopsis, the core of this pathway is 24-nt siRNAs, usually derived from transposable elements and repeats. RNA polymerase IV (Pol IV) produces single-stranded RNAs from RdDM target loci, the RNAs are converted to double-stranded RNAs by RNA-DEPENDENT RNA POLYMERASE 2 (RDR2), and the double-stranded RNAs are processed by DCL3 to 24-nt siRNA duplexes, which undergo HEN1-mediated methylation [19, 20]. The mature siRNA is loaded into AGO4 and interacts with scaffold RNAs transcribed at the target loci by RNA polymerase V (Pol V); this interaction guides DNA methylation (mainly the CHH type where H represents any nucleotide but G) to result in the silencing of the target loci [19, 20].
Angiosperms (flowering plants), from which most of our knowledge of small RNAs and small RNA machinery has been gained, represent only one of the major land plant lineages, which include both vascular plants and non-vascular plants. There are three major types of non-vascular plants—mosses, liverworts and hornworts—which are collectively called bryophytes; they are simpler than vascular plants in morphology. Vascular plants have evolved water- and nutrient-conducting vascular tissues, which have made them much less dependent on surface water and more widely distributed to diverse terrestrial ecosystems. The dominant group of vascular plants are seed plants, including gymnosperms and angiosperms, whereas lycophytes and ferns are the closest sister groups of seed plants . As sister groups of seed plants, lycophytes and ferns may help us to understand the evolutionary origins and diversification histories of the small RNA machinery and miRNAs . In particular, the closest relatives to seed plants are ferns, which are also much more diverse than lycophytes; therefore, information from ferns provides an important reference for comparison with angiosperms and gymnosperms. However, only one lycophyte, Selaginella moellendorffii, has a sequenced genome, and none of the fern genomes has been sequenced, making it difficult to include them in comparative and evolutionary studies and limiting our understanding.
Most evolutionary studies on small RNA pathways in land plants rely heavily or exclusively on the bryophyte Physcomitrella patens and the lycophyte S. moellendorffii as representative sister groups of seed plants [23–26]. While these studies clearly reveal the existence of small RNA machinery in the common land plant ancestor, the paucity of sister groups of seed plants in these studies precluded a comprehensive picture of small RNA pathway evolution in land plants. For example, in angiosperms, DCL and AGO genes have diversified into four and three clades, respectively, representing functional diversification of small RNA pathways [25, 26]. Without information from ferns, the closest sister group of seed plants, the timing and patterns of small RNA pathway diversification were unknown or inconclusive [4, 26, 27]. Examples include the timing of the DCL2/4 divergence, AGO family expansion, and distinction between Pol IV and Pol V. Plant-specific Pol IV and Pol V are derived from Pol II with innovations in the usage of novel subunits. Some subunits that distinguish Pol IV/V from Pol II, namely the first, second, and seventh, are present in P. patens and S. moellendorffii, indicating early divergence from Pol II . But the divergence between Pol IV and Pol V in land plants is more ambiguous. Based on the presence of proteins with domain structures similar to the largest subunits of Pol IV and Pol V in P. patens, it was concluded that Pol IV and Pol V diverged in the most recent common ancestor of land plants. But genes encoding distinct largest subunits of Pol IV and Pol V are not found in the lycophyte S. moellendorffii .
In recent years, with the development of high throughput sequencing technology, numerous miRNAs have been identified in various plant species, ranging from green algae to angiosperms. In miRBase v21 (http://www.mirbase.org), over 8000 miRNAs from 73 plant species are included. This information led to the deduction of sets of conserved miRNA families in angiosperms, seed plants, and land plants . However, owing to lagging genome sequencing, the information on lycophyte and fern miRNAs is limited. The only whole-genome-sequenced lycophyte, S. moellendorffii, shows a miRNA profile different from that in angiosperms . More recently, a number of conserved miRNAs in the fern Pleopeltis minima have been discovered using bioinformatic prediction methods . Although comparative studies with existing datasets led to important revelations about the evolution of miRNAs and miRNA–target relationships [31–35], the limited knowledge of miRNAs from major vascular plant lineages hinders a comprehensive view of land plant miRNA evolution.
In order to better understand the molecular evolution of small RNA pathways as well as miRNAs themselves in land plants, we generated and analyzed transcriptomes and small RNAomes of lycophytes and ferns, as well as the transcriptome of the hornwort Folioceros fuciformis (a bryophyte). Four species representing all three orders of lycophytes and 21 species representing 11 orders of ferns were included. We identified gene families encoding major components of the small RNA machinery (biogenesis, degradation, and mode of action) from these sister species of seed plants. This allowed us to perform phylogenetic analyses on the small RNA machinery with representatives from all major land plant lineages (three green algae, three bryophytes, four lycophytes, 21 ferns, and selected seed plants). These analyses confirmed the existence of both posttranscriptional and transcriptional gene silencing pathways in ancient land plants, but more importantly, they provided unprecedented insights into the diversification of small RNA pathways in land plant evolution. The three major AGO clades found in angiosperms are present in bryophytes, lycophytes and ferns, indicating that AGO family diversification occurred early in land plant evolution. Intriguingly, we found an AGO clade present in bryophytes, lycophytes, ferns and a gymnosperm but absent in angiosperms, implicating the presence of a novel class of sRNAs in non-angiosperm species with potentially distinct functions from those in angiosperms. With regard to RdDM, our findings agree with previous reports of early divergence of Pol IV/V from Pol II , but support a later distinction between Pol IV and Pol V in the common ancestor of ferns and seed plants. Analyses of miRNAs and their targets (through prediction and degradome/PARE sequencing) refined the timing of origination of conserved miRNAs and revealed conserved as well as fluid miRNA–target relationships. This study provides a comparative and genome-wide view of small RNAs and small RNA machinery in sister species of seed plants and fills a major gap in the knowledge of small RNA evolution in land plants.
Diversification of DCL and AGO genes in land plants
AGO genes encode proteins that serve as effectors of various small RNAs and, in angiosperms, form three major phylogenetic clades that can be dated back to the most recent common ancestors of land plants, each with distinct functions through binding to different groups of small RNAs [25, 27, 44, 45]. In bryophytes, lycophytes, ferns, and one gymnosperm, the AGO genes formed four clades (Fig. 2b), three of which corresponded to the three clades in angiosperms (Additional file 2: Figure S2). In each of the three clades, the AGO genes evolved independently in each land plant lineage, such that the gene tree mimicked that of the species tree (Additional file 2: Figure S2). Thus, the AGO diversity in each of the three clades in seed plants occurred after the fern/seed plant divergence. In the AGO1/5/10 and AGO2/3/7 clades, expansion occurred in leptosporangiate ferns, the largest lineage including Polypodiales and Salviniales species  (Additional file 2: Figure S2a, b). Thus, one or more ancient duplications likely occurred in this lineage after splitting from Osmundales (arrowheads in Additional file 2: Figure S2). The additional clade of AGO genes (Fig. 2c) in the hornwort F. fuciformis, lycophytes, ferns, and the gymnosperm P. abies encoded AGO proteins containing the functional domains as well as the catalytic residues as in angiosperm AGO proteins (Additional file 2: Figure S3). The presence of AGO members of this clade in the hornwort, lycophytes, ferns, and the gymnosperm suggests an early origin of this clade but a subsequent loss in angiosperms.
Conservation of the miRNA machinery in land plants
We identified homologs of angiosperm genes involved in miRNA biogenesis, such as DCL1, SE, and HEN1, in miRNA degradation, such as HESO1, URT1, and SDN, and in miRNA activity, such as AGO1, from bryophytes, lycophytes, and ferns (Additional file 1: Table S2). DCL1 encoding the major enzyme in miRNA biogenesis was conserved in all land plant lineages analyzed (Fig. 2a). The DCL1 orthologs in bryophytes, lycophytes, and ferns formed a monophyletic group with the DCL1 genes in seed plants (Additional file 2: Figure S1), separate from other DCL clades, indicating early divergence of the miRNA pathway from siRNA pathways in land plants. The AGO1 gene belongs to the AGO1/5/10 clade in angiosperms [14, 27]. The aforementioned phylogenetic analyses of AGO genes in bryophytes, lycophyes, ferns, and seed plants indicated that the AGO1/5/10 clade originated in the most recent common ancestor of land plants (Additional file 2: Figure S2a). Phylogenetic analyses with homologs of SE, HEN1, HESO1, URT1, and SDN showed that homologs from all land plants formed a monophyletic group for each of the genes (Additional file 2: Figure S4), suggesting that each gene existed in the most recent common ancestor of land plants. Homologs of HEN1, HESO1, and URT1 were found as single copy in each bryophyte, lycophyte, and fern species, raising the possibility that they are orthologs (Additional file 2: Figure S4a, d), whereas those of SE had multiple copies in some of the species (Additional file 2: Figure S4c). Together, these findings suggest that the mechanisms of miRNA biogenesis and degradation were established in the most recent common ancestor of land plants.
The unicellular green alga Chlamydomonas reinhartii has miRNAs [46, 47]. This raises the question of whether land plant miRNA pathways already existed in the common ancestor of green plants. We searched for homologs of DCL1, SE, HEN1, AGO1, SDN, HESO1, and URT1 in C. reinhardtii  and two multicellular green algae, Volvox carteri  and Klebsormidium flaccidum . Algal homologs for all genes except for SE were found, and phylogenetic analyses showed that algal HEN1, SDN, HESO1, and URT1 genes each formed a monophyletic group with their land plant homologs, implying that these genes (all encoding enzymes) may have similar molecular functions to their land plant counterparts. However, the functions of these genes in Arabidopsis are not restricted to miRNAs, e.g., HEN1 also acts on siRNAs  and HESO1 and URT1 also act on long RNAs [52, 53]; thus, the phylogenetic conservation in these genes could not be interpreted to support the presence of a common miRNA pathway in algae and land plants.
As the diversification of DCL and AGO genes in land plants reflects the functional diversification of small RNA pathways (such as miRNA vs. siRNA), we turned to examine whether DCL and AGO diversification already occurred in the common ancestor of green plants. AGO genes in green algae clustered separately from those in any other plant species (Fig. 2b), suggesting that the four land plant AGO clades were established after the algae/land plant split. Similarly, all algal DCL genes were outgroups to all land plant DCL clades (Additional file 2: Figure S1), suggesting that DCL diversification occurred in the common ancestor of land plants. Thus, an ancient small RNA-based silencing pathway existed in the common ancestor of green plants (as shown by the presence of DCL, AGO, and HEN1 genes in algae and land plants), but the land plant miRNA machinery probably became specialized after the algae/land plant split.
The RdDM machinery was not fully established in ancient land plants
RdDM is a transcriptional gene silencing process that involves Pol IV and Pol V in angiosperms . RDR2 also acts in RdDM while its paralog in Arabidopsis, RDR6, acts in posttranscriptional gene silencing. In order to evaluate the evolution of RdDM in land plants, we identified genes encoding key subunits of each of the five RNA polymerases (Pol I, II, III, IV, and V), as well as RDR genes in green algae, bryophytes, lycophytes, ferns, and seed plants, and performed phylogenetic analyses (Additional file 2: Figure S5). In land plants, two separate monophyletic groups, RDR1/2 and RDR6, were found, indicating that RDR1/2 and RDR6 diverged from each other early in land plants (Additional file 2: Figure S5d) and suggesting the existence of both transcriptional and posttranscriptional gene silencing in ancient land plants. Homologs of RDR genes in green algae clustered exclusively from those in all examined land plants, suggesting that the RDR diversification into the posttranscriptional and transcriptional gene silencing roles occurred after the algae/land plant split.
To evaluate the divergence of Pol IV/Pol V from Pol II, we examined the phylogeny of the second, fourth, and seventh subunits that are specific to, and shared by, Pol IV and Pol V in angiosperms . NRPA2/B2/C2, encoding the second largest subunit of Pol I, II, and III, respectively, formed three monophyletic groups, respectively, showing that they are distinct from one another and extremely conserved across green plant lineages. Homologs of NRPD2 were found in almost all bryophytes, lycophytes, and ferns examined (Additional file 1: Table S2), and the phylogeny of the genes showed early divergence from NRPB2 in land plant evolution (Additional file 2: Figure S5b). Similarly, NRPD7 from all land plants examined formed a monophyetic group separate from that of NRPB7 (Additional file 2: Figure S5c). Together, the NRPD2 and NRPD7 phylogenies indicate that a Pol IV- or Pol V-like polymerase diverged from Pol II in the most recent common ancestor of land plants. However, we did not detect any NRPD4 genes in any of the bryophyte, lycophyte, fern or gymnosperm species, suggesting that this subunit of Pol IV/V evolved specifically in angiosperms.
In addition to sequence similarity, previous studies also considered the domain structures of NRPD1 and NRPE1 to distinguish the two . NRPD1 and NRPE1 in angiosperms contain an N-terminal domain similar to that in NRPB1 (RPB domain) and a C-terminal DeCL domain. The region between the two domains is long in NRPE1 and short in NRPD1 in angiosperms (Fig. 3). We found that this was not a reliable feature to distinguish the two proteins. The fern proteins that grouped with angiosperm NRPE1 with good bootstrap support did not have the DeCL domain (Fig. 3). Given the poor support for the clustering of NRPD1/E1-like genes from bryophytes and lycophytes with either NRPD1 or NRPE1, we conclude that the divergence of Pol IV and Pol V probably occurred in the most recent common ancestor of ferns and seed plants. The sister group of current ferns and seed plants probably had a single Pol II derivative.
The 24-nt small RNA class is missing in many samples
Identification of miRNAs that are conserved among vascular plants
Although the 24-nt peak was variable in abundance and possibly existence in lycophytes and ferns, the 21-nt peak, largely composed of miRNAs in angiosperms , was clearly discernable in nearly all lycophytes and ferns (Fig. 4a, b; Additional file 2: Figure S6). A gold standard to validate miRNAs in plants  is to interrogate the secondary structures of putative precursors. However, the lycophytes and ferns in this study have not been genome-sequenced except for S. moellendorffii, and the precursors of miRNAs are difficult to detect by RNA-seq because of their low abundance. Therefore, we focused on conserved miRNAs (miRNAs with sequence similarity to annotated miRNAs) as well as validated miRNAs using the genomic sequences of S. moellendorffii.
Previous findings in P. patens and S. moellendorffii revealed that some miRNAs were conserved with those in angiosperms . To find conserved miRNAs in the lycophytes and ferns, we adopted and modified the method described in Chávez Montes et al.  (see “Methods” for details). Because of the existence of homologs of miRNA modification enzymes like HESO1 and URT1 in these species (Additional file 2: Figure S4d), we took 3′ truncation and tailing of miRNAs into account and combined predicted miRNA candidates with identical 1–16 nucleotides from their 5′ ends into one cluster, from which the most abundant one was used as the representative (Additional file 2: Figure S7). As a result, 2675 miRNA clusters from 258 miRNA families matching reported plant miRNAs were identified (Additional file 3; Additional file 1: Table S3).
To confirm the reliability of prediction of conserved miRNAs, we sought to validate the predicted miRNAs in genome-sequenced S. moellendorffii. We first mapped the miRNA candidates to the assembled transcripts from our RNA-seq datasets, and discovered nine transcripts containing hairpin structures accommodating mature miRNAs, indicating that these transcripts may be the precursors to these miRNAs (Additional file 1: Table S4). Of these nine putative precursors, seven contained annotated miRNAs, including miR1081, miR1086, miR1098, miR1105, miR1107, miR1113, and miR171c. The same transcript containing miR171c also contained miR171c*, which was detected in small RNA-seq. The remaining two transcripts supported the prediction of two new miRNAs, miR5054.2429 and miR536.2447. About 49% of the small RNAs from our small RNA-seq from S. moellendorffii were mappable to the S. moellendorffii genome. This low mapping rate might result from sequencing error or incompleteness of the genome. Among the 209 miRNA candidates identified in our study, 69 could be mapped to the genome; in addition, 41 out of the 69 mapped candidates were accommodated in hairpin structures in the genome (Additional file 1: Table S4), indicating high confidence in miRNA prediction. Among the 69 candidates, 25 were among the 64 annotated S. moellendorffii miRNAs in miRBase v21 (Additional file 1: Table S4). Two predicted Smo-miR164 isoforms (not among the annotated miRNAs) mapped to an unusually high number of loci in the genome (Additional file 1: Table S4) compared with other miRNAs, suggesting that these two small RNAs were likely generated from repetitive sequences and were probably siRNAs. Other predicted but not previously annotated miRNA candidates may be true miRNAs. For example, the miR6300 family mapped to genomic regions containing hairpin structures, and this miRNA was found in all four lycophytes and 21 ferns (see below).
Features of lycophyte and fern miRNAs
The 5′ nucleotide
Because the nature of the 5′ nucleotide of small RNAs is a critical feature relevant to their sorting into different AGOs , we examined the 5′ nucleotide identity of these miRNA candidates. In all lycophyte and fern species, the most prevalent 5′ nucleotide of miRNA candidates was U (Fig. 5d), which is also the most prevalent 5′ nucleotide in angiosperm miRNAs , a feature of miRNAs that is probably related to AGO1’s preference for 5′ U . Interestingly, the second most prevalent 5′ nucleotide in lycophyte and fern miRNA candidates was C, as opposed to A in angiosperms (Fig. 5d). In addition, by comparing the 5′ U prevalence between ferns and lycophytes and between lycophytes and other land plants (P. patens, A. trichopoda, O. sativa, Glycine max, and A. thaliana), we found that 5′ U was significantly more prevalent in lycophytes than in ferns (P value < 3.87e-11, χ2 test) or in other plants (P value < 6.17e-12, χ2 test). This implicates different AGO sorting patterns in lycophytes. To determine the 5′ nucleotide identity in individual miRNA families, we also focused on the 25 most conserved miRNA families mentioned above. The identities of the 5′ nucleotides were different among these miRNA families (Fig. 5e). For example, over half of miR6300-3p family members had a 5′ G, and the majority of miR7767 had a 5′ C, which were consistent with the situations in soybean and Brachypodium distachyum, respectively [62, 63]. However, the 5′ C prevalence in miR394s in lycophytes and ferns is not found in the currently annotated miR394s in angiosperms (miRBase v21), suggesting an early divergence of miR394 in land plants.
Isoforms and/or sequence variations
To understand further the conservation/divergence of miRNAs, we examined sequence similarities of conserved miRNA candidates in lycophytes and ferns. To minimize the effects of sequencing error, we focused only on the top one or two most abundant isoforms in each species, and calculated nucleotide variation across the lycophytes and fern species for each conserved family (defined as being detectable in over 15 species of lycophytes and ferns) by comparing to the consensus sequence (Fig. 6c). Many of these miRNA families, including miR158, miR156/7-5p, miR165/6-3p, and miR172-3p, were quite conserved, and had less than one nucleotide variation on average compared to the consensus sequence. Most of the remaining miRNA families varied by less than two nucleotides. However, four families were relatively less conserved; these were miR536, miR159-3p, miR170/1-5p, and miR170/1-3p (Fig. 6c).
Phased siRNAs (phasiRNAs), including trans-acting siRNAs (ta-siRNAs), are a class of secondary siRNAs, the biogenesis of which is triggered by the cleavage of target transcripts (from PHAS and TAS genes) by a few specific miRNAs [67, 68]. Known phasiRNA-triggering miRNAs in angiosperms include miR161 targeting PPR genes, miR168 targeting AGO1, miR173 targeting TAS1 and TAS2, miR390 targeting TAS3, miR393 targeting F-box genes, and miR828 targeting TAS4 in Arabidopsis , and others such as miR4392 in soybean , and miR2118 and miR2275 in monocots . We searched for homologs of the angiosperm phasiRNA-triggering miRNAs in lycophytes and ferns. miR161 was detected in nine species of lycophytes and ferns (Fig. 7; Additional file 1: Table S3). Interestingly, some phasiRNA-triggering miRNAs were detected in ferns but not in lycophytes, including miR168 and miR390 (Fig. 7; Additional file 1: Table S3). It is thought that miR390 is conserved in land plants, as in the moss P. patens, which is the sister group of vascular plants, miR390 targets TAS to generate secondary siRNAs [68, 71]. To further shed light on phasiRNA evolution, we tried to identify phased siRNA clusters in the lycophyte S. moellendorffii genome, but we were unable to find any. miR390 was also not found in our small RNA-seq or in the genome of S. moellendorffii. miR168 was known to be present in the ancient euphyllophytes, since it was identified in the fern M. quadrifolia and in angiosperms . As miR168 targets AGO1 in angiosperms, we interrogated whether this miR-target relationship was established in ferns. We found that only in E. ramosissimum did a miR168 candidate (Era-miR168.921) potentially target Eram1374, an AGO in the AGO1/5/10 clade (Additional file 1: Table S2 and S5). Interestingly, fern miRNA candidates from two other families, Ani-miR848.276 and Sun-miR159-5p.2545, could potentially target AGO homologs Anim17854 (in the AGO2/3/7 clade) and Sunm18764 (in the AGO1/5/10 clade) (Additional file 1: Table S5). Thus, the miR168-AGO1 relationship in angiosperms was likely established after the divergence of ferns and seed plants.
miRNA targets are conserved among vascular plants
Information on miRNA candidates and target transcripts in various species
Number of miRNA candidates
Number of predicted targets
Number of miRNA candidates with targets
Small RNAs constitute an important population of the RNA complement in eukaryotes. Our current knowledge of small RNAs has been derived mainly from model plants with sequenced genomes, most of which are angiosperms. In angiosperms, most 21-nt small RNAs are miRNAs, and most 24-nt small RNAs are generated by Pol IV and act in the RdDM pathway. Sister species of seed plants, including lycophytes and ferns, are underrepresented in the small RNA field due to the lag in genome sequencing. This has precluded a holistic picture of small RNA pathways in land plants. Our characterization of small RNAs and identification of small RNA pathway genes in lycophytes and ferns, two major sister lineages of seed plants, filled a major gap in our knowledge of small RNAs. The inclusion of all major lycophyte and fern lineages in phylogenetic analyses of small RNA pathway genes, which was not previously possible, led to new insights into small RNA pathway evolution in land plants.
Conservation and diversification of small RNA pathways in land plants
Although RNA-seq-based gene identification may miss some genes due to their spatiotemporally restricted expression, the inclusion of multiple species in each phylogenetic group helped to minimize the influence of incomplete sampling of tissues. As a result, homologs of angiosperm genes in small RNA pathways were identified from most species of lycophytes and ferns. Homologs of these genes were also found in the sequenced genomes of two byrophytes and three algae. Thus, it can be concluded that small RNA-based RNA silencing was established in the common ancestor of green plants. Our phylogenetic analyses reveal that small RNA pathways diversified and specialized in the most recent common ancestor of land plants. For example, all angiosperms have at least four classes of DCLs that generate different types of small RNAs (miRNAs and various endogenous and viral siRNAs). Each DCL class is a monophyletic group in land plants (Additional file 2: Figure S1), indicating ancient divergence of the DCL family and implying ancient diversification of small RNA pathways in land plants. DCL2 genes were not detected in lycophytes and some ferns, and was absent in the genome of the bryophyte P. patens, suggesting that DCL2 was lost in some bryophytes, lycophytes, and some ferns or it evolved after the divergence between lycophytes and other vascular plants.
Consistent with the early diversification of DCLs, the AGO family also diversified early in land plants, as all three major clades of angiosperm AGOs have counterparts in bryophytes. As different AGO proteins bind to and mediate the activities of different classes of small RNAs, the early diversification of the AGO family supports ancient diversification of small RNA pathways in land plants. We also discovered differences in AGO evolution compared to that of DCL genes. The AGO genes of vascular plants form several separate groups (Additional file 2: Figure S2) in each of three conserved clades. This indicates that the expansion of AGO genes in each of the three clades occurred in parallel in seed plants and their sister species. For example, specific AGO genes in angiosperms, such as AthAGO10, which sequesters miR166 from AGO1 in Arabidopsis , and OsAGO18, which functions in miRNA sequestration in rice , emerged after the divergence of ferns and seed plants. Thus, the functions of these genes in Arabidopsis and rice do not apply to ferns and lycophytes. In addition, the expansion of the AGO1/5/10 and AGO2/3/7 clades in sister species of seed plants is limited to leptosporangiates, the most prosperous lineage of ferns, including Polypodiales, Salvinales, and other orders (Additional file 2: Figure S2a, b). This observation raised the possibility that AGO gene expansion and functional divergence of small RNA pathways could have contributed to plant survival.
Our studies also shed light on the evolution of RdDM in land plants. Although DNA methylation has been described in the moss P. patens and the lycophyte S. moellendorffii, evidence for the existence of RdDM in other lycophytes was lacking [54, 77]. Here we identified many key genes involved in RdDM not only in ferns but also in lycophytes, including subunits specific to Pol IV/Pol V. This implies a developed RdDM pathway in lycophytes as in ferns. However, mirroring previous findings, we did not find abundant 24-nt small RNAs in many species, including two lycophytes and ten ferns. Most of the ferns possessing a 24-nt small RNA peak are in Polypodiales, the most diversified order among extant ferns (Fig. 4a; Additional file 2: Figure S6). The earth underwent a vegetation change from a landscape dominated by gymnosperms and seed-free vascular plants to one populated mainly by angiosperms . In this change most ancient species were compromised when the angiosperms began to bloom , while Polypodiales was an exception, which expanded as flowering plants flourished according to fossil and living records , and accounts for more than 80% of all extant fern species [80, 81]. The existence of 24-nt small RNAs and the expansion of AGOs in Polypodiales implied the emergence of a sophisticated system of generating and utilizing 24-nt small RNAs. We spectulate that the well developed regulatory system might have helped plants adapt to environments to facilitate survival  in two successful lineages of land plants, Polypodiales and angiosperms. It is possible that once the AGO family expanded to develop the capability of binding the 24-nt small RNAs, this class of small RNAs began to be predominant in the small RNA population and became vital in gene and genome regulation.
Our phylogenetic analyses show that ferns, but not lycophytes or bryophytes, have clear NRPD1 and NRPE1 genes. We prospose a model of the evolution of Pol IV and Pol V (Fig. 4d). An NRPD1/E1-like gene diverged from NRPB1 in ancient land plants. As two P. patens NRPD1/E1-like genes have an NRPE1-like domain configuration (Fig. 3), the ancestral NRPD1/E1-like gene might have been more like NRPE1, but this is largely speculative. In ferns and angiosperms, NRPD1 and NRPE1 evolved from the NRPD1/E1-like ancestral gene. NRPE1 in ferns lost the DeCL domain while NRPE1 in angiosperms retained the DeCL domain. Notably, the role of NRPD1 in generating 24-nt siRNAs in angiosperms may be acquired later in evolution, as in lycophytes and ferns, a correlation between 24-nt siRNAs and NRPE1 expression was found (Fig. 4c).
Insights into miRNA evolution in land plants
The molecular framework of miRNA biogenesis, degradation, and mode of action was likely established in the common ancestor of land plants, as major components of the miRNA pathway as we understand in angiosperms have homologs in bryophytes, lycophytes, and ferns, including DCL1 and SE in miRNA biogenesis, HEN1 in miRNA stability, AGO1 in miRNA binding and activity, and SDN, HESO1, and URT1 in miRNA turnover. We found many truncated and tailed isoforms in miRNA candidates, with the miR165/6 family from S. moellendorffii being a prominent example (Fig. 6b). This suggests that the mechanisms of miRNA degradation are conserved in land plants. Degradome/PARE analysis of S. moellendorffii not only confirmed our miRNA–target predictions but also demonstrated that miRNA-guided target RNA cleavage occurs in a lycophyte.
Our identification of conserved miRNAs in lycophytes and ferns, together with previous studies of miRNAs in two ferns, M. quadrifolia and P. minima [28, 30], has enriched our understanding of the evolution of miRNAs. These studies point to approximately 12 miRNA families that were present in the most recent common ancestor of vascular plants by adding more lycophytes into the species pool. In addition, our study helped time the origination of a few well-known, conserved miRNAs. We found that some well-known, conserved miRNAs were missing in lycophytes, including miR172, miR390, miR160, miR530, miR168, miR394, and miR169 (Fig. 7). Since miR172 was not found in the moss P. patens  or the liverworts Pellia endiviifolia  and M. polymorpha , it is probable that miR172 evolved only in the most recent common ancestor of ferns and seed plants to regulate AP2 genes. Many miR172-AP2 pairs were found in ferns, but no AP2 genes were among the predicted miRNA targets in S. moellendorffii and other lycophytes, except for a miR171-3p-AP2 pair in L. cernuum (Additional file 1: Table S5). This implies that lycophyte AP2 genes are not regulated by miR172 or any miRNA except for L. cernuum, in which they are regulated by miR171-5p.1360. Also, as a trigger for phasiRNA biogenesis, miR390 was considered conserved in land plants due to the presence of this miRNA and its target TAS3 in the moss P. patens . In our study, no miR390 candidates were found in any of the lycophytes, raising the possibility that the phasiRNA pathway was not established in lycophytes. The absence of several other phasiRNA-triggering miRNAs in lycophytes as well as the absence of PHAS or TAS genes or phased siRNAs in S. moellendorffii support this hypothesis. Further genome information of these species would help evaluate the existence/absence of secondary siRNAs in lycophytes.
This work also revealed fluid miRNA–target relationships in evolution. While AGO1 is conserved in land plants, miR168, which targets AGO1 in angiosperms, probably evolved in the most recent common ancestor of vascular plants . In some lycophytes, miRNAs other than miR168 target AGO1 (Additional file 1: Table S5). Thus, different miRNAs are employed to target AGO1 in different lineages. Another fluid relationship is AGO–miRNA association. In angiosperms, AGO10 specifically associates with miR165/6 and sequesters it from AGO1 . While the miR165/6 family is conserved in land plants, AGO10 only emerged in angiosperms after the fern–seed plant divergence. Thus, the specific AGO10-miR165/6 relationship in angiosperms evolved after this divergence.
This study on lycophytes and ferns, two major land plant lineages that are extremely underrepresented in small RNA studies, sheds light on the evolution of small RNA pathways and miRNAs in land plants and provides valuable information from sister lineages of seed plants for comparative studies. Three DCL and four AGO clades formed early in land plants, implicating functional diversification of small RNAs early in land plant evolution. The molecular framework for miRNA biogenesis, degradation, and activity was likely established in the common ancestor of land plants. The lack of certain subunits of Pol IV/Pol V together with the absence of prominent 24-nt siRNAs in lycophytes and some ferns suggests stepwise assembly of the RdDM machinery in land plant evolution. The existence of an AGO clade in bryophytes, lycophytes, ferns, and possibly gymnosperms but not angiosperms strongly suggests differences in RNA silencing between angiosperms and other land plants. Our analyses of miRNAs have enriched the landscape of conserved miRNA families in major land plant lineages. The landscape of miRNAs in sister species of seed plants also has ramifications on the origin of phasiRNAs.
Plant sample collection and total RNA extraction
A total of four lycophytes and 21 fern species were selected following these rules: 1) at least one representative in each of the three and 11 current orders of lycophytes and ferns, respectively; 2) more species in family-rich orders; 3) priority given to ones with sequenced genomes. Other information about the selected species is detailed in Additional file 1: Table S1. Among these species, only S. moellendorffii has a published whole-genome sequence . For most samples, young aerial parts were collected and total RNA was extracted from ground plant tissues using a modified CTAB method as described by Zhang et al. .
mRNA library construction, sequencing, and data processing
RNA-seq libraries were constructed using TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001 and RS-122-2002), and pooled and sequenced (paired-end, 125 bp) on the Illumina Hiseq 2500 platform at Berry Genomics (Beijing, China) or on the Illumina Hiseq 3000 platform (paired-end, 150 bp) at Genergy (Shanghai, China). All sequences were used for de novo transcript assembly using Trinity v2.1.1  with parameters “--trimmomatic --quality_trimming_params ‘ILLUMINACLIP:/usr/local/bin/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 LEADING:10 TRAILING:10 MINLEN:70’ --normalize_max_read_cov 100 --min_kmer_cov 2”. Assembled transcripts over 100 nt were named by a combination of species abbreviation, “m” meaning “mRNA”, and a uniform serial number, such as Pcum53368. Afterwards, proteins were predicted from the assembled transcripts using TransDecoder with default parameters, which is integrated in Trinity, and used for protein domain search with hmmsearch .
Phylogenetic analysis of proteins related to small RNA pathways
Proteins that are putative components of small RNA pathways were identified through hmmsearch using an HMM profile built from their homologs in A. thaliana, O. sativa, A. trichopoda, S. moellendorffii, and P. patens obtained from Phytozome v12 (https://phytozome.jgi.doe.gov). The identified protein sequences were aligned by MUSCLE v3.8.31 with default parameters  and optimized manually. The corresponding coding nucleotide sequences (CDS) from the protein alignment were extracted and aligned, and the nucleotide alignment was used for subsequent phylogenetic analyses. The maximum likelihood (ML) trees were inferred using RAxML v8.2.4  with the parameter “-f a -m GTRCAT -N 1000” and drawn by MEGA7 . Genes in each tree were labeled with the species names, and their nucleotide sequences are included in Additional file 3.
Small RNA library construction, sequencing, and data processing
Total RNA (20 μg) from each sample was resolved in a 15% polyacryladmide/urea gel. Gel slices corresponding to RNA sizes of 15–40 nt were excised, and RNA was extracted using the TRIzol@ reagent (ThermoFisher, 15596026). The RNA was then used to construct small RNA libraries according to instructions from NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, E7300S). The small RNA libraries were then pooled and sequenced (single-end reads of 50 bp) on the Illumina HiSeq 2500 platform at Berry Genomics (Beijing, China). The adapter sequence was removed from the output reads using cutadapt v1.10 , and only 16–26-nt-long reads were retained. The rRNA, tRNA, snoRNA, and snRNA fragments were filtered against the S. moellendorffii genome with bowtie v1.1.2  allowing for two mismatches and removed. Any 3′ U tails were shortened to 1 nt to minimize the influence on subsequent analyses. The prediction of conserved miRNAs was conducted following the method described in . Only those with less than 3-nt mismatches and less than 2-nt differences in length were recognized as miRNA candidates and assigned as the closest homologs to the reported plant miRNAs. In this way, similar miRNA families could be combined into one family, such as miR156/157, miR165/166, and miR170/171. Predicted miRNAs with identical 5′ nucleotides 1–16 were combined into one miRNA cluster with the most abundant one as the representative (Additional file 2: Figure S8), and labeled with a uniform serial number followed by the raw read counts, such as Smo-miR170/1-3p.2380_3761. The abundance of these miRNA candidates was calculated as reads per million (RPM) total reads of 18–26 nt small RNAs in each species. The miRNA candidates with more than ten raw reads or five in RPM (whichever is higher) were retained. All identified miRNA candidates are included in Additional file 4.
Degradome/PARE library construction, sequencing, and data processing
The S. moellendorffii degradome/PARE library was constructed with 75 μg of total RNA as described . The library was sequenced on the Illumina HiSeq 2500 platform (single end, 50 bp). After removing adaptor sequences, reads shorter than 19 nt were removed. Retained reads were then mapped to the transcripts assembled from mRNA-seq using ShortStack with default parameters. A local algorithm with requirements for peak calling was employed: 1) at least 12 unique tags were mapped to the transcript; 2) the peak position is among the top 12 positions with mapped reads in this transcript; 3) the RPM of the peak is over 5; 4) the RPM of the peak is larger than the mean plus five times standard error of RPM of all positions with mapped reads on this transcript.
Genome mapping of small RNAs in S. moellendorffii
The small RNA reads in S. moellendorffii were mapped to the genome using ShortStack  allowing for no mismatches. The 400-bp flanking sequences of aligned hits were extracted and subjected to secondary structure prediction using RNAfold in ViennaRNA packages 2  with default parameters. The miRNA candidates with less than four mismatches in the hairpin structures were retained.
miRNA target analysis
The prediction of miRNA targets in each species was performed using TarHunter (https://github.com/XMaBio/TarHunter) with a cutoff of 2.5. Predicted targets were searched for known protein domains using hmmsearch with the Pfam-A.hmm file downloaded from Pfam (http://pfam.xfam.org). Orthologous targets in all species were also predicted by TarHunter, and orthologous groups present in over 15 species were retained for analysis of sequence variations. Aligned nucleotide sequences within a group were divided into 30-nt sliding windows to calculate nucleotide variation as compared to the ancestral sequence calculated by MEGA7.
We thank Dr. Bailin Hao and Dr. Chien-Hsun Huang from Fudan University and Dr. Wenbo Ma from University of California Riverside for discussions, and Dr. Fay-Wei Li from Duke University for providing materials.
This project is supported by NSFC (31571332, 91440105), Guangdong Innovation Research Team Fund (2014ZT05S078), China Postdoctoral Science Foundation (009339), Natural Science Foundation of SZU (827-000191), National Institutes of Health (GM061146), and Gordon and Betty Moore Foundation (GBMF3046).
Availability of data and materials
Most species in this study were from Fairylake Botanical Garden, Shenzhen, China (Additional file 1: Table S1; http://www.szbg.ac.cn/), and all plant voucher specimens were deposited at Shenzhen University, China. All messenger RNA sequencing data generated in this study were deposited in NCBI SRA under the accession SRP106198, and small RNA sequencing data were deposited in NCBI GEO under the accession GSE98408.
CY, JC, and XC designed the project. LYK and XQ determined the list of species to be included. JC, HW, and XQ collected samples and performed the experiments, and CJ performed the bioinformatics analysis. CY and JC wrote the manuscript. LYK, HM, BM, and XC revised the manuscript. All authors read and approved the final manuscript.
Ethics approval and consent to participate
Consent for publication
The authors declare that they have no competing interests.
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