De novo transcriptome analysis of Medicago falcata reveals novel insights about the mechanisms underlying abiotic stress-responsive pathway
- Zhenyan Miao†1, 4,
- Wei Xu†2,
- Daofeng Li1, 5,
- Xiaona Hu1,
- Jiaxing Liu1,
- Rongxue Zhang1,
- Zongyong Tong1,
- Jiangli Dong1,
- Zhen Su3,
- Liwei Zhang3,
- Min Sun2,
- Wenjie Li2,
- Zhenglin Du2,
- Songnian Hu†2Email author and
- Tao Wang†1Email author
© Miao et al. 2015
Received: 4 April 2015
Accepted: 7 October 2015
Published: 19 October 2015
The entire world is facing a deteriorating environment. Understanding the mechanisms underlying plant responses to external abiotic stresses is important for breeding stress-tolerant crops and herbages. Phytohormones play critical regulatory roles in plants in the response to external and internal cues to regulate growth and development. Medicago falcata is one of the stress-tolerant candidate leguminous species and is able to fix atmospheric nitrogen. This ability allows leguminous plants to grow in nitrogen deficient soils.
We performed Illumina sequencing of cDNA prepared from abiotic stress treated M. falcata. Sequencedreads were assembled to provide a transcriptome resource. Transcripts were annotated using BLASTsearches against the NCBI non-redundant database and gene ontology definitions were assigned. Acomparison among the three abiotic stress treated samples was carried out. The expression of transcriptswas confirmed with qRT-PCR.
We present an abiotic stress-responsive M. falcata transcriptome using next-generation sequencing data from samples grown under standard, dehydration, high salinity, and cold conditions. We combined reads from all samples and de novo assembled 98,515 transcripts to build the M. falcata gene index. A comprehensive analysis of the transcriptome revealed abiotic stress-responsive mechanisms underlying the metabolism and core signalling components of major phytohormones. We identified nod factor signalling pathways during early symbiotic nodulation that are modified by abiotic stresses. Additionally, a global comparison of homology between the M. falcata and M. truncatula transcriptomes, along with five other leguminous species, revealed a high level of global sequence conservation within the family.
M. falcata is shown to be a model candidate for studying abiotic stress-responsive mechanisms in legumes. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in the acclimation to abiotic stresses. Our data provides many gene candidates that might be used for herbage and crop breeding. Additionally, FalcataBase (http://bioinformatics.cau.edu.cn/falcata/) was built for storing these data.
KeywordsMedicago falcata Transcriptome Legume Phytohormones Nodule
Abiotic stresses such as low temperature, high salinity, and drought adversely affect plant growth and productivity worldwide. The entire world is facing an increasing food requirement as the population grows continuously while crop and herbage productivity diminishes due to the deteriorating environment. Therefore, our understanding of the mechanisms underlying plant responses to external abiotic stresses is very important for breeding stress-tolerant crops and herbages, as well as sustaining the agricultural industry .
A variety of adaptive strategies to cope with abiotic stresses have evolved in plants. These include morphological, physiological, biochemical, and molecular responses [1–5]. Hundreds of plant genes are differentially regulated in response to abiotic stresses, as demonstrated by RNA-seq analyses. The complex network of regulatory genes necessary to sense and respond to abiotic stresses has been addressed. Regulatory component identified so far include transcription factors (TFs), plant hormones, noncoding RNAs, protein modifiers and epigenetic modifications [6–9].
The growth and development of all plants is determined by the interactions between their genome and growing environment. A multitude of complex signalling systems have evolved in plants to respond to external and internal cues to regulate growth and development under abiotic stresses. Phytohormones play critical regulatory roles in these processes. Generally, phytohormones control various developmental events throughout the plant life cycle, such as patterning, cell identity, and differentiation, as well as the coordinated growth of various reproductive organs . In recent years, the metabolism and core signalling components of major phytohormones, such as abscisic acid (ABA), ethylene, jasmonic acid (JA), auxins, and gibberellins (GA), have been revealed . In plants, the response to abiotic stresses is through the modulation of gene expression by phytohormone-mediated signalling processes. As summarised in recent reviews, ABA remains the best-studied hormone for plant stress responses [12–16]. However, other hormones, such as ethylene, JA, GA, and auxins, are being studied to a limited extent for abiotic stress responses [17–20].
Medicago falcata, which is closely related to alfalfa (Medicago sativa), is an economically and ecologically important legume herbage and is widely distributed throughout the world. M. falcata is especially attractive because it can be grown in adverse environment regions, such as infertile and sandy soils, and is, thus more tolerant against drought and cold compared with alfalfa [21, 22]. The combination of these traits makes M. falcata one of the best stress-tolerant candidate plant species. M. falcata also consists of numerous different genotypes, each of which has diverse growth and agricultural characteristics, indicating its agricultural importance . A variety of genes were reported involved in tolerant mechanism of M. falcata. Expression of multiple genes encoding myo-inositol phosphate synthase (MIPS), galactinol synthase (GolS), early light induced protein (ELIP), hybrid proline rich protein (HyPRP), S-adenosylmethionine synthetase (SAMS), and a myo-inositol transporter-like (INTlike) in response to low temperature is also associated with cold tolerance in M. falcata plants [24–28]. Temperature-induced lipocalin (TILs) have initially been detected as massively increased proteins in response to low temperatures. Arabidopsis TIL1 is localized in the plasma membrane and its temperature response suggested a function in membrane stabilization during freezing stress . A partial-length cDNA clone encoding a TIL has been obtained in M. falcata responsive to cold , implying its potential role in cold tolerance of M. falcata. As a legume species, M. falcata has the ability to fix atmospheric nitrogen through the establishment of a symbiotic association with bacteria called rhizobia, and this ability allows leguminous plants to grow in soils that are deficient in nitrogen, decreasing both the need for costly nitrogen fertilisers and the water pollution they may cause . An organ, the root nodule, is formed to house this symbiosis. Within this organ, there is an exchange of nutrients: the bacteria provide the plant with ammonia, and the plant provides the bacteria with carbohydrates. Over the past several years, hundreds of plant and bacterial genes displaying differential expression during the nodulation process have been identified by transcriptome analyses in Medicago truncatula and Sinorhizobium meliloti [32–40], and many factors have been shown to control the nodulation process . Studies of bacterial and plant mutants have led to the identification of plant genes involved in the early stages of symbiotic nodulation . However, a transcriptomic analysis of nodulation signalling pathway gene expression in response to abiotic stresses is lacking in the literature.
The emergence of next-generation sequencing (NGS) technologies has allowed further study of species in which the genome sequence is available or previously unexplored species in re-sequencing and de novo sequencing aspects . The technology, which allows the sequencing of the entire transcriptome (RNA-Seq), could provide expression profiles of either coding or non-coding RNAs, making important contributions to genome annotation [44, 45]. Transcriptome sequencing has become more and more popular in many research areas, especially for model species such as Arabidopsis , Cotton , Soybean , M. tuncatula [38, 39, 49–51] and non-model species, such as alfalfa [52–55], lentil , pea , pigeon pea  and cucurbits . Although often used in species with a sequenced genome and high-quality gene predictions, the rapid development of software tools has allowed researchers to undertake the de novo assembly of a transcriptome based on only short sequence fragments, which has been widely applied in many plants [52, 60–63].
In this work, we present the expression profiles of M. falcata in plants grown under dehydration, high salinity, and cold conditions. We also explore evidence for novel abiotic stress-induced phytohormone metabolism and nodulation signalling. This is the first high-throughput transcriptomic study in stress-tolerant legume herbage, and we hope that it will be a valuable resource for breeding crops and herbages with enhanced abiotic stress-resistance abilities in legumes or other species.
Evaluation of cold, dehydration and salt stresses response of three Medicago genotypes
In order to assess the resistance ability of M. falcata (PI502449), we test Medicago truncatula ecotypes A17 and R108 under different abiotic stresses, including cold, drought and salt stresses. The methods referred to Medicago Handbook  and was modified. Firstly, in the cold stress test, we find that the differences in mortalities (%) and root to aerial part ratios between M. falcata and M. truncatula are significant. After the treatment under −6 °C for 10 h, the mortality of PI502449 is 80 %, whereas the mortalities of A17 and R108 are both 100 %. Under −6 °C for 6 h, the mortalities of PI502449, A17, and R108 are 0 %, 85 %, and 100 %, respectively. Under −6 °C for 8 h, the mortalities of PI502449 is 20 %, the other two are 100 % (results are shown in Additional file 1D). Since the cold stress can inhibit the growth of roots, therefore, the root to aerial ratio, which is defined as the ratio between fresh weights of root to that of aerial part, can characterize the ability of alfalfa’s resistance to cold stress. The results show that, as the cold stress time becomes longer, the root of PI502449 can still grow in compare to that of R108 and A17 (Additional file 1A). Therefore, it is obvious that the PI502449 processes a stronger ability to resist the cold stress. Secondly, drought stress is applied 7 days (control), 10 days, 12 days and 14 days, respectively, followed by re-hydration, three replicates. Fresh weight and ratio of root to aerial part were measured. The results showed that the roots of PI502449 have relative higher water contents. PI502449 has the highest ratio of root to aerial part among R108, A17, and PI502449. To sum up, the M. falcata PI502449 has the strongest ability to resist drought. In the salt stress test, we treated the soil with 0 mM (Control), 100 mM, 150 mM and 200 mM NaCl, and then collect the content of soluble carbohydrate using a phenol-sulfuric acid method. The contents of soluble carbohydrate can be used as criteria for salt stress resistance, because the carbohydrate will increase under the salt stress to reduce the damage of NaCl to plantlet. Based on the results, we can conclude that A17 has the strongest ability to resist the salt stress, PI502449 the weakest (Additional file 1C). These results suggested that M. falcata PI502449 is more tolerant against drought and cold stresses compared with M. truncatula. Based on these results, we attend to reveal mechanisms involved in M. falcata response to abiotic stresses by using RNA-seq technology.
RNA-seq using the Illumina platform and the de novo assembly of the transcriptome
In order to find out the early response genes of PI502449 under abiotic stresses, we analyzed the electrolyte leakage after the rapid stresses (Additional file 2). We picked the optimal stress treatment under which electrolyte leakage increased 2-fold or more compared with standard conditions for RNA-Seq. Plant materials were collected under dehydration (dehydrated for 2 h), high salinity (1 M NaCl for 2 h), or cold (0 °C for 8 h) treatment and then RNA were extracted. We developed complementary DNA (cDNA) libraries derived from M. falcata PI502449 grown under abiotic stress and standard conditions: dehydration stress plantlets (DS), high salinity stress plantlets (SS), cold stress plantlets (CS), and standard conditions (SC). Two libraries were constructed for one sample respectively, resulting in a total of eight cDNA libraries for the RNA-Seq analysis. A total of 33,432,584,900 nt of raw sequencing data were generated from the eight cDNA libraries. After a stringent quality filtration of the raw read data using the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html), a total of 31,591,337,787 nt filtered data were selected for further analysis (Additional file 3).
To obtain a better assembly result, two assembly methods (single k-mer method and multiple k-mer method) were used for the de novo assembly of our sequencing data. The parameters used for the two methods are described in the Methods section. The de novo assembled transcripts were combined with 98,515 unique sequences (Additional file 4). The total base count of the assembly sequences was 84,416,200 nt, with the unique sequence lengths ranging from 200 to 14,802 nt. In order to explicitly evaluate the quality of the transcripts generated by assembly, we download 913 mRNAs already characterized in M. falcata from NCBI EST database. BLASTn comparisons were performed between assembly sequences and EST dataset. Total 869 (95.2 %) mRNAs had significant hits to assembly sequences. Putative functions for the assembly sequences were assigned using BLASTX searches against the non-redundant (nr) NCBI database, UniProt database, and M. truncatula proteome (for details, see the “Methods”; annotation files available at http://bioinformatics.cau.edu.cn/falcata). Putative functions were assigned for 50 % of the sequences. We also assigned gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classes. Annotations for genes and pathways analysed in greater detail throughout this paper were manually curated to ensure accurate analysis and interpretation. In addition, we have pursued systemic co-expression/network analysis with our RNA-seq dataset using WGCNA software  and we integrated the results into FalcataBase (http://bioinformatics.cau.edu.cn/falcata/network/). Users can explore the players that contribute to cold, salt and dehydration response conveniently.
We identified putative housekeeping genes that displayed little variation in expression but were expressed at relatively high levels (Additional file 5). To identify housekeeping genes, we first selected genes with an average RPKM-normalised transcript count greater than 10. We next selected the top 10 % of genes (938) with the lowest coefficient of variation (SD/mean) . Finally, we picked up 587 single copy genes with the length more than 1000 nt. These housekeeping genes may be useful as reference genes in quantitative real-time PCR (qRT-PCR) or other experiments to normalise gene expression levels across different conditions .
Posttranscriptional regulation by microRNAs (miRNAs) is an important response to nutritional, biotic, and abiotic stresses [69, 70]. The sequencing of miRNAs requires special library construction. Therefore, the identification of mature miRNAs is beyond the scope of this study. However, transcripts regulated by miRNAs should contain sequences with almost perfect complementarity to known miRNAs. We used the psRNATarget programme  to screen the transcripts we identified as differentially expressed due to abiotic stresses for sequences potentially regulated by miRNAs using mature miRNAs from miRBase as queries. We identified 1,132 transcripts potentially regulated by 818 miRNAs (Additional file 6). Two of the 818 miRNAs identified in this analysis (miR166 and miR399) have been previously shown to directly regulate cold and salt responses . Additionally, researchers have identified a number of miRNAs that are regulated by abiotic stresses [73–75]. Several of these miRNAs were also identified in this analysis.
Differential expression of transcripts due to abiotic stresses
A total of 6,158 transcripts were differentially expressed in response to abiotic stresses: 4,460 genes in DS versus SC comparison, 2,356 genes in SS versus SC comparison, and 2,293 genes in CS versus SC comparison (Fig. 1; Additional file 7). Of the 4,442 differentially expressed transcripts identified in DS, 2,806 transcripts were up-regulated, whereas 1,636 were down-regulated. Of the 2,320 differentially expressed transcripts identified in SS, 1,533 transcripts were up-regulated, whereas 787 were down-regulated. Of the 2,252 differentially expressed transcripts identified in CS, 1,123 transcripts were up-regulated, whereas 1,129 were down-regulated. Additionally, 362 transcripts were induced and 288 transcripts were inhibited by all three stresses concurrently.
TFs differentially expressed due to abiotic stresses
ABA signalling and its key role in the adaptation of plants to stress conditions has been the focus of many studies since the early 1990s . Thus, we queried the database for differentially expressed transcripts related to ABA biosynthesis enzymes, such as Crtz (beta-carotene 3-hydroxylase), ZEP (zeaxanthin epoxidase), and NCED (9-cis-epoxycarotenoid dioxygenase), as well as AAO (abscisic-aldehyde oxidase) and ABA catabolism enzymes, such as CYP707A (Fig. 2). As expected, most of the transcripts for the ABA biosynthesis enzyme genes displayed enhanced expression in DS, SS, and CS. However, transcripts for the ABA catabolism enzyme genes showed decreased expression in DS, SS, and CS. Unexpectedly, transcripts for the AAO gene, which encodes for an enzyme that catalyses the final step of ABA biosynthesis, showed different levels of decreased expression in all stress-treated samples. Meanwhile, we determined the content of ABA after cold treatment. Compared with M. truncatula, the content of ABA in M. falcata dropped significantly (Additional file 9). Furthermore, PYR/PYL (Pyrabactin Resistance 1/Pyrabactin Resistance 1-Like) genes, identified as ABA receptors, showed obvious decreased expression in DS, SS, and CS. ABF transcription factors are the key regulators of ABA signalling. Interestingly, transcripts for a member of this family, named ABF1, and exhibiting differential expression were found; up-regulated expression was observed in the DS and SS samples, while down-regulated expression was observed in the CS samples. Together with ABA, gibberellins (GAs) act as a main regulating factor in seed germination; however, their role is antagonistic compared with ABA. A principal pathway for GA plant hormones can be drawn from GA12-aldehyde. A stepwise analysis of GA metabolism revealed the conversion of GA12-aldehyde to bioactive GA4 and inactive GA34 . In our transcriptome data, the GA 20-oxidase and 3β-hydroxylase transcripts showed different levels of decreased expression in all stress-treated samples; however, the 2β-hydroxylase transcripts displayed the respective increased expression in these samples (Fig. 2). Interestingly, we identified some transcripts for a GA receptor named GID1 (GA-INSENSITIVE DWARF1) exhibiting differential expression. Compared with the down-regulated expression in the CS sample, these transcripts showed up-regulated expression in the DS and SS samples.
Confirmation of the RNA-Seq expression profiles with qRT-PCR
Nodule receptor kinase
RNA-Seq expression validation by qRT-PCR
Transcripts known to be involved in the abiotic stress response (such as dehydration, high salinity, and cold) were confirmed by qRT-PCR to have expression patterns similar to those measured by RNA-Seq. Additionally, the expression profiles of transcripts involved in phytohormone metabolism and symbiotic nodulation signal transduction were also measured by qRT-PCR (Additional files 10 and 11). Finally, transcripts involved in auxin transport were identified in the assembly and used to design primers for qRT-PCR analysis to measure the expression profiles in plants treated with IAA. In total, 56 transcripts were evaluated by qRT-PCR, with 95.2 % consistent with the RNA-Seq data (Table 2).
Comparative transcriptomics of M. falcata and with the other legume species
To examine the degree of conservation between M. falcata and other sequenced legume species, six pairwise tBLASTn comparisons were performed between M. falcata and each of the six legume species (Fig. 5c). M. truncatula had the highest number of sequences with significant hits to the M. falcata database (e ≤ 1e−5 and ≥70 % positive match percent), and the greatest proportion of peptides with significant matches (36,869/62,318). All six species had at least 42 % of their proteins significantly represented in the M. falcata database. A global view of the top M. falcata transcripts and their similarity to each M. truncatula peptide (primary transcripts only) is shown in Additional file 12C. Of the M. truncatula loci, 6,743 of 62,318 had transcripts with >70 % similarity and >70 % coverage in the M. falcata transcriptome.
To more closely examine the level of global sequence conservation between M. falcata and M. truncatula, we further examined a BLASTx comparison of the M. falcata transcriptome assembly with the M. truncatula peptide database (primary transcripts only). The relative homology of each predicted peptide to the most similar M. truncatula protein was measured by the percent of positive sequence similarity (Additional file 12A) and percent coverage (Additional file 12B). A smooth scatter plot representing the percent similarity and percent coverage for each M. falcata sequence compared with the closest M. truncatula peptide sequence is shown in Additional file 12C. A proportion (>40 %) of transcripts possessed at least 70 % similarity to a M. truncatula protein. A total of 13,538 M. falcata transcripts had at least one match to a M. truncatula gene, with >70 % similarity/>70 % coverage. Of the M. falcata transcripts, 1,454 had ≥95 % similarity and coverage, 2,029 transcripts were between 80-95 % similarity and coverage, 730 transcripts were between 70–80 % similarity and coverage, 7,458 transcripts were < 70 % similarity and coverage, and 49,400 transcripts lacked a significant BLASTx hit (e ≤ 1e−5) to a M. truncatula peptide.
Several studies utilising microarrays and RNA-Seq have documented the responses of plants to abiotic stresses. In this study, we extended our fundamental understanding of plant acclimation to abiotic stresses through an RNA-Seq whole transcriptome analysis of dehydration, high salinity, and cold treatment in M. falcata. Although our analysis primarily focused on phytohormone metabolism and signalling, we also explored the effect of abiotic stresses on nod factor signalling pathways during early symbiotic nodulation. Our data provide the foundation for what to our knowledge is the first M. falcata gene index (MFGI). We report 98,515 unique sequences, of which more than 6,000 respond to abiotic stresses. Moreover, we report previously unrecognised transcriptional responses to abiotic stresses.
Comparing the M.falcata transcriptome with other legume transcriptomes
We sequenced, assembled, and annotated the M. falcata transcriptome. The draft transcriptome consists of 98,515 unique sequences, of which 51,040 were annotated and the functions of the rest transcripts were unknown. Of these transcripts, 34.5 % were most similar to M. truncatula genes, and 52 % had top hits in the legume, indicating a high level of sequence conservation across the family. BLAST comparisons between M. falcata and six other sequenced legume species showed that our M. falcata transcriptome has good coverage of homologous sequences. Compared with the other species, M. truncatula had the largest proportion of peptides with significant matches (36,869/62,318). In total, all of these six species had 107,779 proteins significantly represented in the M. falcata database. We inferred that multiple sequences in the M. falcata assembly may divide from one single protein-coding transcript. These analyses are consistent with previous phylogenetic findings that M. falcata is more closely related to M. truncatula than other species . The M. falcata transcriptome will provide evidence for the expression of predicted genes in the M. truncatula genome.
Genes commonly expressed under abiotic stresses
We identified 166 transcripts containing sequences homologous to 71 identified helicase proteins in other plants. Nine transcripts were induced by all three stresses. These transcripts were homologous to seven helicase proteins in plants, including Ricinus communis, Vitis vinifera, and Arabidopsis lyrata, indicating that at least seven helicase genes in M.falcata could be induced to respond to dehydration, high salinity, and cold. The helicase involved in the abiotic stress response was first identified in the legume pea . In the pea, DNA helicase 47 (PDH47, GenBank accession number: AAN74636.1) was only induced by salt and cold stress and not by dehydration stress. This induction was also tissue-specific and regulated by responses to heat and ABA stress. In our data, three transcripts were similar to a DEAD-box ATP-dependent RNA helicase (GenBank accession number: XP_002527090.1), and one transcript was similar to a RNA helicase (GenBank accession number: AAF40306.1). The importance of RNA helicases in stress responses was also reviewed in a previous research study . An increased expression level was also observed in genes encoding for RNA polymerases. Eight transcripts corresponding to eight proteins from four species were induced by all three stresses and accounted for 2.8 % of all of the polymerase transcripts identified. The relationship between poly (ADP-ribose) polymerase (PARP) and abiotic stresses has been studied in the soybean, and this enzyme was found to mediate DNA repair and programmed cell death processes during responses to mild and severe stresses, respectively . In addition, PARP inactivation has been reported to increase the tolerance of plants against a broad range of abiotic stresses by inhibiting the processes of cell death and reducing energy consumption . Choline, an important precursor of the membrane phospholipid phosphatidylcholine, is used to produce glycine betaine, which functions as an osmoprotectant conferring salt, drought, and other stress tolerance in plants [90, 91]. Phosphoethanolamine N-methyltransferase (PEAMT, EC 18.104.22.168) is believed to be a key enzyme of the choline biosynthesis pathway. Note that two transcripts with sequences homologous to a putative PEAMT protein from R. communis were up-regulated by all three stresses.
TF expression is altered by abiotic stresses
Interestingly, all the major TF families induced by abiotic stresses are directly related to either a general stress response (NAC, MYB, bHLH, and WORKY) or a specific hormone pathway (AP2-EREBP, ARF, and Pseudo-ARR). The largest class of TFs induced by abiotic stresses in the three stressed samples was the NAC TF family. A total of 62, 33, and 12 NACs were up-regulated due to dehydration, high salinity, and cold stress, respectively. NAC is regarded as a plant-specific transcription factor family member and expressed in many tissues and during many developmental stages . A further systemic analysis of the NAC transcription factor family at the genome-wide level reported that approximately 30 % of members of the NAC family are up-regulated during abiotic stress in rice, with 11 members induced by at least three types of abiotic stresses . Additionally, in our data, the largest class of TFs induced by cold stress was the MYB TF family. A total of 16 MYBs were up-regulated by cold stress, suggesting that this TF family plays a major role in cold tolerance. A R2R3-type MYB has been identified as a master regulator of the cold stress response , and these results are consistent with our RNA-Seq data. Interestingly, in our transcriptome data, lower numbers of TFs were up-regulated by cold stress than the other two stresses, potentially because the response to cold stress appears to be less active than dehydration and salt stresses. In our opinion, because M. falcata was originally grown in extremely cold environments, the cold-responsive genes were already expressed at a higher level. This hypothesis was inspired by a study in Arabidopsis and salt cress, which illustrated that the stress tolerance of salt cress was due to stress-inducible genes that were constitutively overexpressed in salt cress but inducible in Arabidopsis .
Abiotic stresses modify phytohormone metabolism and signal transduction
Previous studies have demonstrated that abiotic stresses have a striking effect on phytohormone metabolism and signalling. Transcriptomic and metabolomic analyses have demonstrated increased ABA, ethylene, and JA metabolism in several plants [12–20]. We not only reconfirm these initial findings but also extend our understanding of modified phytohormone metabolism in plants. The process from stress signal perception and the trigger of ABA biosynthesis to the dynamic regulation of the ABA level is an important stress signalling pathway in cells. Our data demonstrate the enhanced transcript expression involved in most steps of ABA biosynthesis, including transcripts for Crtz, ZEP, and NCED. The enhanced expression of ABA biosynthesis pathway genes may lead to increased endogenous ABA. Interestingly, transcripts for the AAO gene, which encodes for an enzyme that catalyses the final step of ABA biosynthesis, showed decreased expression in all stress-treated samples. Meanwhile, transcripts for the CYP707A gene, which encodes for an enzyme that catalyses ABA catabolism, showed increased expression in all stress-treated samples. Together with the ABA content determined under cold stress, we hypothesise that increased endogenous ABA may inhibit ABA biosynthesis and advance ABA catabolism to some extent, which is aimed at the dynamic regulation of the ABA level and maintaining the ABA level in balance. ABA perception through PYR/PYL receptors is required for the basal ABA signalling that promotes plant growth and normal seed production and that regulates steady state transpiration . The expression of transcripts for PYR/PYL genes was inhibited by all three stressed samples. Compared with cold stress, the dehydration and high salinity stresses both enhanced the expression of the ABF1 genes observably and induced the expression of ABA-responsive genes further. In contrast, compared with enhancing ABA biosynthesis, all three abiotic stresses inhibited the conversion of GA12-aldehyde to bioactive GA4 and advanced the conversion of bioactive GA4 to inactive GA34, indicating that GA plays an antagonistic role in response to abiotic stresses in M. falcata compared with ABA. Additionally, the antagonistic role of GA is further confirmed by the expression pattern of GA receptors, namely GID1, being contrary to ABA receptors in the DS and SS samples.
The process from stress signal perception to the dynamic regulation of ethylene and JA metabolism is an important abiotic stress signalling pathway in plants. Compared with the downstream events in ethylene and JA signal transduction, the studies in this field are relatively lagging. Our discovery sheds new light on abiotic stress-induced ethylene and JA metabolic responses. We found evidence for pathways that lead to enhanced ethylene and JA biosynthesis. In our transcriptome data, we detected three key enzymes related to the ethylene biosynthesis pathway. All of the transcripts for ethylene biosynthesis enzyme genes showed enhanced expression in all three stressed samples. Consistent with ethylene, JA biosynthesis-related transcripts exhibited similar expression patterns. Upon further analysis, we noted that all three abiotic stresses increased the abundance of transcripts related to the JA metabolic pathway, which would contribute to the increased formation of the bioactive JA compound. Based on this knowledge, we infer that ethylene and JA have synergistically positive effects on resisting abiotic stresses. The ERF gene is an upstream component in both JA and ethylene signalling. The expression pattern of the ERF gene was also up-regulated, further supporting our hypothesis.
Abiotic stresses modify the nod factor signalling pathways during early symbiotic nodulation
Early symbiotic nodulation involves four major developmental programmes: (1) the perception of nod factor, (2) the activation of calcium spiking, (3) root hair deformation and infection, and (4) early nodulin gene induction and nodule primordium formation. A comprehensive transcriptomic analysis of nodulation signalling pathway gene expression in response to abiotic stresses is lacking in the literature. We detected several transcripts for key genes involved in the nodulation signalling pathway. NFR genes are nod factor receptors and play a crucial role in the perception of nod factor. All three stresses increased the expression of the NFR genes. The DMI1 and DMI2 genes displayed similar expression patterns. In accordance with biotic stress, we hypothesise that all three abiotic stresses may enhance the perception of nod factor and the activation of calcium spiking. DMI3, which exhibits different expression patterns between abiotic stresses, may affect the perception of calcium spiking and deformation of root hairs. The expression of the DMI3 genes was down-regulated in the CS sample but up-regulated in the DS and SS stressed samples. The expression of the ENOD genes was down-regulated all together by the three stresses because the expression pattern of the ENOD transcriptional regulators ERN and NSP were altered by these stresses. NSP genes exhibiting decreased expression levels were predominantly due to the up-regulated RR genes. We hypothesise that NSP genes are targets of the RRs-dependent signalling pathway and that miR171h gene is crucial to regulate their expression in response to abiotic stresses and during early nodule development. Interestingly, the expression of the ENOD genes showed less of a decrease in the dehydration -stressed sample compared with the other two stressed samples, which may be due to the increased expression of ERN genes. Upon the above analyses, we concluded that all three stresses might negatively regulate the formation of nodule primordia.
The role of auxin in root responses to cold stress
The cold-stressed root transcripts reported here were derived from our RNA-Seq data and thus reflect the expression of genes not only involved in a generalised root response to cold stress but also transcripts directly related to root development. We found that cold stress reduced lateral root formation, nodule number, and root length. In addition, we found that IAA application can increase the number of lateral roots and nodules, suggesting that the cold-induced decrease of lateral root formation and nodule number are dependent upon a reduction in auxin availability. AUX is an important auxin transporter. Our qTR-PCR results indicate that cold application appears to inhibit AUX expression. The expression of AUX increased after the application of exogenous IAA. We hypothesise that cold-induced reductions in auxin availability may depend on the decreased expression levels of AUX genes. Interestingly, IAA application is unable to increase the length of the main root. We hypothesise that the development of the main root requires the synergy of auxins and other hormones.
To our knowledge, we here present the first whole transcriptome analysis of abiotic stresses using M. falcata and an in-depth RNA-seq analysis of its transcriptomes under optimal treatment conditions. Overall, these experiments and results have confirmed previously reported responses to abiotic stresses while addressing previously unknown details and fundamentally advancing our understanding of how modified gene expression patterns facilitate acclimation to abiotic stresses. We revealed the abiotic stress-responsive mechanisms underlying the metabolism and core signalling components of major phytohormones. In addition, we identified nod factor signalling pathways during early symbiotic nodulation that are modified by abiotic stresses.
M. falcata seeds were obtained from the Agricultural Research Service (ARS) GRIN system (http://www.ars-grin.gov/), US Department of Agriculture (USDA). Seeds originating from Russia (accession number PI502449) were used for this work. Accession PI502449 is regarded as the most tolerant to winter injury  and was identified as diploid M. falcata . Seeds of Medicago truncatula A17 and R108 were provided by BRC, UMR 1097, INRA, Montpellier, France. Seed treatments for germination have been published previously . After germination, the plantlets were grown in a soil/vermiculite (3:1, v/v) mixture in a chamber incubated under controlled environment conditions (14-h photo-period, 60 μmol photons m−2 s−1, 22°/18 °C day/night regime, 70 % relative humidity).
Evaluate the effect of cold, drought and salt stresses on M. truncatula 108-R, M. truncatula A17 and M.falcata PI502449
Plants grown for these assays were germinated as described above. After germination, 4-week-old plants grown in a soil/vermiculite (3:1, v/v) mixture at 24 °C under a 14-h photoperiod were used for abiotic stress treatments (14-h photo-period, 60 μmol photons m−2 s−1, 22°/18 °C day/night regime, 70 % relative humidity). For cold treatment, the plantlets were incubated at 0 °C (freezing chamber RuMED4001) for 6 h, 8 h, and 10 h under dim light (0.7-0.8 μmol sec−1 m−2). For drought treatment, the plants were grown without watering for 10 d, 12 d, and 14 d under dim light (0.7-0.8 μmol sec−1 m−2). For salinity treatment, the plants were irrigated with NaCl solution at 100 mM, 150 mM, and 200 mM for 10 d under dim light (0.7-0.8 μmol sec−1 m−2). After treatment, leaves and roots were collected respectively, and then measured the weight, mortality and soluble carbohydrates content. Three independent experiments were performed.
Electrolyte leakage assays
Plants grown for electrolyte leakage assays were germinated as described above. After germination, 4-week-old plants grown in a soil/vermiculite (3:1, v/v) mixture at 24 °C under a 16-h photoperiod were used for abiotic stress treatments (14-h photo-period, 60 μmol photons m−2 s−1, 22°/18 °C day/night regime, 70 % relative humidity). For cold treatment, the plantlets were incubated at 0 °C (freezing chamber RuMED4001) for 2 h, 4 h, 6 h, 8 h, and 10 h under dim light (0.7-0.8 μmol sec−1 m−2). For dehydration treatment, the plantlets were transferred to dry Whatman 3 MM paper  for 0.5 h, 1 h, 1.5 h, and 2 h under dim light (0.7-0.8 μmol sec−1 m−2). For high salinity treatment, the plantlets were irrigated with NaCl solution at 200 mM, 400 mM, 600 mM, 800 mM, and 1 M for 2 h under dim light (0.7-0.8 μmol sec−1 m−2). After treatment, leaves were collected, and the electrolyte leakage was measured as previously described . Three independent experiments were performed.
Abiotic stress treatment for sequencing samples
Plants grown for abiotic stress treatment were germinated as described above. Dehydration, cold, and high salinity stress treatments were applied essentially as reported previously . For dehydration treatment, plants were harvested from pots and desiccated on Whatman 3MM paper for 2 h at 24 °C under dim light (0.7-0.8 μmol sec−1 m−2). For cold stress, we transferred the plantlets to 0 °C (freezing chamber RuMED4001) for 8 h under dim light (0.7-0.8 μmol sec−1 m−2). For high salinity stress, we irrigated the plantlets with 1 M NaCl solution for 2 h under dim light (0.7-0.8 μmol sec−1 m−2). Plantlets without stress treatment were used as the standard condition, and all materials were stored in liquid nitrogen immediately after treatment and harvest. Two biological replicates per condition were used for further analysis. In every biological replicate, we mix five plantlets together.
cDNA library preparation and sequencing
Total RNA from each sample was isolated using the TRIzol reagent (Invitrogen), and genomic DNA was digested using DNase (New England Biolabs). We used the OligoTex mRNA mini kit (Qiagen) to purify poly (A) mRNA from the total RNA. The protocol for cDNA synthesis has been previously described . The mRNA was fragmented using an RNA fragmentation kit (Ambion). The first cDNA strand was synthesised using random hexamer primers, and the second cDNA strand was subsequently synthesised.
The sequencing library was constructed according to the manufacturer’s instructions (Illumina) for high-throughput sequencing. Fragments of approximately 300 nt were excised and enriched by 18 PCR cycles. The PCR products were sequenced using the Illumina HiSeq 2000 platform using101-cycle paired-end reads. Initial base calling and quality filtering of the Illumina GA-IIx image data were performed using the default parameters of the Illumina GA Pipeline GERALD stage (http://www.illumina.com). All sequencing reads were deposited into the Short Read Archive (SRA) of the National Center for Biotechnology Information (NCBI), and can be accessed under the accession number (SRR1956534, SRR1956535, SRR1956716, SRR1956718, SRR1956719, SRR1957050, SRR1956913, SRR1956721, SRR1982256, SRR1982261, SRR1982264 and SRR1982268).
De novo transcriptome assembly
To obtain a better assembly result, two assembly methods (single k-mer (SK) method and multiple k-mer (MK) method) were used for the de novo assembly of these sequencing data. We first performed a test assembly using Illumina reads derived from the SC sample rep1 library with a series of k-mers (28–56) using ABySS . To select an optimal k-mer parameter, we compared the summary statistics, including N50s, total contig number, and the total assembly size generated by each k-mer (Additional file 13). After careful consideration, k-mer = 41 was chosen for accuracy and the length of the assembled transcripts. Using these identified parameters, a total of 31,591,337,787 nt reads generated from all eight libraries ((dehydration, salt, cold and standard) × (two replicates)) were de novo assembled into contigs. Additionally, Trinity  has been shown to be the best SK assembler for transcriptome assembly . Trinity was implemented with default parameters on our 8 library datasets. The results of the MK and SK were combined using the CAP3 programme with default parameters . Finally, the redundant sequences were collapsed using the CD-HIT-EST algorithm , producing a total of 98,515 sequences. These sequences span 84,416,200 nt, with an average length of 857 nt. The assembly sequences were listed at (http://bioinformatics.cau.edu.cn/falcata/sequences/all.transcripts).
Putative function, GO, and KEGG orthology annotations
The assembled reference sequences were aligned to NCBI nr database using BLASTx  with a threshold of e-value ≤1e−6, and the best three hits were chosen for putative function annotation. KAAS (KEGG Automatic Annotation Server) was used to identify biochemical pathways and to calculate the statistical significance of each pathway . The GO annotations were obtained from scanning the transcriptome by using InterProScan .
Differentially expressed transcripts
The sequencing reads of the four samples were mapped to the M. falcata transcriptome by SOAPaligner , with a maximum of three mismatches. Gene expression levels were calculated by RPKM. The expression difference was identified by DEGseq , in which Fisher’s exact test and the likelihood ratio were proposed to identify differentially expressed genes, and the P- and Q-values for each gene were calculated. Differentially expressed genes identified by DESeq were required to have a 2-fold change and P ≤ 0.05.
We first selected six expressed and relatively stable genes displayed in the RNA-Seq data as internal control candidates. Two reference genes (ID: Mf94657 and Mf85797) were determined by geNorm  for qRT-PCR analysis. After the total RNA was extracted, reverse transcription was performed using M-MLV Reverse Transcriptase (Promega). The quantitative real-time PCR analysis was conducted using a CFX-96 Real-Time System (Bio-Rad) and SYBR Premix Ex Taq (TaKaRa). All of the specific primers used in this work are listed in Additional file 14.
Determine ABA content
ABA content was measured as previously described . For cold stress, we transferred the plantlets (4-week-old) to 0 °C (freezing chamber RuMED4001) for 0 h, 2 h, 4 h, 6 h under dim light (0.7-0.8 μmol sec-1 m-2). After cold stress, a total of 20 mg of homogenized M. falcata (PI 502449) and M. truncatula (A17) leaves were soaked in 1 ml of ABA extraction buffer (10 mM HCl and 1 % polyvinylpolypyrrolidone in methanol) and shaked at 4 °C for 16 h. After neutralization with 15 μl of 1 M NaOH, the supernatant was dried and resuspended in TBS. The ABA content was quantified using a Phytodetek ABA Test Kit (Agdia, USA). These experiments were repeated three times with similar results.
Auxin treatment experiment
Plants grown for the auxin treatment experiment were germinated as described above, except that the plantlets were transferred to large Petri pots containing Fahraeus medium  vertically and inoculated with Sinorhizobium meliloti strain 1021 in Bergensen’s modified medium adjusted to an optical density at 600 nm [OD600] = 0.1. There were four plantlets per pot. Each pot was two-thirds covered with black paper on the outside. These pots were placed in a growth chamber at 24 °C under long days (16 h light, 8 h dark) for 72 h, and the pots were then divided into three sets. (a) Plantlets were supplemented with IAA to a final concentration of 10−8 M and grown at 4 °C under long days for 10 days before being transferred to 24 °C. (b) Plantlets were supplemented with IAA to a final concentration of 10−8 M and maintained at 24 °C under long days. (c) Plantlets were supplied with an equal amount of distilled water and maintained at 24 °C under long days. All of these plants were collected after 21 days for root measurements and RNA extraction.
This work was supported by grants from the National Basic Research Program of China (973 Program, 2012CB215301) and the Hi-Tech Research and Development (863, 2011AA100209) Program. We thank Dr. Jean Marie Prosperi and Magalie Delalande (BRC for Medicago truncatula, UMR 1097, INRA, Montpellier, France) for providing seeds of Medicago truncatula A17 and R108. We thank the US National Plant Germplasm System (NPGS) in US Department of Agriculture (USDA) for providing Medicago falcata (PI502449) seeds.
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