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. 2019 Nov 14;42(3):611–623. doi: 10.1590/1678-4685-GMB-2018-0235

Genome-wide identification and characterization of R2R3-MYB genes in Medicago truncatula

Wei Li 1,*, Ying Liu 1,*, Jinyue Zhao 1, Xin Zhen 1, Changhong Guo 1, Yongjun Shu 1
PMCID: PMC6905446  PMID: 31188936

Abstract

MYB is a large family of plant transcription factors. Its function has been identified in several plants, while there are few reports in Medicago truncatula. In this study, we used RNA-seq data to analyze and identify R2R3-MYB genes in the genome of Medicago truncatula. Phylogenetic analysis classified 150 MtMYB genes into 21 subfamilies with homologs. Out of the 150 MtMYB genes, 139 were distributed among 8 chromosomes, with tandem duplications (TD) and segment duplications (SD). Microarray data were used for functional analysis of the MtMYB genes during growth and developmental processes providing evidence for a role in tissues differentiation, seed development processes, and especially the nodulation process. Furthermore, we investigated the expression of MtMYB genes in response to abiotic stresses using RNA-seq data, which confirmed the critical roles in signal transduction and regulation processes under abiotic stress. We used quantitative real-time PCR (qRT-PCR) to validate expression profiles. The expression pattern of M. truncatula MYB genes under different abiotic stress conditions suggest that some may play a major role in cross-talk among different signal transduction pathways in response to abiotic stresses. Our study will serve as a foundation for future research into the molecular function of M. truncatula R2R3-MYB genes.

Keywords: Medicago truncatula, MYB, abiotic stress, qRT-PCR

Introduction

Myeloblastosis (MYB) genes are one of the largest transcription factors families in the plant kingdom (Romero et al., 1998; Rosinski and Atchley, 1998). MYB typically contain an MYB-binding domain at the N-terminus, composed of 1-4 imperfect repeats, with approximately 51-52 amino acid residues of incomplete conserved peptides encoding three α-helices (Kanei-Ishii et al., 1990; Lipsick, 1996; Stracke et al., 2001). These three α-helices form a helix-turn-helix (HTH) structure and fold with three relatively conserved tryptophan residues, separated by 18-19 amino acid residues of regular arrangement, and further participate in the formation of hydrophobic interactions (Ogata et al., 1995). The structure of the MYB domain reveals that the HTH interacts with the major groove of DNA (Ogata et al., 1994). MYB-containing genes have a diverse number of MYB proteins containing incomplete repeats and are divided into four categories, 1R-MYB, R2R3-MYB, R1R2R3-MYB, and 4R-MYB (Jin and Martin, 1999).

In the MYB gene family, R2R3-MYB is the largest category in plants and yeast (Martin and Pazares, 1997; Jin and Martin, 1999). To date, 126 R2R3-MYB genes have been identified in Arabidopsis (Stracke et al., 2001), 157 in maize (Du et al., 2012a), 244 in soybean (Du et al., 2012b), 205 in Gossypium raimondii (He et al., 2016), and 166 in cassava (Liao et al., 2016). R2R3-MYB transcription factors are involved with abiotic stress response, reactive oxygen species signaling pathways, secondary metabolism, and hormone signaling pathways. AtMYB41 from Arabidopsis is induced in response to high salinity, drought, cold, and abscisic acid (Lippold et al., 2009). AtMYB102 are rapidly induced by osmotic stress and abscisic acid (ABA) treatment (Denekamp and Smeekens, 2003). OsMYB55 is induced in rice by high temperature and over-expression of OsMYB55 resulted in improved plant growth under high temperature (Elkereamy et al., 2012). Meanwhile, OsMYB91 plays a role in plant growth regulation and salt stress tolerance in rice (Zhu et al., 2015). TaMYB4 of wheat is induced by salicylic acid, ethylene, abscisic acid, and methyl jasmonate, demonstrating a role of TaMYB4 in response to biotic stress (Al-Attala et al., 2014). GbMYB5 from Gossypium barbadense is positively involved in response to drought stress during plant development (Chen et al., 2015). GbMYBFL, involving in flavonoid biosynthesis, is most closely related to R2R3-MYB and displays high similarity to MYB from other plants (Zhang et al., 2017).

Medicago truncatula is a model plant for genetic research of legume plants (Young and Udvardi, 2009), as it has a small genome, high genetic transformation efficiency, self-pollination, nitrogen fixing, along with high biological diversity. Crop improvement of legume breeding has become an important subject (Lee et al., 2017). MtERF and MtMAPKKK gene families of M. truncatula are valuable for characterizing molecular function to improve stress tolerance in plants (Li et al., 2016; Shu et al.. 2016). However, the R2R3-MYB family is poorly identified on a genomic level in M. truncatula.

In this study, we performed a genome-wide analysis of the R2R3-MYB gene family in M. truncatula, including multiple alignment analysis, phylogenetic analysis, chromosome localization, gene duplication analysis, and expression profiling. We used quantitative real-time reverse transcription (qRT-PCR) experiments to compare and analyze five stress treatments (ABA, cold, freezing, drought, and salt) with a control treatment. Our study will serve as a foundation for future research into the molecular function of M. truncatula R2R3-MYB genes.

Materials and Methods

Plant growth and treatment

M. truncatula (cv. JemalongA17) seeds were grown in a growth chamber (Conviron E15), between 18ºC (night) and 24ºC (day), with humidity ranging from 60% to 80%, and a 14/10 h light-dark period (light, 06:00–20:00). The seedlings were irrigated with half-strength Hoagland solution once every other day. At 8 weeks, M. truncatula were randomly divided into six groups for stress treatments. Plants treated with cold stress (B group) and freezing stress (C group) were transferred to chambers set at 4 ºC and -8 ºC, respectively. Plants treated with drought stress (D group) and salt stress (E group) were respectively treated with 300 mM mannitol and 200 mM NaCl solutions. Plants in the ABA (F group) treatment group were sprayed with 100 μM ABA solution. The control (untreated, A group) and treated (B-F groups) seedlings were harvested 3 h after treatment. For each group, five randomly chosen whole seedlings were pooled to form a biological replicate. All plant samples were frozen in liquid nitrogen and stored at -80 ºC until use.

Database search for MYB proteins in M. truncatula

M. truncatula genome and protein sequences were downloaded from JCVI (http://jcvi.org/medicago/, Mt4.0) (Young et al., 2011). R2R3-MYB protein sequences of Arabidopsis were obtained from TAIR (http://www.arabidopsis.org/) (Poole, 2007) and served as queries to search against the M. truncatula proteins using the BLASTP program with e-values of 1E-3. All BLAST hits were retrieved and searched using the Hidden Markov Model (HMM) profile of the R2R2-MYB DNA-binding domain (PF000249), which was downloaded from the Pfam website (http://pfam.xfam.org/) (Finn et al., 2014).

Phylogenetic analysis of the M. truncatula R2R3-MYB gene family

Phylogenetic analysis was performed using MEGA (Version 5.0), and constructed using neighbor-joining (NJ) methods. The NJ method used the following parameters: Poisson correction, pair-wise deletion, and 1000 bootstrap analysis for statistical reliability (Tamura et al., 2011).

Chromosomal location and gene duplication of R2R3-MYB gene family

The location of R2R3-MYB genes were mapped to different chromosomes using the Circos software (http://circos.ca/) (Krzywinski et al., 2009). If two genes with similarities of more than 85% were separated by four or fewer gene loci, they were identified as tandem duplications (TD). Otherwise, they were classified as segmental duplications (SD). The duplications with R2R3-MYB genes were identified by plant genome duplications (PGDD, http://chibba.agtec.uga.edu/duplication/) (Lee et al., 2012, Shu et al., 2016), and duplicated genes between different chromosomes or loci were linked in the diagrams.

Expression analysis of R2R3-MYB genes in plant growth and development using high throughput data

We studied the expression analysis of R2R3-MYB genes during growth and development and under different abiotic stress treatments. Gene expression data were downloaded from the Medicago truncatula Gene Expression Atlas (MtGEA) Project (MtGEA, http://mtgea.noble.org/v3/) (Benedito et al., 2008). Genome-wide transcriptome data from M. truncatula in different tissues during development were downloaded from the NCBI short read archive database (SRA database) (http://www.ncbi.nlm.nih.gov).

Expression analysis of R2R3-MYB genes under different abiotic stress treatment conditions

Under six different abiotic stress treatments, MtMYB gene expressional values were evaluated using the TopHat (Trapnell et al., 2009) and Cufflinks (Trapnell et al., 2012) software. The data were analyzed, clustered, and displayed using the ggplot2 of R software (Version 3.1.0), as our previous research described (Shu et al., 2016).

Quantitative reverse transcription PCR (qRT-PCR) analysis of R2R3-MYB genes expressed in M. truncatula

Ten R2R3-MYB genes were selected and quantitative primers were designed based on genes sequences, while the ACTIN and GAPDH genes served as reference genes (see Table S1 (98.3KB, pdf) ). Total RNA was extracted from M. truncatula grown under the six conditions (control, ABA, drought, salt, cold, and freezing) using a total RNA kit (Tiangen, Beijing, China) according to the manufacturer’s instructions. The RNA extracts were reverse transcribed to cDNA, using a PrimeScript RT reagent Kit (Toyobo, Shanghai, China). qRT-PCR was performed using the LightCycler®96 System (Roche, Rotkreuz, Switzerland) with SYBR Premix Ex TaqTM II (Toyobo, Shanghai, China). The experiments were repeated for three biological replicates and the PCR conditions were set as follows: 95 ºC for 2 min, 40 cycles of 95 ºC for 30 s, 55 ºC for 30 s, and 72 º for 1 min. The fold change value was calculated using the expression abundances, which based on the 2-ΔΔCT method.

Results

Identification and classification of R2R3-MYB genes in M. truncatula

To identify R2R3-MYB genes in M. truncatula, Arabidopsis R2R3-MYB gene sequences were used as queries with e-value set as 1E-3. The gene name, gene locus, chromosome location, amino acid sequence, introns, family groups, and isoelectric point (pI) are described in Table 1. Out of the 150 MtMYB genes, 139 genes were distributed across 8 chromosomes of M. truncatula. The remaining 11 MtMYB genes were MtMYB5, 6, 7, 13, 14, 16, 34, 35, 36, 37, and 52. The length of these 139 R2R3-MYB ranged from 194 to 1514 amino acids, with an intron distribution of 0-12, and the isoelectric point were distributed from 4.77 to 9.93.

Table 1. List of all MtMYB genes identified in the Medicago truncatula genome.

Gene Name Gene Locus Chromosome Location AA Introns Family Group pI
MtMYB001 Medtr3g039990 chr3:13992780-13994617 312 2 1 5.44
MtMYB002 Medtr6g012180 chr6:3615718-3617850 319 2 1 5.76
MtMYB003 Medtr7g010210 chr7:2460324-2462646 272 3 1 8.94
MtMYB004 Medtr7g087130 chr7:33927709-33929377 339 2 1 6.54
MtMYB005 Medtr0140s0030 scaffold0140:9682-11671 335 2 1 6.6
MtMYB006 Medtr0489s0020 scaffold0489:9594-10964 335 2 1 6.6
MtMYB007 Medtr0251s0050 scaffold0251:9249-10577 273 1 2 5.09
MtMYB008 Medtr1g043050 chr1:16126632-16128228 255 2 2 5.58
MtMYB009 Medtr1g043080 chr1:16137369-16139502 256 2 2 5.6
MtMYB010 Medtr1g076150 chr1:33730166-33733155 259 2 2 5.31
MtMYB011 Medtr7g096930 chr7:38915313-38918018 279 2 2 5.35
MtMYB012 Medtr7g115650 chr7:47812651-47813895 208 2 2 8.51
MtMYB013 Medtr0008s0390 scaffold0008:236494-237588 273 1 2 5.55
MtMYB014 Medtr0008s0470 scaffold0008:261364-262450 292 1 2 5.34
MtMYB015 Medtr2g067420 chr2:28203900-28207822 330 2 3 4.74
MtMYB016 Medtr0063s0090 scaffold0063:54059-56064 224 2 3 5.78
MtMYB017 Medtr4g073420 chr4:27807701-27809440 286 1 4 8.65
MtMYB018 Medtr4g485530 chr4:33337240-33340075 194 2 4 9.68
MtMYB019 Medtr5g079670 chr5:34066783-34068495 214 2 4 9.14
MtMYB020 Medtr8g095390 chr8:39916215-39917940 316 2 4 9.14
MtMYB021 Medtr4g100720 chr4:41544004-41544940 176 3 5 8.25
MtMYB022 Medtr4g125520 chr4:52070924-52072242 308 2 5 8.34
MtMYB023 Medtr8g020490 chr8:7194946-7196540 255 2 5 8.55
MtMYB024 Medtr5g078800 chr5:33679342-33680505 266 2 6 8.76
MtMYB025 Medtr5g078860 chr5:33697936-33699039 307 2 6 8.76
MtMYB026 Medtr5g078910 chr5:33733725-33736557 301 2 6 9.06
MtMYB027 Medtr5g078930 chr5:33748446-33750303 220 2 6 9.74
MtMYB028 Medtr5g078950 chr5:33762292-33763827 266 2 6 9.14
MtMYB029 Medtr5g079120 chr5:33821199-33824299 307 3 6 9.12
MtMYB030 Medtr5g079220 chr5:33865422-33867467 277 2 6 8.08
MtMYB031 Medtr5g079290 chr5:33903955-33904999 265 2 6 9.11
MtMYB032 Medtr7g017260 chr7:5468456-5471716 276 2 6 7.59
MtMYB033 Medtr8g060940 chr8:21305461-21306435 245 2 6 5.83
MtMYB034 Medtr0001s0360 scaffold0001:148343-149371 254 2 6 8.13
MtMYB035 Medtr0193s0090 scaffold0193:23279-25596 208 2 6 9.27
MtMYB036 Medtr0197s0010 scaffold0197:3158-6293 230 2 6 5.79
MtMYB037 Medtr0247s0040 scaffold0247:19831-22448 180 2 6 9.56
MtMYB038 Medtr2g034790 chr2:13342703-13345610 333 2 7 5.57
MtMYB039 Medtr4g121460 chr4:50199327-50201231 340 2 7 5.21
MtMYB040 Medtr7g117730 chr7:48891947-48893156 257 1 7 9.19
MtMYB041 Medtr8g027345 chr8:9621235-9622899 301 1 7 7.03
MtMYB042 Medtr1g100653 chr1:45593395-45595446 296 2 9 7.16
MtMYB043 Medtr4g082230 chr4:31939369-31942857 408 2 9 6.02
MtMYB044 Medtr4g082290 chr4:31999665-32001816 408 2 9 5.77
MtMYB045 Medtr6g012690 chr6:3910120-3912657 358 2 9 5.54
MtMYB046 Medtr7g011170 chr7:2948411-2950937 310 2 9 6.57
MtMYB047 Medtr7g076740 chr7:28944308-28947368 305 2 9 8.15
MtMYB048 Medtr8g031360 chr8:11745382-11748030 298 2 9 5.92
MtMYB049 Medtr4g478180 chr4:30006885-30009067 354 3 10 6.36
MtMYB050 Medtr5g007370 chr5:1317895-1319526 300 1 10 6.25
MtMYB051 Medtr5g029840 chr5:12551795-12553088 335 1 10 6.26
MtMYB052 Medtr0008s0280 scaffold0008:117749-119885 232 2 10 6.21
MtMYB053 Medtr2g011660 chr2:2891380-2892991 346 2 11 5.85
MtMYB054 Medtr2g089450 chr2:37807548-37809745 251 2 11 7.62
MtMYB055 Medtr2g089620 chr2:37880385-37882262 327 2 11 6.45
MtMYB056 Medtr4g091490 chr4:36245993-36247326 359 2 11 5.87
MtMYB057 Medtr1g085040 chr1:37962367-37964302 370 2 13 7.1
MtMYB058 Medtr1g085640 chr1:38268101-38269978 389 2 13 6.1
MtMYB059 Medtr1g112760 chr1:51044088-51045093 231 2 13 8.61
MtMYB060 Medtr3g077110 chr3:34625609-34627040 350 2 13 5.71
MtMYB061 Medtr4g105130 chr4:43559175-43561153 362 2 13 5.51
MtMYB062 Medtr7g110830 chr7:45437545-45439504 368 2 13 5.28
MtMYB063 Medtr7g111290 chr7:45674622-45676610 382 2 13 6.26
MtMYB064 Medtr1g017000 chr1:4609270-4612231 253 2 14 6.22
MtMYB065 Medtr1g017140 chr1:4685126-4687287 342 2 14 7.21
MtMYB066 Medtr2g095520 chr2:40818577-40820355 321 2 14 7.02
MtMYB067 Medtr3g103570 chr3:47845667-47847265 348 2 14 6.26
MtMYB068 Medtr4g057635 chr4:21173419-21175385 325 2 14 6.67
MtMYB069 Medtr4g097570 chr4:40253351-40254860 294 2 14 8.04
MtMYB070 Medtr4g128670 chr4:53556826-53558636 351 2 14 5.43
MtMYB071 Medtr5g014990 chr5:5113035-5114677 310 2 14 7.49
MtMYB072 Medtr6g090405 chr6:34357171-34358762 256 2 14 5.53
MtMYB073 Medtr7g102110 chr7:41207062-41209098 273 2 14 6.13
MtMYB074 Medtr1g100667 chr1:45604161-45606367 273 2 16 9.4
MtMYB075 Medtr6g055910 chr6:20067285-20071069 284 2 16 6.55
MtMYB076 Medtr1g083630 chr1:37214098-37220601 631 10 18 8.87
MtMYB077 Medtr1g085770 chr1:38342281-38444471 308 3 18 7.64
MtMYB078 Medtr1g085880 chr1:38446474-38447221 194 1 18 9.25
MtMYB079 Medtr2g088170 chr2:37135155-37138193 460 2 18 5.04
MtMYB080 Medtr5g062790 chr5:26032596-26033729 305 2 18 4.67
MtMYB081 Medtr5g088080 chr5:38180518-38181517 267 2 18 5.06
MtMYB082 Medtr5g088150 chr5:38189614-38190613 267 2 18 5.06
MtMYB083 Medtr5g088610 chr5:38446993-38448346 356 2 18 5.03
MtMYB084 Medtr5g088640 chr5:38455878-38456905 276 2 18 5.06
MtMYB085 Medtr5g488170 chr5:38207742-38208675 245 2 18 8.27
MtMYB086 Medtr5g488210 chr5:38216839-38217838 267 2 18 5.06
MtMYB087 Medtr6g006030 chr6:968935-973160 210 2 19 6.79
MtMYB088 Medtr7g035075 chr7:13292852-13298285 209 2 19 6.07
MtMYB089 Medtr1g086510 chr1:38706430-38707982 266 2 20 6.71
MtMYB090 Medtr1g086530 chr1:38719605-38720569 279 1 20 5.57
MtMYB091 Medtr1g110460 chr1:49847994-49849320 312 2 20 6.97
MtMYB092 Medtr2g033170 chr2:12558787-12561118 330 2 20 5.54
MtMYB093 Medtr4g123040 chr4:50776703-50778712 316 2 20 6.9
MtMYB094 Medtr4g082040 chr4:31789875-31791702 428 2 21 5.48
MtMYB095 Medtr5g041570 chr5:18244022-18246575 439 2 21 5.81
MtMYB096 Medtr6g027340 chr6:9347619-9348708 206 2 21 9.43
MtMYB097 Medtr6g027370 chr6:9359727-9361707 353 2 21 9.13
MtMYB098 Medtr6g074860 chr6:27791872-27795423 242 2 21 8.94
MtMYB099 Medtr7g086960 chr7:33824449-33826853 357 2 21 8.87
MtMYB100 Medtr3g101290 chr3:46598679-46599616 227 0 22 6.39
MtMYB101 Medtr4g094982 chr4:39426938-39428438 272 0 22 5.76
MtMYB102 Medtr5g016510 chr5:5923364-5924314 317 0 22 8.35
MtMYB103 Medtr5g082910 chr5:35747490-35748793 289 1 22 8.33
MtMYB104 Medtr6g015455 chr6:5126272-5138191 1514 9 22 6.6
MtMYB105 Medtr4g019370 chr4:6040082-6046125 351 1 23 6.1
MtMYB106 Medtr3g074520 chr3:33695057-33696802 347 2 24 5.76
MtMYB107 Medtr1g026870 chr1:8820780-8826887 984 10 25 5.45
MtMYB108 Medtr1g045610 chr1:17117606-17119422 259 2 25 9.28
MtMYB109 Medtr1g057980 chr1:25521596-25523733 298 2 25 6.68
MtMYB110 Medtr1g062940 chr1:27632125-27633748 219 3 25 5.7
MtMYB111 Medtr1g073170 chr1:32447073-32448262 258 2 25 7.64
MtMYB112 Medtr2g064160 chr2:27171680-27173646 314 2 25 6.14
MtMYB113 Medtr2g096380 chr2:41173925-41175393 237 2 25 6.2
MtMYB114 Medtr2g097910 chr2:41830130-41832026 320 1 25 5.63
MtMYB115 Medtr2g099740 chr2:42787607-42789410 402 1 25 6.27
MtMYB116 Medtr3g065440 chr3:29570010-29573532 312 3 25 4.81
MtMYB117 Medtr3g077650 chr3:34915543-34917386 448 2 25 6.65
MtMYB118 Medtr3g083540 chr3:37705148-37706353 304 1 25 6.83
MtMYB119 Medtr3g097450 chr3:44673726-44675570 298 2 25 8.71
MtMYB120 Medtr3g110028 chr3:50889343-50895792 904 11 25 5.08
MtMYB121 Medtr3g461490 chr3:24436965-24438138 326 2 25 6.31
MtMYB122 Medtr4g063100 chr4:23343932-23345888 254 2 25 5.44
MtMYB123 Medtr4g065017 chr4:24357511-24360058 333 1 25 5.31
MtMYB124 Medtr4g088015 chr4:34653348-34657396 443 2 25 9.15
MtMYB125 Medtr4g102380 chr4:42421826-42423447 273 1 25 5.26
MtMYB126 Medtr4g105660 chr4:43865250-43867027 431 2 25 6.39
MtMYB127 Medtr5g010020 chr5:2590454-2592700 340 2 25 5.8
MtMYB128 Medtr5g010650 chr5:2899487-2902910 477 7 25 8.32
MtMYB129 Medtr5g038910 chr5:17123381-17129369 391 10 25 6.19
MtMYB130 Medtr5g049190 chr5:21549233-21551259 243 2 25 6.36
MtMYB131 Medtr5g070020 chr5:29670807-29672960 356 2 25 8.58
MtMYB132 Medtr5g078140 chr5:33378172-33380732 321 2 25 5.12
MtMYB133 Medtr6g009430 chr6:2790201-2792486 337 2 25 5.59
MtMYB134 Medtr7g035350 chr7:13467452-13470094 451 2 25 5.66
MtMYB135 Medtr7g037130 chr7:13641861-13644153 359 2 25 8.62
MtMYB136 Medtr7g037260 chr7:13704241-13706602 359 2 25 8.99
MtMYB137 Medtr7g061330 chr7:22157000-22164437 531 7 25 9.15
MtMYB138 Medtr7g061550 chr7:22184367-22187445 360 1 25 9.39
MtMYB139 Medtr7g450950 chr7:17066918-17069310 339 2 25 5.53
MtMYB140 Medtr7g451170 chr7:17173579-17176966 413 2 25 9.22
MtMYB141 Medtr7g461410 chr7:22216202-22220641 567 6 25 8.75
MtMYB142 Medtr8g006470 chr8:571945-573793 288 2 25 6.22
MtMYB143 Medtr8g017340 chr8:5841430-5843448 493 2 25 4.92
MtMYB144 Medtr8g017350 chr8:5847584-5850190 644 3 25 4.79
MtMYB145 Medtr8g017390 chr8:5885779-5887719 476 2 25 5.34
MtMYB146 Medtr8g017440 chr8:5919956-5921521 342 2 25 6.45
MtMYB147 Medtr8g017500 chr8:5958601-5960679 349 2 25 5.96
MtMYB148 Medtr8g017540 chr8:5983119-5985752 395 3 25 6.07
MtMYB149 Medtr8g098860 chr8:41349431-41351751 321 2 25 5.85
MtMYB150 Medtr8g468380 chr8:24758342-24766275 437 12 25 8.72
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Phylogenetic analysis of the R2R3-MYB genes in M. truncatula

To investigate the evolutionary relationships of R2R3-MYB genes, we performed multiple sequence alignment and phylogenetic analysis. MtMYB transcription factors were queried against AtMYB transcription factors using BLASTP, and we constructed phylogenetic trees of the MtMYB transcription factor family using ClustalW2 and MEGA. MtMYB genes were divided into 21 subfamilies (Figure 1) consistent with the distribution of AtMYB gene family members. The subfamily 1 has six members, subfamily 6 has 14 members, subfamily 13 has seven members, subfamily 14 has ten members, and subfamily 18 has eleven members. This is similar to the distribution of the Arabidopsis subfamily members. R2R3-MYB transcription factors appeared to be conserved in plants as the evolution of M. truncatula is present in the evolution of Arabidopsis.

Figure 1. Phylogenetic tree analysis of the R2R3-MYB transcription factors in Medicago truncatula. Red circle: subgroup 1; red square: subgroup 2; red triangle: subgroup 3; red diamond: subgroup 4; blue circle: subgroup five; blue square subgroup six; blue indicates subgroup seven; blue diamond subgroup nine; green circular subgroup ten; green square subgroup 11; green triangle: subgroup 13; green diamond: subgroup 14; pink circle: subgroup 16; pink square: subgroup 18; pink triangle: subgroup 19; pink diamond: subgroup 20; cyan circle: subgroup 21; cyan square: subgroup 22; cyan triangle: subgroup 23; cyan diamond: subgroup 24; yellow circle: subgroup 25.

Figure 1

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Chromosomal location and gene duplication of R2R3-MYB gene family

To determine the evolution and expansion of MYB genes, we used Circos software to construct the distribution of MYB genes across chromosomes (Figure 2). Out of the 150 R2R3-MYB genes, 139 were distributed across 8 chromosomes, mainly chromosome 1, 4, 5, and 7 (MtChr1, MtChr4, MtChr5 and MtChr7, respectively). There were 28 R2R3-MYB genes located on MtChr5 alone. The fewest number of genes were found on MtChr6 with ten R2R3-MYB genes. Using sequence alignment, mainly through gene duplication, 128 out of 139 genes were duplicated and divided into two categories. There were 68 segment duplications (SD) caused by the amplification of R2R3-MYB transcription factor members on different chromosomes and 60 tandem duplications (TD) resulting from the generation of R2R3-MYB transcription factor gene clusters. The SD and TD genes were mainly found on MtChr4, MtChr5, MtChr6, MtChr7, and MtChr8, while other chromosomes only contained SD genes. The regions containing TD genes were hot regions of gene distribution. These duplications may have led to the expansion of the MtMYB gene family in the M. truncatula genome.

Figure 2. Chromosome distribution and expansion analysis of R2R3-MYB transcription factors in Medicago truncatula. The genome locations of R2R3-MYB transcription factors were retrieved from Medicago genome website, and the duplications between R2R3-MYB genes identified using software PGDD and BLAST analysis.

Figure 2

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Expression analysis of R2R3-MYB genes in growth and development

The expression information of 71 R2R3-MYB transcription factors were extracted and analyzed by cluster analysis (Figure 3 and Table S2 (270.9KB, pdf) ) using the annotation information of microarray data based on MtGEA. We clustered the 71 R2R3-MYB transcription factors into four groups (A-D). Group A was mainly concentrated in the roots and nodules of M. truncatula. There was only low expression in other tissues and during developmental processes. Group B was mainly expressed in the development of seed. Group C genes were expressed in various organ tissues. These results indicated that they were both involved in tissues construction process of M. truncatula. Finally, Group D genes were expressed at a low level in various tissues and during developmental processes.

Figure 3. Microarray expression data of R2R3-MYB transcription factors in Medicago truncatula. The heatmap was generated using R gplots package. The expressional values of 71 R2R3-MYB genes were retrieved from MtGEA, and they were normalized and used as input, red represents high expressional levels, while blue represents low expressional level.

Figure 3

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The transcriptome sequencing data of M. truncatula were downloaded from the NCBI SRA database, and the gene expression level was obtained using TopHat2 and Cufflinks analyses. We extracted 67 R2R3-MYB transcription factors (Figure 4 and Table S3 (144KB, pdf) ). Multiple genes with high expression in the roots and nodules were classified into Group E, while Group F contained numbers of paralog genes, which were mainly up-regulated in the flower, the carps, and inflorescence.

Figure 4. RNA-seq analysis of R2R3-MYB transcription factors in Medicago truncatula. The heatmap was generated using R gplots package, and the FPKM values of Medicago truncatula genes were evaluated and normalized based RNA-seq data from NCBI SRA database. The plot data included expressional profiles of 67 R2R3-MYB genes in six tissues, and red represents high expressional levels, while blue represents low expressional level.

Figure 4

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Expression analysis of R2R3-MYB genes under different abiotic stress treatment conditions

RNA-seq was used to investigate the expression of R2R3-MYB transcription factors in response to abiotic stress of M. truncatula. Out of the 150 MtMYB genes, 64 were expressed in response to abiotic stress (cold, freezing, drought, salt and ABA) (Figure 5 and Table S4 (143.3KB, pdf) ). In the control treatment, multiple genes were down-regulated or showed no change in expression, yet few genes were up-regulated. We compared genes regulated in response to abiotic stress to the control treatment and found genes highly up-regulated in response to cold and freezing stresses (50/64, 78.1%). These genes interacted with their paralog genes showing co-expression. In response to drought, high salt, and ABA stresses, multiple genes showed opposing expression and co-expression of the pairs of paralog genes. Significantly, most of these genes showed only low expression or no expression. In particular, some genes were down-regulated and co-expressed in response to ABA stress. It was suggested that the expression of these transcription factors are induced by ABA hormones, which regulate the downstream response genes and affect the response of plants to drought stress and salt stress.

Figure 5. Expression profile analysis of R2R3-MYB transcription factors in response to abiotic stresses in Medicago truncatula. The heatmap was generated using R gplots package, and the FPKM values of Medicago truncatula genes were evaluated and normalized based RNA-seq data from NCBI SRA database. The plot data included expressional profiles of 64 R2R3-MYB genes in response to abiotic stress, and red represents high expressional levels, while blue represents low expressional level.

Figure 5

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qRT-PCR validation of R2R3-MYB genes expression

To validate the reliability of the RNA-seq data under abiotic stress in M. truncatula, we selected 10 R2R3-MYB transcription factors (MtMYB010, MtMYB011, MtMYB012, MtMYB013, MtMYB014, MtMYB054, MtMYB090, MtMYB100, MtMYB108, and MtMYB116) from M. truncatula for qRT-PCR validation. The expression levels of the RNA-seq data and qRT-PCR gene expression analysis resulted in a correlation coefficient of 0.85 (Figure 6). These results suggest the RNA-seq data are highly reliable.

Figure 6. qRT-PCR validation of R2R3-MYB transcription factors in Medicago truncatula. All expressional levels of each R2R3-MYB genes were normalized with control expression value (group A) set as one. The groups B (cold stress), C (freezing stress), D (drought stress), E (salt stress), and F (ABA treatment) were compared with control group, and fold-changes were calculated. The fold-change data was used to create the plot, and the blue indicates RNA-seq results, while pink indicates qRT-PCR analysis results.

Figure 6

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Discussion

To date, R2R3-MYB transcription factors have been identified in plants, including Arabidopsis (126) (Yanhui et al., 2006), maize (157) (Du et al., 2012a), rice (102) (Yanhui et al., 2006), Populus (192) (Wilkins et al., 2009), and cassava (166) (Liao et al., 2016). The M. truncatula genome has been sequenced, yet the R2R3-MYB transcription factors have not been researched. This study performed genome-wide analysis of the R2R3-MYB transcription factors in M. truncatula. We identified 150 R2R3-MYB genes in M. truncatula and compared these with other plants. The R2R3-MYB genes of M. truncatula are similar to their Arabidopsis, maize, and cassava counterparts. The results indicated that R2R3-MYB transcription factors are highly conserved in plants.

Cannon et al. (2004) have shown gene duplication was closely related to plant evolution and played an important role in the gene amplification. Gene duplication analysis showed the same subfamily members were located on different chromosomes, such as the 21 subfamily gene members. These genes were distributed across all chromosomes and occurred as TD and SD. These results were consistent with the results of the phylogenetic tree. Furthermore, distribution of other subfamily members was confirmed based on clustering in the phylogenetic tree. These results suggest that the R2R3-MYB genes in M. truncatula are highly conserved as a result of gene duplication. The duplication pattern of R2R3-MYB genes, are consistent with the expression of R2R3-MYB genes in tomato (Zhao et al., 2014) and Populus (Wilkins et al., 2009). Tandem gene duplication was a major driver of gene expansion in M. truncatula.

MYB genes play a role in plant development and stress tolerance (Martin and Pazares, 1997). We have shown that R2R3-MYB genes were typically expressed in the roots, nodules, seedpods, and flowers. Compared with soybean and Arabidopsis, differential expression was observed during flower development, root formation, and seed development for R2R3-MYB genes (Du et al., 2012b). Nodulation is the result of a symbiosis between legumes and rhizobial bacteria in soil. Libault et al. (2009) have reported a gene named Control of Nodule Development (CND), encoding an MYB transcription factor gene. When the CND gene is silenced, nodulation is reduced (Libault et al., 2009). These results indicate that the MYB transcription factors may play a major role in regulation of legume-specific nodulation.

MYB transcription factor genes have been investigated as regulators for plant responses (Ambawat et al., 2013). Their results show that MYB genes are involved in response to various abiotic stresses in higher plants. Herein, we found that MYB genes were not only down-regulated, but in some cases up-regulated in response to drought and salt stress. A positive response of MYB genes following drought stress, salt stress, and ABA-induced stress has been observed in Arabidopsis (AtMYB002, AtMYB060/AtMYB094, AtMYB044, and AtMYB096) (Cominelli et al., 2005; Jung et al., 2008; Seo et al., 2009; Urao and Shinozaki, 1993), Boea crassifolia (BcMYB1) (Chen et al., 2005), and Saccharum officinarum (ScMYBAS1) (Prabu and Prasad, 2012). However, MtMYB genes were up-regulated in response to cold and freezing stresses, while the opposite is observed in Arabidopsis. Interestingly, our result agrees with the expression profile of cotton in response to drought and salt stress (He et al., 2016). Both cotton and M. truncatula are diploid and their duplication can be divided into TD and SD. The expression pattern of M. truncatula MYB genes under different abiotic stress conditions suggest that some may play a major role in cross-talk among different signal transduction pathways in response to abiotic stresses.

CONCLUSIONS

In summary, we have identified 150 MYB genes in M. truncatula, which were classified into 21 subfamilies based on phylogenetic analysis. Meanwhile, their expression profiles were investigated using microarray and RNA-seq. The results revealed regulatory roles in plant growth and tissue development, and especially nodule development. In addition, we explored the role of the MYB genes in response to abiotic stresses. Our results suggested MYB transcription factors broadly participate in abiotic stress response of M. truncatula, whose function can be carefully explored in future.

Acknowledgments

We thank Miss Jun Zhang and Dr. Lili Song (Harbin Normal University) for their helpful technical supports in plant growth and treatment. The data analysis work was supported by high performance computing center of Harbin Normal University. This work was supported by grants from the National Natural Science Foundation of China (31302019 and 31470571), the China Postdoctoral Science Foundation (2016T90307 and 2015M571430), the University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province (UNPYST-2016071), the MOST 863 Project (2013AA102607-5), and the Heilongjiang Province Postdoctoral Science Foundation (LBH-Z14126).

Supplementary material

The following online material is available for this article

Table S1. PCR primers used for quantitative real-time PCR analysis.
Click here for additional data file. (98.3KB, pdf)
Table S2. Expression data of R2R3-MYB transcription factors in various tissues and development processes.
Click here for additional data file. (270.9KB, pdf)
Table S3. Expression data of R2R3-MYB transcription factors in various tissues.
Click here for additional data file. (144KB, pdf)
Table S4. Expression data of R2R3-MYB transcription factors response to abiotic stresses.
Click here for additional data file. (143.3KB, pdf)

Associate Editor: Hong Luo

Author Contributions

YS and CG conceived and designed the experiments; WL, YL, JZ, and ZX performed the experiments; YS, WL, JZ, and ZX analyzed the data; YS, WL, and CG wrote the paper. All authors read and approved the final version.

Conflict of Interest

The authors declare that there is no conflict of interest regarding the publication of this paper.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Table S1. PCR primers used for quantitative real-time PCR analysis.
Click here for additional data file. (98.3KB, pdf)
Table S2. Expression data of R2R3-MYB transcription factors in various tissues and development processes.
Click here for additional data file. (270.9KB, pdf)
Table S3. Expression data of R2R3-MYB transcription factors in various tissues.
Click here for additional data file. (144KB, pdf)
Table S4. Expression data of R2R3-MYB transcription factors response to abiotic stresses.
Click here for additional data file. (143.3KB, pdf)

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