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作物学报

作物学报 ›› 2023, Vol. 49 ›› Issue (7): 1769-1784.doi: 10.3724/SP.J.1006.2023.24180

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

甘蔗割手密种LRRII-RLK基因家族演化和表达分析

丁洪艳1,2(), 冯晓溪3, 汪柏宇2, 张积森1,2,*()   

  1. 1广西大学农学院, 广西南宁 530004
    2广西大学亚热带农业生物资源保护与利用国家重点实验室, 广西南宁 530004
    3福建农林大学农学院, 福建福州 350002
  • 收稿日期:2022-08-03 接受日期:2022-11-25 出版日期:2023-07-12 网络出版日期:2022-12-14
  • 通讯作者: *张积森, E-mail: zjisen@126.com
  • 作者简介:E-mail: hyding2020@163.com
  • 基金资助:
    本研究由国家重点研发计划项目(2021YFF1000100);广东省重点领域研发计划项目(2019B020238001)

Evolution and relative expression pattern of LRRII-RLK gene family in sugarcane Saccharum spontaneum

DING Hong-Yan1,2(), FENG Xiao-Xi3, WANG Bai-Yu2, ZHANG Ji-Sen1,2,*()   

  1. 1College of Agriculture, Guangxi University, Nanning 530004, Guangxi, China
    2State Key Laboratory of Conservation and Utilization of Agric-Biological Resources, Guangxi University, Nanning 530004, Guangxi, China
    3College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
  • Received:2022-08-03 Accepted:2022-11-25 Published:2023-07-12 Published online:2022-12-14
  • Contact: *E-mail: zjisen@126.com
  • Supported by:
    The National Key Research and Development Program of China(2021YFF1000100);The Science and Technology Planting Project of Guangdong Province(2019B020238001)

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摘要：

LRRII-RLK是一种类受体激酶(receptor-like kinase, RLK), 该基因家族在植物中广泛存在, 在植物的生长发育和生物胁迫中发挥着重要的作用, 但目前在甘蔗中未见对该基因家族的系统鉴定和分析。本研究对甘蔗的LRRII-RLK基因进行分类, 并研究了其结构和功能。结合割手密种基因组和发育组织、叶片发育梯度、昼夜节律和生物胁迫反应转录组数据, 在甘蔗割手密种中共鉴定到27个LRRII-RLK基因, 分布在17条染色体上。系统进化分析发现, 它们分别属NIK、SERK和LRRII-C分支, 其中处于LRRII-C分支的SsLRRII-RLK基因出现了显著扩增。顺式元件分析显示, 它们的启动子共包含32类顺式元件, 其主要参与植物光反应、响应胁迫反应、调控植物激素和植物生长发育。这些基因共有35对共线性基因对, 具有多个保守基序, 主要通过片段复制的方式进行扩增, 且根据Ka/Ks比率发现, 它们在演化过程中经历了严格的纯化选择作用。此外, SsLRRII-RLK基因表达分析显示, 它们在甘蔗不同组织中表达量不同, 其中部分基因在昼夜不同时期表达量呈现差异, 这表明它们参与了植物生长和光合作用的调节。值得注意的是, SsLRRII-RLK基因的表达模式在不同病害(甘蔗梢腐病和花叶病)胁迫下呈现差异, 因此, 我们认为这些基因在病毒复制和发病机制过程中发挥作用。本研究结果有助于深入了解甘蔗LRRII-RLK基因的演化过程, 且为LRRII-RLK基因在甘蔗生长发育、光合作用以及在病害胁迫中的功能研究提供初步的理论基础。

关键词: 割手密种, LRRII-RLK基因, 转录组学, 基因表达分析, 演化分析

Abstract:

It is well-known that LRRII-RLK gene family widely exists in plants. These genes are receptor like kinase (RLK), which play a significant role in plant development and biological stress. Up till now, there is no systematic identification and analysis of the LRRII-RLK gene family in sugarcane. Here, we identified 27 LRRII-RLK genes in Saccharum spontaneum, which were distributed on 17 chromosomes. Phylogenetic tree showed the classification of these genes into three different branches including NIK, SERK, and LRRII-C. Furthermore, we observed the significant amplification in the LRRII-C branch. Next, we characterized the cis-regulatory elements, which identified 32 different types of cis elements in the gene promoters, primarily involved in light response, stress response, regulation of hormone mechanism, and plant growth. Interestingly, SsLRRII-RLK genes were detected to be conserved with 35 collinear gene pairs and multiple conserved motifs. These genes were mainly amplified by segmental replication and had undergone strict purification selection during the evolution, according to their Ka/Ks ratios. Furthermore, the relative expression level of SsLRRII-RLK genes varied in different tissues of sugarcane. Additionally, some genes expressed differently during distinct periods of day and night, suggesting that they were associated with plant growth regulation and photosynthesis. Noticeably, the relative expression pattern of SsLRRII-RLK genes varied significantly under different disease conditions (sugarcane pokkah boeng disease and mosaic disease). In conclusion, these genes might play a role in pathogenesis and viral replication. The results of this study are helpful to further understand the evolutionary process of LRRII-RLK gene in sugarcane. This data provides a preliminary theoretical basis for the functional study of LRRII-RLK gene during photosynthesis, growth and development, and disease conditions in sugarcane.

Key words: Saccharum spontaneum, LRRII-RLK genes, transcriptomics, gene expression analysis, phylogenetic analysis

表1

qPCR引物序列"

基因名称
Gene name		 正向引物
Forward sequence (5'-3')		 反向引物
Reverse sequence (5'-3')
GAPDH CACGGCCACTGGAAGCA TCCTCAGGGTTCCTGATGCC
SsLRRII-RLK1 AGAGCGCCTACTTGTTTATCC GCTTCCTTGCAGACCAATCTA
SsLRRII-RLK4-2 GGATCATGCTTCTGGAGCTTATTA CTTCTCCTTCAGCAGTCCTTTC
SsLRRII-RLK 5 GGCTATGGGATCATGCTTCTT CCCTTCTCTCTGTAGCTTCTTTAC
SsLRRII-RLK 9-3 GCCTTCGTGGATTCTGTATGA GCCAATCTAGTGGAGGTTCAG
SsLRRII-RLK 14 CTACTTCAGGCGGCTCATTAC GCACCAACAATGCTTCCAATAA
SsLRRII-RLK 16-2 CCAGTGTCCTACAACCTCAATAG GCCTCCACCAGAACAGAAAT

表2

甘蔗割手密种LRRII-RLK家族基因和编码蛋白基本信息"

基因编号
No. of genes		 基因
Gene name		 染色体
Chr.		 氨基酸数
NA		 分子量
MW (kD)		 等电点
pI		 不稳定系数
Instability
index		 平均疏水性
Grand average of hydropathicity		 复制类型
Replication
type
Sspon.01G0025910-4D SsLRRII-RLK-1 1D 629 69.86 5.31 31.89 -0.130 4
Sspon.01G0025910-2B SsLRRII-RLK-1-2 1B 384 41.90 6.83 30.59 0.105 4
Sspon.03G0036270-1B SsLRRII-RLK-2 3B 417 45.56 8.85 35.51 -0.022 4
Sspon.03G0036270-2C SsLRRII-RLK-2-2 3C 417 45.51 8.85 35.15 -0.021 4
Sspon.03G0036270-3D SsLRRII-RLK-2-3 3D 410 44.65 7.10 26.89 -0.053 4
Sspon.04G0004390-1A SsLRRII-RLK-3 4A 661 72.62 7.87 38.30 -0.010 4
Sspon.04G0004390-2D SsLRRII-RLK-3-2 4D 626 68.61 7.25 39.69 -0.037 4
Sspon.04G0009850-1A SsLRRII-RLK-4 4A 578 63.63 5.57 44.60 -0.181 4
Sspon.04G0009850-3D SsLRRII-RLK-4-2 4D 625 68.62 5.57 44.03 -0.147 4
Sspon.04G0013270-1A SsLRRII-RLK-5 4A 606 67.54 5.13 35.40 -0.184 4
Sspon.04G0014480-3D SsLRRII-RLK-6 4D 715 79.13 5.68 38.88 -0.107 4
Sspon.05G0010060-2C SsLRRII-RLK-7 5C 458 50.37 5.98 46.82 -0.237 4
Sspon.05G0010060-1A SsLRRII-RLK-7-2 5A 543 60.94 7.06 45.11 -0.243 4
Sspon.06G0005550-1A SsLRRII-RLK-8 6A 982 105.55 10.63 46.16 -0.211 4
Sspon.06G0010230-1A SsLRRII-RLK-9 6A 580 64.21 5.84 43.90 -0.243 4
Sspon.06G0010230-2B SsLRRII-RLK-9-2 6B 586 64.37 5.66 44.92 -0.166 4
Sspon.06G0010230-3C SsLRRII-RLK-9-3 6C 584 64.62 5.77 43.86 -0.221 3
Sspon.06G0016870-1A SsLRRII-RLK-10 6A 581 65.10 5.89 38.07 -0.211 4
Sspon.06G0016880-1A SsLRRII-RLK-11 6A 925 102.95 8.20 45.98 -0.382 4
Sspon.06G0016880-2B SsLRRII-RLK-11-2 6B 619 69.48 5.57 38.08 -0.120 2
Sspon.06G0016880-1P SsLRRII-RLK-12 6B 624 70.00 5.64 38.47 -0.107 4
Sspon.06G0005060-3C SsLRRII-RLK-13 6C 591 66.41 6.35 34.31 -0.092 4
Sspon.06G0035390-1D SsLRRII-RLK-14 6D 473 52.30 8.63 32.14 -0.084 4
Sspon.07G0011930-3D SsLRRII-RLK-15 7D 497 54.79 5.45 39.04 -0.049 4
Sspon.08G0009990-1A SsLRRII-RLK-16 8A 336 37.00 8.70 33.67 -0.025 4
Sspon.08G0009990-2C SsLRRII-RLK-16-2 8C 581 63.95 6.89 39.18 -0.130 1
Sspon.08G0009990-3D SsLRRII-RLK-16-3 8D 551 60.66 7.95 39.71 -0.132 4

图1

甘蔗(Ss)、拟南芥(AT)、水稻(Os)和高粱(Sb) LRRII-RLK蛋白的系统进化树"

图2

17种植物的LRRII-RLK蛋白系统发育关系 树的底部显示了时间Mya (百万年前)的标尺。17种植物包括: 甘蔗割手密种(Saccharum spontaneum)、水稻(Oryza sativa)、二穗短柄草(Brachypodium distachyon)、高粱(Sorghum bicolor)、马铃薯(Solanum tuberosum)、番茄(Solanum lycopersicum)、陆地棉(Gossypium hirsutum)、拟南芥(Arabidopsis thaliana)、萝卜(Raphanus sativus)、甜橙(Citrus sinensis)、柑橘(Citrus clementina)、黄瓜(Cucumis sativus)、草莓(Fragaria vesca)、梨(Pyrus bretschneideri)、苹果(Malus domestica)、梅(Prunus mume)、桃(Prunus persica)。"

图3

甘蔗割手密种LRRII-RLK基因家族蛋白保守基序和基因结构分析 A: SsLRRII-RLK基因结构分析, 不同颜色方框表示不同的基因结构, 黑线表示内含子。B: SsLRRII-RLK蛋白保守基序分析, 不同颜色方框表示不同保守基序, 黑线表示氨基酸序列。"

图4

甘蔗割手密种LRRII-RLK基因顺式元件分析"

图5

SsLRRII-RLK基因在染色体上的分布及共线性关系 内部连线表示甘蔗割手密种LRRII-RLK基因家族间的共线性。"

图6

甘蔗与高粱物种间的共线性分析 灰线表示2个物种基因组间的共线性区块, 红线表示2个物种间LRRII-RLK的共线基因对。"

图7

甘蔗和高粱中同源LRRII-RLK基因对Ka/Ks值分析 *、**分别表示在0.05和0.01概率水平差异显著。"

表3

甘蔗和高粱LRRII-RLK基因、Ks信息和基因分歧时间"

基因编号
Number of genes		 基因名
Gene name		 同义突变频率Ks
Synonymous		 分歧时间
Divergence time (Mya)
Sspon.03G0036270-1B-Sobic.003G051100 SsLRRII-RLK-2-SbLRRII-RLK1 0.1065600 4.512
Sspon.03G0036270-2C-Sobic.003G051100 SsLRRII-RLK-2-2-SbLRRII-RLK1 0.1075050 8.270
Sspon.04G0004390-2D-Sobic.004G252200 SsLRRII-RLK-3-2-SbLRRII-RLK5 0.0616391 4.741
Sspon.04G0009850-3D-Sobic.004G189900 SsLRRII-RLK-4-2-SbLRRII-RLK4 0.0675914 5.199
Sspon.04G0013270-1A-Sobic.004G128200 SsLRRII-RLK-5-SbLRRII-RLK3 0.0586529 4.512
Sspon.04G0014480-3D-Sobic.004G104800 SsLRRII-RLK-6-SbLRRII-RLK2 0.0743093 5.716
Sspon.06G0005550-1A-Sobic.007G142900 SsLRRII-RLK-8-SbLRRII-RLK12 0.2812260 21.633
Sspon.06G0010230-1A-Sobic.007G059600 SsLRRII-RLK-9-SbLRRII-RLK9 0.0693491 5.335
Sspon.06G0010230-2B-Sobic.007G059600 SsLRRII-RLK-9-2-SbLRRII-RLK9 0.1305250 10.040
Sspon.06G0016880-1A-Sobic.005G182400 SsLRRII-RLK-11-SbLRRII-RLK7 0.0387034 2.977
Sspon.06G0016880-2B-Sobic.005G182400 SsLRRII-RLK-11-2-SbLRRII-RLK7 0.0373593 2.874
Sspon.08G0009990-2C-Sobic.010G115300 SsLRRII-RLK-16-2-SbLRRII-RLK15 0.0964024 7.416
Sspon.08G0009990-3D-Sobic.010G115300 SsLRRII-RLK-16-3-SbLRRII-RLK15 0.0919244 7.071
Sspon.06G0035390-1D-Sobic.005G182400 SsLRRII-RLK-14-SbLRRII-RLK7 0.1044750 8.037

图8

SsLRRII-RLK基因在甘蔗不同组织, 叶片发育梯度和昼夜节律中的表达 Sd: 苗期; PM: 成熟前期; M: 成熟期; SL: 苗期叶; SS: 苗期茎; LR: 卷叶; LF: 正叶; BZ: 基部区; TZ: 过渡区; MZ1: 成熟区1; MZ2: 成熟区2。"

图9

SsLRRII-RLK基因表达模式的qRT-PCR验证"

图10

SsLRRII-RLK基因在不同病害(梢腐病和花叶病)侵染甘蔗中的表达热图 P1: CK; P2: 轻微; P3: 严重; S1: CK; S2: 脱毒; S3: 侵染后。"

[1] Shiu S H. Plant receptor-like kinase gene family: diversity, function, and signaling. Sci STKE, 2001, 2001: re22.
[2] Shiu S H, Bleecker A B. Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc Natl Acad Sci USA, 2001, 98: 10763-10768.
doi: 10.1073/pnas.181141598 pmid: 11526204
[3] Shiu S H, Karlowski W M, Pan R, Tzeng Y H, Mayer K F, Li W H. Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell, 2004, 16: 1220-1234.
doi: 10.1105/tpc.020834
[4] Sun X, Wang G L. Genome-wide identification, characterization and phylogenetic analysis of the rice LRR-kinases. PLoS One, 2011, 6: e16079.
doi: 10.1371/journal.pone.0016079
[5] Shiu S H, Bleecker A B. Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc Natl Acad Sci USA, 2001, 98: 10763-10768.
doi: 10.1073/pnas.181141598 pmid: 11526204
[6] Tang P, Ying Z, Sun X, Tian D, Yang S, Jing D. Disease resistance signature of the leucine-rich repeat receptor-like kinase genes in four plant species. Plant Sci, 2010, 179: 399-406.
doi: 10.1016/j.plantsci.2010.06.017
[7] Fischer I, Diévart A, Droc G, Dufayard J F, Chantret N. Evolutionary dynamics of the leucine-rich repeat receptor-like kinase (LRR-RLK) subfamily in angiosperms. Plant Physiol, 2016, 170: 1595-1610.
doi: 10.1104/pp.15.01470 pmid: 26773008
[8] Nikolaev S V, Penenko A V, Lavreha V V, Mjolsness E D, Kolchanov N A. A model study of the role of proteins CLV1, CLV2, CLV3, and WUS in regulation of the structure of the shoot apical meristem. Russ J Dev Biol, 2007, 38: 383-388.
doi: 10.1134/S1062360407060069
[9] Gómez-Gómez L, Boller T. FLS2: an LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis. Mol Cell, 2000, 5: 1003-1011.
doi: 10.1016/s1097-2765(00)80265-8 pmid: 10911994
[10] Zipfel C, Kunze G, Chinchilla D, Caniard A, Jones J D G, Boller T, Felix G. Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts Agrobacterium-mediated transformation. Cell, 2006, 125: 749-760.
doi: 10.1016/j.cell.2006.03.037 pmid: 16713565
[11] Jia L, Wen J, Lease K A, Doke J T, Walker J C. BAK1, an Arabidopsis LRR receptor-like protein kinase, interacts with BRI1 and modulates brassinosteroid signaling. Cell, 2002, 110: 213-222.
doi: 10.1016/s0092-8674(02)00812-7 pmid: 12150929
[12] Chinchilla D, Shan L, He P, De Vries S, Kemmerling B. One for all: the receptor-associated kinase BAK1. Trends Plant Sci, 2009, 14: 535-541.
doi: 10.1016/j.tplants.2009.08.002 pmid: 19748302
[13] Mariano A C, Andrade M O, Santos A A, Carolino S, Oliveira M L, Baracat-Pereira M C, Brommonshenkel S H, Fontes E. Identification of a novel receptor-like protein kinase that interacts with a geminivirus nuclear shuttle protein. Virology, 2004, 318: 24-31.
doi: 10.1016/j.virol.2003.09.038 pmid: 14972531
[14] Zorzatto C, Machado J P, Lopes K V, Nascimento K J, Pereira W A, Brustolini O J, Reis P A, Calil I P, Deguchi M, Sachetto-Martins G, Gouveia B C, Loriato V A, Silva M A, Silva F F, Santos A A, Chory J, Fontes E P. NIK1-mediated translation suppression functions as a plant antiviral immunity mechanism. Nature, 2015, 520: 679-682.
doi: 10.1038/nature14171
[15] Fontes E P, Santos A A, Luz D F, Waclawovsky A J, Chory J. The geminivirus nuclear shuttle protein is a virulence factor that suppresses transmembrane receptor kinase activity. Genes Dev, 2004, 18: 2545-2556.
doi: 10.1101/gad.1245904
[16] Santos A A, Lopes K V, Apfata J A, Fontes E P. NSP-interacting kinase, NIK: a transducer of plant defence signalling. J Exp Bot, 2010, 61: 3839-3845.
doi: 10.1093/jxb/erq219 pmid: 20624762
[17] Ali A, Khan M, Sharif R, Mujtaba M, Gao S J. Sugarcane Omics: an update on the current status of research and crop improvement. Plants (Basel), 2019, 8: 344.
doi: 10.3390/plants8090344
[18] Zhang J, Zhang X, Tang H, Zhang Q, Hua X, Ma X, Zhu F, Jones T, Zhu X, Bowers J. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat Genet, 2018, 50: 1565-1573.
doi: 10.1038/s41588-018-0237-2
[19] Viklund H K, Elofsson A. Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci, 2004, 13: 1908-1917.
pmid: 15215532
[20] Price M N, Dehal P S, Arkin A P. FastTree 2: approximately maximum-likelihood trees for large alignments. PLoS One, 2010, 5: e9490.
doi: 10.1371/journal.pone.0009490
[21] Yuan Y, Yang X, Feng M, Ding H, Khan M T, Zhang J, Zhang M. Genome-wide analysis of R2R3-MYB transcription factors family in the autopolyploid Saccharum spontaneum: an exploration of dominance expression and stress response. BMC Genomics, 2021, 22: 1-18.
doi: 10.1186/s12864-020-07350-y
[22] Katoh K, Standley D M. Katoh K, Standley D M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol, 2013, 30: 772-780.
doi: 10.1093/molbev/mst010 pmid: 23329690
[23] Sun J, Li L, Wang P, Zhang S, Wu J. Genome-wide characterization, evolution, and expression analysis of the leucine-rich repeat receptor-like protein kinase (LRR-RLK) gene family in Rosaceae genomes. BMC Genomics, 2017, 18: 763.
doi: 10.1186/s12864-017-4155-y pmid: 29017442
[24] Magalhães D M, Scholte L, Silva N V, Oliveira G C, Zipfel C, Takita M A, Souza A D. LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects. BMC Genomics, 2016, 17: 623.
doi: 10.1186/s12864-016-2930-9 pmid: 27515968
[25] Yuan N, Rai K M, Balasubramanian V K, Upadhyay S K, Luo H, Mendu V. Genome-wide identification and characterization of LRR-RLKs reveal functional conservation of the SIF subfamily in cotton (Gossypium hirsutum). BMC Plant Biol, 2018, 18: 185.
doi: 10.1186/s12870-018-1395-1
[26] Wang J, Hu T, Wang W, Hu H, Wei Q, Bao C. Investigation of evolutionary and expressional relationships in the function of the leucine-rich repeat receptor-like protein kinase gene family (LRR-RLK) in the radish (Raphanus sativus L.). Sci Rep, 2019, 9: 6937.
doi: 10.1038/s41598-019-43516-9
[27] Wei Z, Wang J, Yang S, Song Y. Identification and expression analysis of the LRR-RLK gene family in tomato (Solanum lycopersicum) Heinz 1706. Genome, 2015, 58: 121-134.
doi: 10.1139/gen-2015-0035 pmid: 26207619
[28] Li X, Ahmad S, Guo C, Yu J, Cao S, Gao X, Li W, Li H, Guo Y. Identification and characterization of LRR-RLK family genes in potato reveal their involvement in peptide signaling of cell fate decisions and biotic/abiotic stress responses. Cells, 2018, 7: 120.
doi: 10.3390/cells7090120
[29] Yu J, Zhang B, Liu S, Guo W, Gao Y, Sun H. Genome-wide characterization, evolution and expression analysis of the leucine-rich repeat receptor-like kinase (LRR-RLK) gene family in cucumbers. Plant Prot Sci, 2022, 58: 125-138.
doi: 10.17221/131/2021-PPS
[30] Hu B, Jin J, Guo A Y, Zhang H, Luo J, Gao G. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 2015, 31: 1296-1297.
doi: 10.1093/bioinformatics/btu817 pmid: 25504850
[31] Bailey T L, Boden M, Buske F A, Frith M, Grant C E, Clementi L, Ren J, Li W W, Noble W S. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res, 2009, 37: W202-W208.
[32] Wang Y, Tang H, Debarry J D, Tan X, Li J, Wang X, Lee T H, Jin H, Marler B, Guo H. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res, 2012, 40: e49.
doi: 10.1093/nar/gkr1293
[33] Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones S J, Marra M A. Circos: an information aesthetic for comparative genomics. Genome Res, 2009, 19: 1639-1645.
doi: 10.1101/gr.092759.109 pmid: 19541911
[34] Tang H, Bowers J E, Wang X, Ming R, Alam M, Paterson A H. Synteny and collinearity in plant genomes. Science, 2008, 320: 486-488.
doi: 10.1126/science.1153917 pmid: 18436778
[35] Wang D, Zhang Y, Zhang Z, Zhu J, Yu J. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genom Proteom Bioinf, 2010, 8: 77-80.
doi: 10.1016/S1672-0229(10)60008-3 pmid: 20451164
[36] Gaut B S, Morton B R, Mccaig B C, Clegg M T. Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci USA, 1996, 93: 10274-10279.
doi: 10.1073/pnas.93.19.10274 pmid: 8816790
[37] Chen Y, Zhang Q, Hu W, Zhang X, Wang L, Hua X, Yu Q, Ming R, Zhang J. Evolution and expression of the fructokinase gene family in Saccharum. BMC Genomics, 2017, 18: 197.
doi: 10.1186/s12864-017-3535-7 pmid: 28222695
[38] Zhang Q, Hua X, Liu H, Yuan Y, Shi Y, Wang Z, Zhang M, Ming R, Zhang J. Evolutionary expansion and functional divergence of sugar transporters in Saccharum (S. spontaneum and S. officinarum). Plant J, 2021, 105: 884-906.
doi: 10.1111/tpj.v105.4
[39] Li Z, Hua X, Zhong W, Yuan Y, Wang Y, Wang Z, Ming R, Zhang J. Genome-wide identification and expression profile analysis of WRKY family genes in the autopolyploid Saccharum spontaneum. Plant Cell Physiol, 2019, 61: 616-630.
doi: 10.1093/pcp/pcz227
[40] Livak K J, Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 2001, 25: 402-408.
doi: 10.1006/meth.2001.1262 pmid: 11846609
[41] Ling H, Wu Q, Guo J, Xu L, Que Y. Comprehensive selection of reference genes for gene expression normalization in sugarcane by real time quantitative RT-PCR. PLoS One, 2015, 10: e0118444.
doi: 10.1371/journal.pone.0118444
[42] Swift M L. GraphPad prism, data analysis, and scientific graphing. J Chem Inf Comput Sci, 1997, 37: 411-412.
doi: 10.1021/ci960402j
[43] Wang P, Moore B M, Panchy N L, Meng F, Lehti-Shiu M D, Shiu S H. Factors influencing gene family size variation among related species in a plant family, Solanaceae. Genome Biol Evol, 2018, 10: 2596-2613.
doi: 10.1093/gbe/evy193 pmid: 30239695
[44] Zhang J, Zhang Q, Li L, Tang H, Zhang Q, Chen Y, Arrow J, Zhang X, Wang A, Miao C. Recent polyploidization events in three Saccharum founding species. Plant Biotechnol J, 2019, 17: 264-274.
doi: 10.1111/pbi.2019.17.issue-1
[45] Goswami D, Handique P J, Deka S. Rhamnolipid biosurfactant against Fusarium sacchari—the causal organism of pokkah boeng disease of sugarcane. J Basic Microbiol, 2014, 54: 548-557.
doi: 10.1002/jobm.v54.6
[46] Xu S, Wang J, Wang H, Bao Y, Li Y, Govindaraju M, Yao W, Chen B, Zhang M. Molecular characterization of carbendazim resistance of Fusarium species complex that causes sugarcane pokkah boeng disease. BMC Genomics, 2019, 20: 115.
doi: 10.1186/s12864-019-5479-6 pmid: 30732567
[47] Singh A, Chauhan S S, Singh A, Singh S B. Deterioration in sugarcane due to pokkah boeng disease. Sugar Technol, 2006, 8: 187-190.
doi: 10.1007/BF02943659
[48] Yang Z N, Mirkov T E. Sequence and relationships of sugarcane mosaic and sorghum mosaic virus strains and development of RT-PCR-Based RFLPs for strain discrimination. Phytopathology, 1997, 87: 932-939.
doi: 10.1094/PHYTO.1997.87.9.932 pmid: 18945064
[49] Xu D L, Park J W, Mirkov T E, Zhou G H. Viruses causing mosaic disease in sugarcane and their genetic diversity in southern China. Arch Virol, 2008, 153: 1031-1039.
doi: 10.1007/s00705-008-0072-3 pmid: 18438601
[50] Chauhan R P, Rajakaruna P, Verchot J. Complete genome sequence of nine isolates of canna yellow streak virus reveals its relationship to the sugarcane mosaic virus (SCMV) subgroup of potyviruses. Arch Virol, 2015, 160: 837-844.
doi: 10.1007/s00705-014-2327-5 pmid: 25567205
[51] Zhou F, Guo Y, Qiu L J. Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean. BMC Plant Biol, 2016, 16: 58.
doi: 10.1186/s12870-016-0744-1 pmid: 26935840
[52] Santos A, Lopes K, Apfata J, Fontes E. NSP-interacting kinase, NIK: a transducer of plant defence signalling. J Exp Bot, 2010, 2010, 61: 3839-3845.
doi: 10.1093/jxb/erq219 pmid: 20624762
[53] Hu H, Xiong L, Yang Y. Rice SERK1 gene positively regulates somatic embryogenesis of cultured cell and host defense response against fungal infection. Planta, 2005, 222: 107-117.
doi: 10.1007/s00425-005-1534-4 pmid: 15968510
[54] Kim C, Wang X, Lee T H, Jakob K, Lee G J, Paterson A H. Comparative analysis of Miscanthus and Saccharum reveals a shared whole-genome duplication but different evolutionary fates. Plant Cell, 2014, 26: 2420-2429.
doi: 10.1105/tpc.114.125583
[55] Sakamoto T, Deguchi M, Brustolini O J, Santos A A, Silva F F, Fontes E P. The tomato RLK superfamily: phylogeny and functional predictions about the role of the LRRII-RLK subfamily in antiviral defense. BMC Plant Biol, 2012, 12: 229.
doi: 10.1186/1471-2229-12-229 pmid: 23198823
[56] Cannon S B, Mitra A, Baumgarten A, Young N D, May G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol, 2004, 4: 10.
doi: 10.1186/1471-2229-4-10
[57] Zhang Z, Li X. Genome-wide identification of AP2/ERF superfamily genes and their expression during fruit ripening of Chinese jujube. Sci Rep, 2018, 8: 15612.
doi: 10.1038/s41598-018-33744-w pmid: 30353116
[58] Guo B, Wei Y, Xu R, Lin S, Luan H, Lyu C, Zhang X, Song X, Xu R. Genome-wide analysis of APETALA2/ethylene-responsive factor (AP2/ERF) gene family in barley (Hordeum vulgare L.). PLoS One, 2016, 11: e0161322.
doi: 10.1371/journal.pone.0161322
[59] Niehrs C, Pollet N. Synexpression groups in eukaryotes. Nature, 1999, 402: 483-487.
doi: 10.1038/990025
[60] He K, Gou X, Yuan T, Lin H, Asami T, Yoshida S, Russell S D, Li J. BAK1 and BKK1 regulate brassinosteroid-dependent growth and brassinosteroid-independent cell-death pathways. Curr Biol, 2007, 17: 1109-1115.
doi: 10.1016/j.cub.2007.05.036 pmid: 17600708
[61] Jin Y L, Tang R J, Wang H H, Jiang C M, Bao Y, Yang Y, Liang M X, Sun Z C, Kong F J, Li B. Overexpression of Populus trichocarpa CYP85A3 promotes growth and biomass production in transgenic trees. Plant Biotechnol J, 2017, 15: 1309-1321.
doi: 10.1111/pbi.12717 pmid: 28258966
[62] Lakhssassi N, Liu S, Bekal S, Zhou Z, Colantonio V, Lambert K, Barakat A, Meksem K. Characterization of the soluble NSF attachment protein gene family identifies two members involved in additive resistance to a plant pathogen. Sci Rep, 2017, 7: 45226.
doi: 10.1038/srep45226 pmid: 28338077
[63] Pérez-Pérez J, Esteve-Bruna D, González-Bayón R, Kangasj R S, Caldana C, Hannah M A, Willmitzer L, Micol P. Functional redundancy and divergence within the Arabidopsis RETICULATA-RELATED gene family. Plant Physiol, 2013, 162: 589-603.
doi: 10.1104/pp.113.217323 pmid: 23596191
[64] Lakhssassi N, Doblas V G, Rosado A, Del Valle A E, Posé D, Jimenez A J, Castillo A G, Valpuesta V, Borsani O, Botella M A. The Arabidopsis TETRATRICOPEPTIDE THIOREDOXIN-LIKE gene family is required for osmotic stress tolerance and male sporogenesis. Plant Physiol, 2012, 158: 1252-1266.
doi: 10.1104/pp.111.188920 pmid: 22232384
[65] Ni Z, Kim E D, Ha M, Lackey E, Liu J, Zhang Y, Sun Q, Chen Z J. Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature, 2009, 457: 327-331.
doi: 10.1038/nature07523
[66] Michael T P, Salome P A, Yu H J, Spencer T R, Sharp E L, McPeek M A, Alonso J M, Ecker J R, McClung C R. Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science, 2003, 302: 1049-1053.
doi: 10.1126/science.1082971 pmid: 14605371
[67] Giuliano G, Hoffman N E, Ko K, Scolnik P A, Cashmore A R. A light-entrained circadian clock controls transcription of several plant genes. EMBO J, 1988, 7: 3635-3642.
doi: 10.1002/j.1460-2075.1988.tb03244.x pmid: 3208743
[68] Green R M, Tingay S, Wang Z Y, Tobin E M. Circadian rhythms confer a higher level of fitness to Arabidopsis plants. Plant Physiol, 2002, 129: 576-584.
doi: 10.1104/pp.004374
[69] Chen X, Zuo S, Schwessinger B, Chern M, Canlas P E, Ruan D, Zhou X, Wang J, Daudi A, Petzold C J, Heazlewood J L, Ronald P C. An XA21-associated kinase (OsSERK2) regulates immunity mediated by the XA21 and XA3 immune receptors. Mol Plant, 2014, 7: 874-892.
doi: 10.1093/mp/ssu003 pmid: 24482436
[70] Chaparro-Garcia A, Wilkinson R C, Gimenez-Ibanez S, Findlay K, Coffey M D, Zipfel C, Rathjen J P, Kamoun S, Schornack S. The receptor-like kinase SERK3/BAK1 is required for basal resistance against the late blight pathogen Phytophthora infestans in Nicotiana benthamiana. PLoS One, 2011, 6: e16608.
doi: 10.1371/journal.pone.0016608
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