Genome-Wide Identification, Characterization, and Expression Analysis of the NAC Gene Family in Litchi chinensis

: NAC proteins play an essential role in the growth and development of litchi, especially during reproductive development. However, a comprehensive analysis of the litchi NAC gene family is currently absent. Based on information from the litchi genome, we found that the 112 NAC genes of litchi show an uneven distribution on the chromosomes. Phylogenetic and conserved structural domain analyses indicated that different types of variability were exhibited in the family of litchi NACs (LcNACs). Gene covariance analysis showed that the LcNACs showed better similarity in the same genus than with Arabidopsis . We further investigated the differential expression patterns of LcNACs in buds and rudimentary leaves of litchi. qRT-PCR results implied that they were involved in the process. Profiling of LcNAC promoter elements in litchi showed that they were extensively involved in light response, phytohormone regulation, abiotic stress response, and plant growth and development processes. This study provides new insights into the identification, structural characterization, tissue-specific expression analysis, and promoter response elements of LcNACs . It reveals the characteristics of the LcNACs and lays the foundation for the subsequent understanding of its biological functions and molecular regulatory mechanisms

[1]  X. Wang,et al.  The unique sweet potato NAC transcription factor IbNAC3 modulates combined salt and drought stresses. , 2022, Plant physiology.

[2]  Peng Wu,et al.  Identification of the NAC Transcription Factors and Their Function in ABA and Salinity Response in Nelumbo nucifera , 2022, International journal of molecular sciences.

[3]  Chi Zhang,et al.  HemI 2.0: an online service for heatmap illustration , 2022, Nucleic Acids Res..

[4]  Biyan Zhou,et al.  LcNAC13 Is Involved in the Reactive Oxygen Species-Dependent Senescence of the Rudimentary Leaves in Litchi chinensis , 2022, Frontiers in Plant Science.

[5]  D. Grierson,et al.  NAC Transcription Factor Family Regulation of Fruit Ripening and Quality: A Review , 2022, Cells.

[6]  D. Sankoff,et al.  Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars , 2022, Nature Genetics.

[7]  C. Gu,et al.  The NAM/ATAF1/2/CUC2 transcription factor PpNAC.A59 enhances PpERF.A16 expression to promote ethylene biosynthesis during peach fruit ripening , 2021, Horticulture research.

[8]  Dayong Li,et al.  ONAC066, A Stress-Responsive NAC Transcription Activator, Positively Contributes to Rice Immunity Against Magnaprothe oryzae Through Modulating Expression of OsWRKY62 and Three Cytochrome P450 Genes , 2021, Frontiers in Plant Science.

[9]  P. A. Reis,et al.  Senescence-Associated Glycine max (Gm)NAC Genes: Integration of Natural and Stress-Induced Leaf Senescence , 2021, International journal of molecular sciences.

[10]  S. Masiero,et al.  The NAC side of the fruit: tuning of fruit development and maturation , 2021, BMC Plant Biology.

[11]  F. Lisacek,et al.  Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users , 2021, Nucleic Acids Res..

[12]  Zhaohui Xue,et al.  The interplay between ABA/ethylene and NAC TFs in tomato fruit ripening: a review , 2021, Plant Molecular Biology.

[13]  Huicong Wang,et al.  LcERF2 Modulates Cell Wall Metabolism by Directly Targeting a UDP-glucose 4-epimerase Gene to Regulate Pedicel Development and Fruit Abscission of Litchi. , 2021, The Plant journal : for cell and molecular biology.

[14]  Tian Li,et al.  miR164-targeted TaPSK5 encodes a phytosulfokine precursor that regulates root growth and yield traits in common wheat (Triticum aestivum L.) , 2020, Plant Molecular Biology.

[15]  Haisen Guo,et al.  Heat map visualization for electrocardiogram data analysis , 2020, BMC Cardiovascular Disorders.

[16]  Xuncheng Liu,et al.  KNOX protein LcKNAT1 regulates fruitlet abscission in litchi by repressing ethylene biosynthetic genes. , 2020, Journal of experimental botany.

[17]  Biyan Zhou,et al.  Comparative proteomics of phloem exudates reveals long-distance signals potentially involved in Litchi chinensis flowering , 2020 .

[18]  Margaret H. Frank,et al.  TBtools - an integrative toolkit developed for interactive analyses of big biological data. , 2020, Molecular plant.

[19]  Qiang Zhao,et al.  Isolation, sequencing, and expression analysis of 30 AP2/ERF transcription factors in apple , 2020, PeerJ.

[20]  Dayong Li,et al.  NAC transcription factors in plant immunity , 2019, Phytopathology Research.

[21]  Z. Zheng,et al.  Identification and Characterization of HAESA-Like Genes Involved in the Fruitlet Abscission in Litchi , 2019, International journal of molecular sciences.

[22]  Sergio Gonzalez,et al.  Identification and expression analysis of NAC transcription factors potentially involved in leaf and petal senescence in Petunia hybrida. , 2019, Plant science : an international journal of experimental plant biology.

[23]  M. Lercher,et al.  Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees , 2019, Nucleic Acids Res..

[24]  Xiaofei Song,et al.  Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri) , 2019, BMC Plant Biology.

[25]  A. Khan,et al.  Genomics, molecular and evolutionary perspective of NAC transcription factors , 2019, bioRxiv.

[26]  Hong Zhu,et al.  LcNAC13 Physically Interacts with LcR1MYB1 to Coregulate Anthocyanin Biosynthesis-Related Genes during Litchi Fruit Ripening , 2019, Biomolecules.

[27]  Jer-Chia Chang,et al.  Leafless Inflorescence Produces More Female Flowers and Fruit Yield Than Leafy Inflorescence in ‘Yu Her Pau’ Litchi , 2019, HortScience.

[28]  Biyan Zhou,et al.  Genome-wide transcriptome analysis reveals the molecular mechanism of high temperature-induced floral abortion in Litchi chinensis , 2019, BMC Genomics.

[29]  Qiusheng Xiao,et al.  Genome-wide identification and involvement of litchi SPL genes in flowering in response to cold and leaf maturity , 2018, The Journal of Horticultural Science and Biotechnology.

[30]  Silvio C. E. Tosatto,et al.  The Pfam protein families database in 2019 , 2018, Nucleic Acids Res..

[31]  Xiaomei Liu,et al.  Genome-wide identification and expression profile analysis of the NAC transcription factor family during abiotic and biotic stress in woodland strawberry , 2018, PloS one.

[32]  Shuxun Yu,et al.  Functional analysis of nine cotton genes related to leaf senescence in Gossypium hirsutum L , 2018, Physiology and Molecular Biology of Plants.

[33]  Sudhir Kumar,et al.  MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. , 2018, Molecular biology and evolution.

[34]  Hye-Ji Kim,et al.  Reactive oxygen species and nitric oxide induce senescence of rudimentary leaves and the expression profiles of the related genes in Litchi chinensis , 2018, Horticulture Research.

[35]  B. Mueller‐Roeber,et al.  NAC transcription factor JUNGBRUNNEN1 enhances drought tolerance in tomato , 2017, Plant biotechnology journal.

[36]  Feng Chen,et al.  Litchi Fruit LcNAC1 is a Target of LcMYC2 and Regulator of Fruit Senescence Through its Interaction with LcWRKY1 , 2017, Plant & cell physiology.

[37]  H. Nam,et al.  Regulatory network of NAC transcription factors in leaf senescence. , 2016, Current opinion in plant biology.

[38]  Po-An Chen,et al.  Temperature model of litchi flowering—From induction to anthesis , 2016 .

[39]  Jun Liang,et al.  De novo analysis of transcriptome reveals genes associated with leaf abscission in sugarcane (Saccharum officinarum L.) , 2016, BMC Genomics.

[40]  L. Tang,et al.  Characterization of generative development in early maturing litchi ‘Early Big’, a novel cultivar in Taiwan , 2015 .

[41]  Wei Hu,et al.  Genome-Wide Identification and Expression Analysis of the NAC Transcription Factor Family in Cassava , 2015, PloS one.

[42]  Xuede Wang,et al.  Molecular evolution and species-specific expansion of the NAP members in plants. , 2015, Journal of integrative plant biology.

[43]  Jiang Li,et al.  An improved fruit transcriptome and the identification of the candidate genes involved in fruit abscission induced by carbohydrate stress in litchi , 2015, Front. Plant Sci..

[44]  H. Endo,et al.  NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants , 2015, Front. Plant Sci..

[45]  S. Masiero,et al.  Transcriptomic Signatures in Seeds of Apple (Malus domestica L. Borkh) during Fruitlet Abscission , 2015, PloS one.

[46]  L. Xiong,et al.  Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice , 2014, Journal of experimental botany.

[47]  Yupeng Wang,et al.  MCScanX-transposed: detecting transposed gene duplications based on multiple colinearity scans , 2013, Bioinform..

[48]  Félix Romojaro,et al.  Transcriptomic Events Involved in Melon Mature-Fruit Abscission Comprise the Sequential Induction of Cell-Wall Degrading Genes Coupled to a Stimulation of Endo and Exocytosis , 2013, PloS one.

[49]  J. A. Gil-Amado,et al.  Transcriptome analysis of mature fruit abscission control in olive. , 2013, Plant & cell physiology.

[50]  Vladimir N Uversky,et al.  Multifarious Roles of Intrinsic Disorder in Proteins Illustrate Its Broad Impact on Plant Biology , 2013, Plant Cell.

[51]  Birthe B Kragelund,et al.  Order by disorder in plant signaling. , 2012, Trends in plant science.

[52]  Manoj Prasad,et al.  NAC proteins: regulation and role in stress tolerance. , 2012, Trends in plant science.

[53]  Jeremy D. DeBarry,et al.  MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.

[54]  Narmada Thanki,et al.  CDD: a Conserved Domain Database for the functional annotation of proteins , 2010, Nucleic Acids Res..

[55]  M. K. Jensen,et al.  The Arabidopsis thaliana NAC transcription factor family: structure-function relationships and determinants of ANAC019 stress signalling. , 2010, The Biochemical journal.

[56]  K. Theres,et al.  Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana. , 2008, The Plant journal : for cell and molecular biology.

[57]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[58]  Yongfeng Guo,et al.  AtNAP, a NAC family transcription factor, has an important role in leaf senescence. , 2006, The Plant journal : for cell and molecular biology.

[59]  Addie Nina Olsen,et al.  NAC transcription factors: structurally distinct, functionally diverse. , 2005, Trends in plant science.

[60]  John B. Anderson,et al.  CDD: a Conserved Domain Database for protein classification , 2004, Nucleic Acids Res..

[61]  Ron D. Appel,et al.  ExPASy: the proteomics server for in-depth protein knowledge and analysis , 2003, Nucleic Acids Res..

[62]  B. Zhou,et al.  Low temperature-induced leaf senescence and the expression of senescence-related genes in the panicles of Litchi chinensis , 2016, Biologia Plantarum.

[63]  Amarjeet Singh,et al.  Primer design using Primer Express® for SYBR Green-based quantitative PCR. , 2015, Methods in molecular biology.

[64]  S. Zhong,et al.  Identification of nitric oxide responsive genes in the floral buds of Litchi chinensis , 2014, Biologia Plantarum.

[65]  H. Xin,et al.  Comprehensive analysis of NAC domain transcription factor gene family in Vitis vinifera , 2012, Plant Cell Reports.

[66]  Kathleen Marchal,et al.  PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences , 2002, Nucleic Acids Res..