Identification of NAC Gene Family and Screening of Cold Stress-Responsive Genes in Catalpa bungei

doi:10.7525/j.issn.1673-5102.2026.03.005

Abstract

Abstract:

NAC（NAM， ATAF， and CUC） transcription factors are plant-specific transcriptional regulators that play crucial roles in plant growth， development， and responses to abiotic stresses. To systematically characterize the molecular evolutionary features of theNAC gene family in Catalpa bungei and elucidate its regulatory mechanisms under cold stress， NAC gene family members were comprehensively identified based on the whole-genome sequence of C. bungei. Comprehensive analyses were performed， including physicochemical properties， phylogenetic topology， gene structure conservation， cis-acting elements in promoter regions， cold-responsive expression patterns， and weighted gene co-expression network analysis（WGCNA）. The results demonstrated that a total of 65 CbuNAC genes were identified in the C. bungei genome and classified into four highly conserved subfamilies based on phylogenetic analysis. Chromosomal mapping revealed that these genes were unevenly distributed across 16 chromosomes， displaying a distinct clustered distribution pattern. Gene structure and conserved motif analyses indicated that members within the same subfamily exhibited highly similar intron-exon organization and conserved motif composition，which not only supported the reliability of the phylogenetic classification but also implied potential functional redundancy and evolutionary divergence within subfamilies. Collinearity analysis indicated that segmental duplication， rather than tandem duplication， was the predominant driving force for the expansion and evolutionary divergence of the CbuNAC gene family. Time-series transcriptome analysis under cold stress revealed that CbuNAC15， CbuNAC30， and CbuNAC36 were significantly upregulated， exhibiting strong and temporally dynamic responses to low-temperature stress. Furthermore， WGCNA revealed that the three core genes not only coordinately regulated the classical ICE1-CBF cold-signaling pathway but were also closely associated with downstream genes involved in osmotic adjustment and hormone metabolism. In summary， this study systematically characterized the genomic features of the NAC gene family in C. bungei and identified three key candidate genes associated with cold-tolerance， thereby providing valuable theoretical insights and candidate targets for elucidating abiotic stress adaptation mechanisms in woody plants and advancing marker-assisted breeding.

Key words: Catalpa bungei, NAC gene family, low-temperature stress, expression pattern, gene identification

CLC Number:

Q949.777.9

Pingan BAO, Boxin LIU, Yaxin HE, Pengyue FU, Shuo YU, Jingshuang SUN, Wenjun MA, Guanzheng QU, Junhui WANG, Ruiyang HU. Identification of NAC Gene Family and Screening of Cold Stress-Responsive Genes in Catalpa bungei[J]. Bulletin of Botanical Research, 2026, 46(3): 434-448.

Figures/Tables 9

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References 35

[1]	李银梅，贠慧玲，杨海裕，等.二十九个楸树无性系苗期年生长规律分析［J］.南方农业，2024，18（15）：9-14.
	LI Y M， YUN H L， YANG H Y，et al.Analysis on the annual growth law of twenty-nine Catalpa bungei clones at seedling stage［J］.South China Agriculture，2024，18（15）：9-14.
[2]	彭方仁，郝明灼，梁有旺，等.我国楸树种质资源现状及开发利用策略［J］.林业科技开发，2011，25（6）：1-5.
	PENG F R， HAO M Z， LIANG Y W，et al.Current status and strategies for exploitation and utilization of Catalpa bungei germplasm resources in China［J］.China Forestry Science and Technology，2011，25（6）：1-5.
[3]	赵鲲，王军辉，麻文俊，等.杂交新品种“百日花”楸树选育与栽培试验研究［J］.安徽林业科技，2020，46（6）：15-18.
	ZHAO K， WANG J H， MA W J，et al.Study on breeding and cultivation experiment of the new hybrid cultivar “Bairihua” of Catalpa bungei ［J］.Anhui Forestry Science and Technology，2020，46（6）：15-18.
[4]	MAUGARNY-CALÈS A， GONÇALVES B， JOUANNIC S，et al.Apparition of the NAC transcription factors predates the emergence of land plants［J］.Molecular Plant，2016，9（9）：1345-1348.
[5]	FUERTES-AGUILAR J， MATILLA A J.Transcriptional control of seed life：new insights into the role of the NAC family［J］.International Journal of Molecular Sciences，2024，25（10）：5369.
[6]	XIONG H Y， HE H D， CHANG Y，et al.Multiple roles of NAC transcription factors in plant development and stress responses［J］.Journal of Integrative Plant Biology，2025，67（3）：510-538.
[7]	XU P P， MA W， FENG H F，et al.The NAC056 transcription factor confers freezing tolerance by positively regulating expression of CBFs and NIA1 in Arabidopsis ［J］.Plant Communications，2024，5（7）：100923.
[8]	HAO Y J， WEI W， SONG Q X，et al.Soybean NAC transcription factors promote abiotic stress tolerance and lateral root formation in transgenic plants［J］.The Plant Journal，2011，68（2）：302-313.
[9]	QUACH T N， TRAN L S P， VALLIYODAN B，et al.Functional analysis of water stress-responsive soybean GmNAC003 and GmNAC004 transcription factors in lateral root development in Arabidopsis ［J］.PLoS One，2014，9（1）：e84886.
[10]	YANG X F， KIM M Y，HA J，et al.Overexpression of the soybean NAC gene GmNAC109 increases lateral root formation and abiotic stress tolerance in transgenic Arabidopsis plants［J］.Frontiers in Plant Science，2019，10：1036.
[11]	YARRA R， WEI W.The NAC-type transcription factor GmNAC20 improves cold，salinity tolerance，and lateral root formation in transgenic rice plants［J］.Functional & Integrative Genomics，2021，21（3/4）：473-487.
[12]	WANG F， CHEN Y， YANG R S，et al.Identification of ZmSNAC06，a maize NAC family transcription factor with multiple transcripts conferring drought tolerance in Arabidopsis ［J］.Plants，2025，14（1）：12.
[13]	孔洁玙，杨妮，罗微，等.茶树NAC转录因子CsNAC79和CsNAC9的鉴定及对非生物胁迫的响应分析［J］.西北植物学报，2024，44（4）：572-581.
	KONG J Y， YANG N， LUO W，et al.Identification and response to different abiotic stress of NAC transcription factors CsNAC79 and CsNAC9 in tea plants［J］.Acta Botanica Boreali-Occidentalia Sinica，2024，44（4）：572-581.
[14]	邹霈怡，刘美艳，王颖，等.狗枣猕猴桃AkNAC2的克隆及功能研究［J］.中国农业科学，2025，58（19）：3985-3999.
	ZOU P Y， LIU M Y， WANG Y，et al.Cloning and functional study of AkNAC2 from Actinidia kolomikta ［J］.Scientia Agricultura Sinica，2025，58（19）：3985-3999.
[15]	李畅，牛薪雅，彭金铭，等.黑壳楠低温响应关键基因LmNAC19克隆与功能分析［J］.植物生理学报，2025，61（11）：1534-1544.
	LI C， NIU X Y， PENG J M，et al.Cloning and functional analysis of LmNAC19，a key cold responsive gene in Lindera megaphylla ［J］.Plant Physiology Journal，2025，61（11）：1534-1544.
[16]	林海育.水曲柳FmNACs基因克隆及耐低温功能研究［D］.沈阳：沈阳农业大学，2025.
	LIN H Y.Cloning and functional study on low-temperature resistance of FmNACs gene in Fraxius mandshurica ［D］.Shenyang：Shenyang Agricultural University，2025.
[17]	WANG Q， ZHOU L， YUAN M，et al.Genome-wide identification of NAC gene family members of tree peony （Paeonia suffruticosa Andrews） and their expression under heat and waterlogging stress［J］.International Journal of Molecular Sciences，2024，25（17）：9312.
[18]	TIAN A G， WANG J， CUI P，et al.Characterization of soybean genomic features by analysis of its expressed sequence tags［J］.Theoretical and Applied Genetics，2004，108（5）：903-913.
[19]	NIE G， YANG X Y， YANG Z F，et al.Genome-wide investigation of the NAC transcript factor family in perennial ryegrass （Lolium perenne L.） and expression analysis under various abiotic stressor［J］.Genomics，2020，112（6）：4224-4231.
[20]	HAN K， ZHAO Y， LIU J，et al.Genome-wide investigation and analysis of NAC transcription factor family in Populus tomentosa and expression analysis under salt stress［J］.Plant Biology，2024，26（5）：764-776.
[21]	OOKA H， SATOH K，DOI K，et al.Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana ［J］.DNA Research，2003，10（6）：239-247.
[22]	NURUZZAMAN M， MANIMEKALAI R， SHARONI A M，et al.Genome-wide analysis of NAC transcription factor family in rice［J］.Gene，2010，465（1/2）：30-44.
[23]	CUTLER S R， RODRIGUEZ P L， FINKELSTEIN R R，et al.Abscisic acid：emergence of a core signaling network［J］.Annual Review of Plant Biology，2010，61（1）：651-679.
[24]	ZHU J K.Abiotic stress signaling and responses in plants［J］.Cell，2016，167（2）：313-324.
[25]	KANG X K， WEI F， CHAI S L，et al.The OST1-HOS1-HAT1 module regulates cold response in Arabidopsis thaliana ［J］.New Phytologist，2025，247（1）：209-223.
[26]	AN J P， LI R， QU F J，et al.R2R3-MYB transcription factor MdMYB23 is involved in the cold tolerance and proanthocyanidin accumulation in apple［J］.The Plant Journal，2018，96（3）：562-577.
[27]	JIANG H F， SHI Y T， LIU J Y，et al.Natural polymorphism of ZmICE1 contributes to amino acid metabolism that impacts cold tolerance in maize［J］.Nature Plants，2022，8（10）：1176-1190.
[28]	YANG L， FANG S Y， LIU L，et al.WRKY transcription factors：hubs for regulating plant growth and stress responses［J］.Journal of Integrative Plant Biology，2025，67（3）：488-509.
[29]	ZHANG L H， XU Y， LV L，et al.MbbHLH93，a transcription factor associated with cold and drought tolerance in Malus baccata ［J］.Fruit Research，2024，4：e038.
[30]	EVANS K V， RANSOM E， NAYAKOTI S，et al.Expression of the Arabidopsis redox-related LEA protein，SAG21 is regulated by ERF，NAC and WRKY transcription factors［J］.Scientific Reports，2024，14（1）：7756.
[31]	KOVACS D， KALMAR E， TOROK Z，et al.Chaperone activity of ERD10 and ERD14，two disordered stress-related plant proteins［J］.Plant Physiology，2008，147（1）：381-390.
[32]	RUIZ-CASTILLO A C， BONILLA-CÓRDOBA D J， CISNEROS-HERNÁNDEZ I，et al.The tps5，tps10 and tps11 class II trehalose phosphate synthase mutants alter carbon allocation to starch and organic and amino acids at two different photoperiods in Arabidopsis ［J］.Planta，2025，261（6）：122.
[33]	YANG G H， CHEN Y X， YU H，et al.Raspberry （Rubus idaeus L.） NCED1 gene enhances high salinity and cold tolerance in Arabidopsis ［J］.In Vitro Cellular & Developmental Biology - Plant，2021，57（5）：811-819.
[34]	ZHAO Y， XING L， WANG X G，et al.The ABA receptor PYL8 promotes lateral root growth by enhancing MYB77-dependent transcription of auxin-responsive genes［J］.Science Signaling，2014，7（328）：ra53.
[35]	BAO P A， SUN J S， QU G Z，et al.Identification and expression analysis of CCCH gene family and screening of key low temperature stress response gene CbuC3H24 and CbuC3H58 in Catalpa bungei ［J］.BMC Genomics，2024，25（1）：779.