Genome-wide identification of IQ67 domain (IQD) gene families in Chinese jujube (Ziziphus jujuba Mill.) and expression profiles in response to cold stress

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

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Genome-wide identification and analysis of the CNGC gene family in maize

PeerJ ◽

10.7717/peerj.5816 ◽

2018 ◽

Vol 6 ◽

pp. e5816 ◽

Cited By ~ 4

Author(s):

Lidong Hao ◽

Xiuli Qiao

Keyword(s):

Gene Family ◽

Expression Profiles ◽

Gene Families ◽

Regulatory Elements ◽

Vital Role ◽

Signal Pathways ◽

Cis Acting ◽

Genome Wide ◽

Gramineous Plant ◽

Gated Channel

As one of the non-selective cation channel gene families, the cyclic nucleotide-gated channel (CNGC) gene family plays a vital role in plant physiological processes that are related to signal pathways, plant development, and environmental stresses. However, genome-wide identification and analysis of the CNGC gene family in maize has not yet been undertaken. In the present study, twelve ZmCNGC genes were identified in the maize genome, which were unevenly distributed on chromosomes 1, 2, 4, 5, 6, 7, and 8. They were classified into five major groups: Groups I, II, III, IVa, and IVb. Phylogenetic analysis showed that gramineous plant CNGC genes expanded unequally during evolution. Group IV CNGC genes emerged first, whereas Groups I and II appeared later. Prediction analysis of cis-acting regulatory elements showed that 137 putative cis-elements were related to hormone-response, abiotic stress, and organ development. Furthermore, 120 protein pairs were predicted to interact with the 12 ZmCNGC proteins and other maize proteins. The expression profiles of the ZmCNGC genes were expressed in tissue-specific patterns. These results provide important information that will increase our understanding of the CNGC gene family in maize and other plants.

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Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments

Genome ◽

10.1139/gen-2017-0163 ◽

2018 ◽

Vol 61 (2) ◽

pp. 121-130 ◽

Cited By ~ 4

Author(s):

Chenghao Zhang ◽

Wenqi Dong ◽

Zong-an Huang ◽

MyeongCheoul Cho ◽

Qingcang Yu ◽

...

Keyword(s):

Capsicum Annuum ◽

Abiotic Stresses ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Families ◽

Environmental Stresses ◽

Transcriptional Level ◽

Specific Expression ◽

Capsicum Annuum L ◽

Genome Wide

Auxin plays key roles in regulating plant growth and development as well as in response to environmental stresses. The intercellular transport of auxin is mediated by the following four gene families: ATP-binding cassette family B (ABCB), auxin resistant1/like aux1 (AUX/LAX), PIN-formed (PIN), and PIN-like (PILS). Here, the latest assembled pepper (Capsicum annuum L.) genome was used to characterise and analyse the CaLAX and CaPIN gene families. Genome-wide investigations into these families, including chromosomal distributions, phytogenic relationships, and intron/exon structures, were performed. In total, 4 CaLAX and 10 CaPIN genes were mapped to 10 chromosomes. Most of these genes exhibited varied tissue-specific expression patterns assessed by quantitative real-time PCR. The expression profiles of the CaLAX and CaPIN genes under various abiotic stresses (salt, drought, and cold), exogenous phytohormones (IAA, 6-BA, ABA, SA, and MeJA), and polar auxin transport inhibitor treatments were evaluated. Most CaLAX and CaPIN genes were altered by abiotic stress at the transcriptional level in both shoots and roots, and many CaLAX and CaPIN genes were regulated by exogenous phytohormones. Our study helps to identify candidate auxin transporter genes and to further analyse their biological functions in pepper development and in its adaptation to environmental stresses.

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Genome-wide identification of MAPKKK genes and their responses to phytoplasma infection in Chinese jujube (Ziziphus jujuba Mill.)

BMC Genomics ◽

10.1186/s12864-020-6548-6 ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 1

Author(s):

Zhiguo Liu ◽

Lixin Wang ◽

Chaoling Xue ◽

Yuetong Chu ◽

Weilin Gao ◽

...

Keyword(s):

Chinese Jujube ◽

Genome Wide ◽

Phytoplasma Infection ◽

Ziziphus Jujuba

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Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis

Genes ◽

10.3390/genes10100730 ◽

2019 ◽

Vol 10 (10) ◽

pp. 730 ◽

Cited By ~ 4

Author(s):

Sun ◽

Wang ◽

Ma ◽

Li ◽

Liu

Keyword(s):

Somatic Embryogenesis ◽

Upland Cotton ◽

Expression Profiles ◽

Gene Families ◽

Early Response ◽

Auxin Signaling ◽

Evolutionary Divergence ◽

Genome Wide ◽

A Genome ◽

Early Response Genes

Auxin is well known to regulate growth and development processes. Auxin early response genes serve as a critical component of auxin signaling and mediate auxin regulation of diverse physiological processes. In the present study, a genome-wide identification and comprehensive analysis of auxin early response genes were conducted in upland cotton. A total of 71 auxin response factor (ARF), 86 Auxin/Indole-3-Acetic Acid (Aux/IAA), 63 Gretchen Hagen3 (GH3), and 194 small auxin upregulated RNA (SAUR) genes were identified in upland cotton, respectively. Phylogenetic analysis revealed that the ARF, GH3, and SAUR families were likely subject to extensive evolutionary divergence between Arabidopsis and upland cotton, while the Aux/IAA family was evolutionary conserved. Expression profiles showed that the ARF, Aux/IAA, GH3, and SAUR family genes were extensively involved in embryogenic competence acquisition of upland cotton callus. The Aux/IAA family genes generally showed a higher expression level in the non-embryogenic callus (NEC) of highly embryogenic cultivar CCRI24 than that of recalcitrant cultivar CCRI12, which may be conducive to initializing the embryogenic transformation. Auxin early response genes were tightly co-expressed with most of the known somatic embryogenesis (SE) related genes, indicating that these genes may regulate upland cotton SE by interacting with auxin early response genes.

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Genome-wide analysis of the WRKY family genes and their responses to cold stress in watermelon

Czech Journal of Genetics and Plant Breeding ◽

10.17221/72/2017-cjgpb ◽

2018 ◽

Vol 54 (No. 4) ◽

pp. 168-176

Author(s):

Yan-Man Li ◽

Lei Zhu ◽

Hua-Yu Zhu ◽

Lu-Qin Guo ◽

Peng-Yao Song ◽

...

Keyword(s):

Cold Stress ◽

Expression Profiles ◽

Citrullus Lanatus ◽

Temperature Treatment ◽

Climate Conditions ◽

Regulatory Pathways ◽

Low Temperature Treatment ◽

Physiological Processes ◽

Genome Wide ◽

Group 2

The WRKY transcription factors play important roles in various physiological processes, especially in regulating plant resistance to environmental stresses. Watermelon (Citrullus lanatus) plants suffer from various stressful climate conditions during their growth, especially cold stress. However, little information about the exact role of WRKYs in watermelon responses to cold was available. In this study, a total of 57 candidate ClWRKY genes from watermelon genome were identified and they were distributed unevenly on 11 chromosomes. After excluding five ClWRKY genes with incomplete WRKY domains, phylogenetic analysis showed that the remaining 52 ClWRKY genes could be divided into three groups with 11 members in Group 1, 34 in Group 2, and seven in Group 3. The ClWRKY genes in group 2 could be further classified into five subgroups with three members in 2a, five in 2b, 13 in 2c, six in 2d, and seven in 2e, respectively. The expression profiles of ClWRKY genes in response to cold stress could be classiﬁed into four types: four ClWRKY genes had little or no change in transcript levels, seven ClWRKY genes had irregular expression patters, 17 ClWRKY genes were upregulated, and 25 ClWRKY genes were downregulated. The different regulation patterns of ClWRKY genes in response to low-temperature treatment revealed that the WRKY gene family was crucial for cold stress tolerance and there were multiple regulatory pathways involved in cold resistance.

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Genome-wide identification, characterization, and expression analysis of the expansin gene family in Chinese jujube (Ziziphus jujuba Mill.)

Planta ◽

10.1007/s00425-018-3020-9 ◽

2018 ◽

Vol 249 (3) ◽

pp. 815-829 ◽

Cited By ~ 9

Author(s):

Lu Hou ◽

Zhiyong Zhang ◽

Suhan Dou ◽

Yadong Zhang ◽

Xiaoming Pang ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Chinese Jujube ◽

Expansin Gene ◽

Genome Wide ◽

Ziziphus Jujuba

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Genome-Wide Identification and Expression Analysis of the Protease Inhibitor Gene Families in Tomato

Genes ◽

10.3390/genes11010001 ◽

2019 ◽

Vol 11 (1) ◽

pp. 1 ◽

Cited By ~ 3

Author(s):

Yuxuan Fan ◽

Wei Yang ◽

Qingxia Yan ◽

Chunrui Chen ◽

Jinhua Li

Keyword(s):

Expression Analysis ◽

Developmental Stages ◽

Expression Profiles ◽

In Silico Analysis ◽

Gene Families ◽

Crop Species ◽

Specific Expression ◽

Transcription Analysis ◽

Genome Wide ◽

Wilt Virus

The protease inhibitors (PIs) in plants are involved primarily in defense against pathogens and pests and in response to abiotic stresses. However, information about the PI gene families in tomato (Solanum lycopersicum), one of the most important model plant for crop species, is limited. In this study, in silico analysis identified 55 PI genes and their conserved domains, phylogenetic relationships, and chromosome locations were characterized. According to genetic structure and evolutionary relationships, the PI gene families were divided into seven families. Genome-wide microarray transcription analysis indicated that the expression of SlPI genes can be induced by abiotic (heat, drought, and salt) and biotic (Botrytis cinerea and tomato spotted wilt virus (TSWV)) stresses. In addition, expression analysis using RNA-seq in various tissues and developmental stages revealed that some SlPI genes were highly or preferentially expressed, showing tissue- and developmental stage-specific expression profiles. The expressions of four representative SlPI genes in response to abscisic acid (ABA), salicylic acid (SA), ethylene (Eth), gibberellic acid (GA). and methyl viologen (MV) were determined. Our findings indicated that PI genes may mediate the response of tomato plants to environmental stresses to balance hormone signals. The data obtained here will improve the understanding of the potential function of PI gene and lay a foundation for tomato breeding and transgenic resistance to stresses.

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