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Ripley DM, Garner T, Stevens A. Developing the 'omic toolkit of comparative physiologists. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101287. [PMID: 38972179 DOI: 10.1016/j.cbd.2024.101287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/22/2024] [Accepted: 07/01/2024] [Indexed: 07/09/2024]
Abstract
Typical 'omic analyses reduce complex biological systems to simple lists of supposedly independent variables, failing to account for changes in the wider transcriptional landscape. In this commentary, we discuss the utility of network approaches for incorporating this wider context into the study of physiological phenomena. We highlight opportunities to build on traditional network tools by utilising cutting-edge techniques to account for higher order interactions (i.e. beyond pairwise associations) within datasets, allowing for more accurate models of complex 'omic systems. Finally, we show examples of previous works utilising network approaches to gain additional insight into their organisms of interest. As 'omics grow in both their popularity and breadth of application, so does the requirement for flexible analytical tools capable of interpreting and synthesising complex datasets.
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Affiliation(s)
- Daniel M Ripley
- Marine Biology Laboratory, Division of Science, New York University Abu Dhabi, United Arab Emirates. https://twitter.com/@ElasmoDan
| | - Terence Garner
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Adam Stevens
- Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.
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Yang M, Umer MJ, Wang H, Han J, Han J, Liu Q, Zheng J, Cai X, Hou Y, Xu Y, Wang Y, Khan MKR, Ditta A, Liu F, Zhou Z. Decoding the guardians of cotton resilience: A comprehensive exploration of the βCA genes and its role in Verticillium dahliae resistance. PHYSIOLOGIA PLANTARUM 2023; 175:e14113. [PMID: 38148227 DOI: 10.1111/ppl.14113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 12/28/2023]
Abstract
Plant Carbonic anhydrases (Cas) have been shown to be stress-responsive enzymes that may play a role in adapting to adverse conditions. Cotton is a significant economic crop in China, with upland cotton (Gossypium hirsutum) being the most widely cultivated species. We conducted genome-wide identification of the βCA gene in six cotton species and preliminary analysis of the βCA gene in upland cotton. In total, 73 βCA genes from six cotton species were identified, with phylogenetic analysis dividing them into five subgroups. GHβCA proteins were predominantly localized in the chloroplast and cytoplasm. The genes exhibited conserved motifs, with motifs 1, 2, and 3 being prominent. GHβCA genes were unevenly distributed across chromosomes and were associated with stress-responsive cis-regulatory elements, including those responding to light, MeJA, salicylic acid, abscisic acid, cell cycle regulation, and defence/stress. Expression analysis indicated that GHβCA6, GHβCA7, GHβCA10, GHβCA15, and GHβCA16 were highly expressed under various abiotic stress conditions, whereas GHβCA3, GHβCA9, GHβCA10, and GHβCA18 had higher expression patterns under Verticillium dahliae infection at different time intervals. In Gossypium thurberi, GthβCA1, GthβCA2, and GthβCA4 showed elevated expression across stress conditions and tissues. Silencing GHβCA10 through VIGS increased Verticillium wilt severity and reduced lignin deposition compared to non-silenced plants. GHβCA10 is crucial for cotton's defense against Verticillium dahliae. Further research is needed to understand the underlying mechanisms and develop strategies to enhance resistance against Verticillium wilt.
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Affiliation(s)
- Mengying Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Muhammad Jawad Umer
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
| | - Heng Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
| | - Jiale Han
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiangping Han
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Qiankun Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
| | - Jie Zheng
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
| | - Xiaoyan Cai
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
- Henan International Joint Laboratory of Cotton Biology, Henan, China
| | - Yuqing Hou
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
| | - Yanchao Xu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
| | - Yuhong Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
| | | | - Allah Ditta
- Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | - Fang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
- National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, China
- Henan International Joint Laboratory of Cotton Biology, Henan, China
| | - Zhongli Zhou
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Henan, China
- Henan International Joint Laboratory of Cotton Biology, Henan, China
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Dong Y, Gupta S, Wargent JJ, Putterill J, Macknight RC, Gechev TS, Mueller-Roeber B, Dijkwel PP. Comparative Transcriptomics of Multi-Stress Responses in Pachycladon cheesemanii and Arabidopsis thaliana. Int J Mol Sci 2023; 24:11323. [PMID: 37511083 PMCID: PMC10379395 DOI: 10.3390/ijms241411323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/26/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The environment is seldom optimal for plant growth and changes in abiotic and biotic signals, including temperature, water availability, radiation and pests, induce plant responses to optimise survival. The New Zealand native plant species and close relative to Arabidopsis thaliana, Pachycladon cheesemanii, grows under environmental conditions that are unsustainable for many plant species. Here, we compare the responses of both species to different stressors (low temperature, salt and UV-B radiation) to help understand how P. cheesemanii can grow in such harsh environments. The stress transcriptomes were determined and comparative transcriptome and network analyses discovered similar and unique responses within species, and between the two plant species. A number of widely studied plant stress processes were highly conserved in A. thaliana and P. cheesemanii. However, in response to cold stress, Gene Ontology terms related to glycosinolate metabolism were only enriched in P. cheesemanii. Salt stress was associated with alteration of the cuticle and proline biosynthesis in A. thaliana and P. cheesemanii, respectively. Anthocyanin production may be a more important strategy to contribute to the UV-B radiation tolerance in P. cheesemanii. These results allowed us to define broad stress response pathways in A. thaliana and P. cheesemanii and suggested that regulation of glycosinolate, proline and anthocyanin metabolism are strategies that help mitigate environmental stress.
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Affiliation(s)
- Yanni Dong
- School of Natural Sciences, Massey University, Tennent Drive, Palmerston North 4474, New Zealand
| | - Saurabh Gupta
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam, Germany
| | - Jason J Wargent
- School of Agriculture & Environment, Massey University, Palmerston North 4442, New Zealand
| | - Joanna Putterill
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Richard C Macknight
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand
| | - Tsanko S Gechev
- Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd., 4000 Plovdiv, Bulgaria
- Department of Plant Physiology and Plant Molecular Biology, University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria
| | - Bernd Mueller-Roeber
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd., 4000 Plovdiv, Bulgaria
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Paul P Dijkwel
- School of Natural Sciences, Massey University, Tennent Drive, Palmerston North 4474, New Zealand
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Han J, Jawad Umer M, Yang M, Hou Y, Gereziher Mehari T, Zheng J, Wang H, Liu J, Dong W, Xu Y, Wang Y, Liu F, Zhou Z, Cai X. Genome-wide identification and functional analysis of ICE genes reveal that Gossypium thurberi "GthICE2" is responsible for cold and drought stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 199:107708. [PMID: 37116225 DOI: 10.1016/j.plaphy.2023.107708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/30/2023] [Accepted: 04/14/2023] [Indexed: 05/23/2023]
Abstract
Cold stress has been found to have a negative impact on cotton growth and annual production. To address this issue, the utilization of cold-tolerant gene resources from wild species of Gossypium is crucial for genetic improvements in cultivated cotton. ICE (inducer of CBF expression) are the key regulators of cold tolerance in plants, however, there is relatively little information on ICE genes in cotton. Herein, we performed comprehensive bioinformatics analyses of the ICE gene family in eight cotton species. Phylogenetic analysis showed that 52 ICE genes were clustered into four subgroups. Cis-regulatory elements analysis suggests that the expression of ICE genes might be regulated by light, plant hormones, and various environment stresses. Higher expression of GthICE2 was observed in leaves as compared to roots and stems, in response to cold, drought, and exogenous hormone ABA. Furthermore, overexpression of GthICE2 in A. thaliana led to higher germination and survival rates, longer root length, lower ion leakage, and induction under cold and drought stress. Histochemical staining showed that oxidative damage in transgenic lines was much lower compared to wild-type plants. Lower MDA contents and higher SOD and POD activities were observed in overexpressed plants. Y1H and LUC assays revealed that GthICE2 might activate the expression of GthCBF4, a cold-responsive gene, by connecting with the MYC cis-element present in the promoter of GthCBF4. GthICE2 confers cold and drought stress tolerance in cotton. Our findings add significantly to the existing knowledge regarding cold stress tolerance and helps to elucidate cold response mechanisms in cotton.
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Affiliation(s)
- Jiangping Han
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Mengying Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Teame Gereziher Mehari
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, China
| | - Jie Zheng
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China
| | - Heng Wang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jiajun Liu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wenhao Dong
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yuhong Wang
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fang Liu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China; State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China.
| | - ZhongLi Zhou
- State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xiaoyan Cai
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University/Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China; State Key Laboratory of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China; National Nanfan Research Institute of Chinese Academy of Agriculture Sciences, Sanya, 572025, China.
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Zhang R, Shi PT, Zhou M, Liu HZ, Xu XJ, Liu WT, Chen KM. Rapid alkalinization factor: function, regulation, and potential applications in agriculture. STRESS BIOLOGY 2023; 3:16. [PMID: 37676530 PMCID: PMC10442051 DOI: 10.1007/s44154-023-00093-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/10/2023] [Indexed: 09/08/2023]
Abstract
Rapid alkalinization factor (RALF) is widespread throughout the plant kingdom and controls many aspects of plant life. Current studies on the regulatory mechanism underlying RALF function mainly focus on Arabidopsis, but little is known about the role of RALF in crop plants. Here, we systematically and comprehensively analyzed the relation between RALF family genes from five important crops and those in the model plant Arabidopsis thaliana. Simultaneously, we summarized the functions of RALFs in controlling growth and developmental behavior using conservative motifs as cues and predicted the regulatory role of RALFs in cereal crops. In conclusion, RALF has considerable application potential in improving crop yields and increasing economic benefits. Using gene editing technology or taking advantage of RALF as a hormone additive are effective way to amplify the role of RALF in crop plants.
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Affiliation(s)
- Ran Zhang
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Peng-Tao Shi
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Min Zhou
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Huai-Zeng Liu
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xiao-Jing Xu
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Area, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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