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Backiyarani S, Anuradha C, Thangavelu R, Chandrasekar A, Renganathan B, Subeshkumar P, Giribabu P, Muthusamy M, Uma S. Genome-wide identification, characterization of expansin gene family of banana and their expression pattern under various stresses. 3 Biotech 2022; 12:101. [PMID: 35463044 PMCID: PMC8960517 DOI: 10.1007/s13205-021-03106-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/28/2021] [Indexed: 11/01/2022] Open
Abstract
Expansin, a cell wall-modifying gene family, has been well characterized and its role in biotic and abiotic stress resistance has been proven in many monocots, but not yet studied in banana, a unique model crop. Banana is one of the staple food crops in developing countries and its production is highly influenced by various biotic and abiotic factors. Characterizing the expansin genes of the ancestor genome (M. acuminata and M. balbisiana) of present day cultivated banana will enlighten their role in growth and development, and stress responses. In the present study, 58 (MaEXPs) and 55 (MbaEXPs) putative expansin genes were identified in A and B genome, respectively, and were grouped in four subfamilies based on phylogenetic analysis. Gene structure and its duplications revealed that EXPA genes are highly conserved and are under negative selection whereas the presence of more number of introns in other subfamilies revealed that they are diversifying. Expression profiling of expansin genes showed a distinct expression pattern for biotic and abiotic stress conditions. This study revealed that among the expansin subfamilies, EXPAs contributed significantly towards stress-resistant mechanism. The differential expression of MaEXPA18 and MaEXPA26 under drought stress conditions in the contrasting cultivar suggested their role in drought-tolerant mechanism. Most of the MaEXPA genes are differentially expressed in the root lesion nematode contrasting cultivars which speculated that this expansin subfamily might be the susceptible factor. The downregulation of MaEXPLA6 in resistant cultivar during Sigatoka leaf spot infection suggested that by suppressing this gene, resistance may be enhanced in susceptible cultivar. Further, in-depth studies of these genes will lead to gain insight into their role in various stress conditions in banana. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-021-03106-x.
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Affiliation(s)
- Suthanthiram Backiyarani
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Chelliah Anuradha
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Raman Thangavelu
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Arumugam Chandrasekar
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Baratvaj Renganathan
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Parasuraman Subeshkumar
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Palaniappan Giribabu
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
| | - Muthusamy Muthusamy
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), RDA, Jeonju, 54874 Korea
| | - Subbaraya Uma
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu 620 102 India
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Comparative morphology and transcriptome analysis reveals distinct functions of the primary and secondary laticifer cells in the rubber tree. Sci Rep 2017; 7:3126. [PMID: 28600566 PMCID: PMC5466658 DOI: 10.1038/s41598-017-03083-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/24/2017] [Indexed: 12/27/2022] Open
Abstract
Laticifers are highly specialized cells that synthesize and store natural rubber. Rubber trees (Hevea brasiliensis Muell. Arg.) contain both primary and secondary laticifers. Morphological and functional differences between the two types of laticifers are largely unknown, but such information is important for breeding and cultivation practices. Morphological comparison using paraffin sections revealed only distribution differences: the primary laticifers were distributed randomly, while the secondary laticifers were distributed in concentric rings. Using isolated laticifer networks, the primary laticifers were shown to develop via intrusive "budding" and formed necklace-like morphology, while the secondary laticifers developed straight and smooth cell walls. Comparative transcriptome analysis indicated that genes involved in cell wall modification, such as pectin esterase, lignin metabolic enzymes, and expansins, were highly up-regulated in the primary laticifers and correspond to its necklace-like morphology. Genes involved in defense against biotic stresses and rubber biosynthesis were highly up-regulated in the primary laticifers, whereas genes involved in abiotic stresses and dormancy were up-regulated in the secondary laticifers, suggesting that the primary laticifers are more adequately prepared to defend against biotic stresses, while the secondary laticifers are more adequately prepared to defend against abiotic stresses. Therefore, the two types of laticifers are morphologically and functionally distinct.
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Marowa P, Ding A, Kong Y. Expansins: roles in plant growth and potential applications in crop improvement. PLANT CELL REPORTS 2016; 35:949-65. [PMID: 26888755 PMCID: PMC4833835 DOI: 10.1007/s00299-016-1948-4] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/02/2016] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE Results from various expansin related studies have demonstrated that expansins present an opportunity to improve various crops in many different aspects ranging from yield and fruit ripening to improved stress tolerance. The recent advances in expansin studies were reviewed. Besides producing the strength that is needed by the plants, cell walls define cell shape, cell size and cell function. Expansins are cell wall proteins which consist of four sub families; α-expansin, β-expansin, expansin-like A and expansin-like B. These proteins mediate cell wall loosening and they are present in all plants and in some microbial organisms and other organisms like snails. Decades after their initial discovery in cucumber, it is now clear that these small proteins have diverse biological roles in plants. Through their ability to enable the local sliding of wall polymers by reducing adhesion between adjacent wall polysaccharides and the part they play in cell wall remodeling after cytokinesis, it is now clear that expansins are required in almost all plant physiological development aspects from germination to fruiting. This is shown by the various reports from different studies using various molecular biology approaches such as gene achieve these many roles through their non-enzymatic wall loosening ability. This paper reviews and summarizes some of the reported functions of expansins and outlines the potential uses of expansins in crop improvement programs.
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Affiliation(s)
- Prince Marowa
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China
| | - Anming Ding
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China
| | - Yingzhen Kong
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, People's Republic of China.
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Ikeue D, Schudoma C, Zhang W, Ogata Y, Sakamoto T, Kurata T, Furuhashi T, Kragler F, Aoki K. A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads. PLANT METHODS 2015; 11:34. [PMID: 26052341 PMCID: PMC4458054 DOI: 10.1186/s13007-015-0066-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 03/12/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND The genus Cuscuta is a group of parasitic plants that are distributed world-wide. The process of parasitization starts with a Cuscuta plant coiling around the host stem. The parasite's haustorial organs then establish a vascular connection allowing for access to the phloem content. The host and the parasite form new cellular connections, suggesting coordination of developmental and biochemical processes. Simultaneous monitoring of gene expression in the parasite's and host's tissues may shed light on the complex events occurring between the parasitic and host cells and may help to overcome experimental limitations (i.e. how to separate host tissue from Cuscuta tissue at the haustorial connection). A novel approach is to use bioinformatic analysis to classify sequencing reads as either belonging to the host or to the parasite and to characterize the expression patterns. Owing to the lack of a comprehensive genomic dataset from Cuscuta spp., such a classification has not been performed previously. RESULTS We first classified RNA-Seq reads from an interface region between the non-model parasitic plant Cuscuta japonica and the non-model host plant Impatiens balsamina. Without established reference sequences, we classified reads as originating from either of the plants by stepwise similarity search against de novo assembled transcript sets of C. japonica and I. balsamina, unigene sets of the same genus, and cDNA sequences of the same family. We then assembled de novo transcriptomes from the classified read sets. We assessed the quality of the classification by mapping reads to contigs of both plants, achieving a misclassification rate low enough (0.22-0.39%) to be used reliably for differential gene expression analysis. Finally, we applied our read classification method to RNA-Seq data from the interface between the non-model parasitic plant C. japonica and the model host plant Glycine max. Analysis of gene expression profiles at 5 parasitizing stages revealed differentially expressed genes from both C. japonica and G. max, and uncovered the coordination of cellular processes between the two plants. CONCLUSIONS We demonstrated that reliable identification of differentially expressed transcripts in undissected interface region of the parasite-host association is feasible and informative with respect to differential-expression patterns.
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Affiliation(s)
- Daisuke Ikeue
- />Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1–1 Gakuen–Cho, Naka–Ku, Sakai, Osaka, 599–8531 Japan
| | - Christian Schudoma
- />Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, Potsdam, 14476 Germany
- />Present Address: Bioinformatics Group, The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - Wenna Zhang
- />Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, Potsdam, 14476 Germany
| | - Yoshiyuki Ogata
- />Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1–1 Gakuen–Cho, Naka–Ku, Sakai, Osaka, 599–8531 Japan
| | - Tomoaki Sakamoto
- />Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916–5 Takayama, Ikoma, 630–0192 Japan
| | - Tetsuya Kurata
- />Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916–5 Takayama, Ikoma, 630–0192 Japan
| | - Takeshi Furuhashi
- />Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science (CSRC), 1–7–22 Suehiro, Tsurumi, Yokohama, 230–0045 Japan
- />Present Address: Department of Molecular Systems Biology (Ecogenomics and Systems Biology), Vienna University, Althanstraße 14, Vienna, A–1090 Austria
| | - Friedrich Kragler
- />Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, Potsdam, 14476 Germany
| | - Koh Aoki
- />Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1–1 Gakuen–Cho, Naka–Ku, Sakai, Osaka, 599–8531 Japan
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Tirumalaraju SV, Jain M, Gallo M. Differential gene expression in roots of nematode-resistant and -susceptible peanut (Arachis hypogaea) cultivars in response to early stages of peanut root-knot nematode (Meloidogyne arenaria) parasitization. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:481-92. [PMID: 20863592 DOI: 10.1016/j.jplph.2010.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 08/17/2010] [Accepted: 08/19/2010] [Indexed: 05/10/2023]
Abstract
The peanut root-knot nematode (RKN, Meloidogyne arenaria) can cause significant yield losses in cultivated peanut (Arachis hypogaea). However, molecular events underlying successful RKN infection and host responses in peanut are sparsely understood. Using suppression subtractive hybridization (SSH), cDNA libraries, enriched with differentially expressed ESTs, were constructed from RKN-challenged root tissues in the pre-penetration and early infection stages from near-isogenic nematode-resistant and -susceptible peanut cultivars NemaTAM and Florunner. Following an initial screen of 960 expressed sequence tags (ESTs) for at least three-fold differential expression between the two libraries, 70 ESTs (36 from the NemaTAM-specific library and 34 from the Florunner-specific library) were identified and annotated into seven functional categories (stress responses, metabolism, transcriptional regulation, protein synthesis and/or modification, transport functions, cellular architecture and proteins with unknown functions). Discreet gene tag clusters primarily including pathogenesis related (PR), patatin-like proteins and universal stress related proteins (USPs), as well as those implicated in alleviation of oxidative stress were primarily represented in RKN-infected NemaTAM roots, reflective of a basal level of resistance operative against invading nematodes. However, significant transcriptional reprogramming and upregulation of genes implicated in modification of cellular architecture, adhesion, and proliferation marked an early onset of compatible host-pathogen interactions discernible in Florunner roots.
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