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Genetics, genomics, and evolution of CAM photosynthesis
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Genetics, genomics, and evolution of CAM photosynthesis

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (30 June 2019) | Viewed by 14332

Special Issue Editors

Dr. Xiaohan Yang

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Guest Editor
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Interests: plant synthetic biology; genome editing; comparative genomics; climate change; bioenergy; photosynthesis; plant genomics
Special Issues, Collections and Topics in MDPI journals
Dr. Luciano Freschi

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Guest Editor
Department of Botany, Institute of Biosciences, University of São Paulo (USP), São Paulo, Brazil
Interests: nitric oxide metabolism; signaling processes; fruit physiology; abiotic stress in crop species; ROS and RNS metabolism; antioxidants
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Johan Ceusters

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Guest Editor
Department of Microbial and Molecular Systems, KU Leuven, campus Geel, Geel, Belgium

Special Issue Information

Dear Colleagues,

Crassulacean acid metabolism (CAM) is a special type of photosynthetic pathway, which has evolved multiple times independently from diverse ancestral C3 photosynthesis lineages. In CAM plants, atmospheric CO2 uptake through open stomata takes place predominantly at night when temperature is lower than during the daytime, thereby reducing water loss caused by evaporation and conferring these species much higher water-use efficiency than C3 or C4 photosynthesis plants. CAM is an important carbon concentrating mechanism, in which CO2 released during the day behind closed stomata elevates intracellular CO2 concentrations in the vicinity of ribulose-1,5-bisphosphate carboxylase/oxygenase, essentially creating a temporal “CO2 pump”, which can minimize photorespiration and consequently increase net photosynthesis. Currently, there is a resurgence of interest in understanding the molecular basis and evolution of CAM photosynthesis to facilitate the utilization of CAM for sustainable crop production in dry and marginal lands. This Special Issue focuses on the genetics, genomics and evolution of CAM plants, and welcomes original research articles as well as review articles that summarize recent progress and discuss future needs/opportunities in a wide range of areas including, but not limited to, quantitative genetics, functional genomics, molecular physiology/ecology, metabolic modeling, gene co-expression/regulatory network, genetic diversity, genome-editing, CAM-engineering, and molecular evolution of CAM plants.

Dr. Xiaohan Yang
Dr. Luciano Freschi
Prof. Johan Ceusters
Guest Editors

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Keywords

  • Crassulacean acid metabolism
  • Genetics
  • Genomics
  • Evolution
  • Photosynthesis
  • Gene expression
  • Genome editing
  • Molecular physiology
  • Synthetic biology

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Published Papers (3 papers)

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11 pages, 4667 KiB  
Article
Identification and Expression of SAUR Genes in the CAM Plant Agave
by Gang Deng, Xing Huang, Li Xie, Shibei Tan, Thomas Gbokie, Jr., Yaning Bao, Zhouli Xie and Kexian Yi
Genes 2019, 10(7), 555; https://doi.org/10.3390/genes10070555 - 23 Jul 2019
Cited by 16 | Viewed by 4591
Abstract
Agave species are important crassulacean acid metabolism (CAM) plants and widely cultivated in tropical areas for producing tequila spirit and fiber. The hybrid H11648 of Agave ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for fiber [...] Read more.
Agave species are important crassulacean acid metabolism (CAM) plants and widely cultivated in tropical areas for producing tequila spirit and fiber. The hybrid H11648 of Agave ((A. amaniensis × A. angustifolia) × A. amaniensis) is the main cultivar for fiber production in Brazil, China, and African countries. Small Auxin Up-regulated RNA (SAUR) genes have broad effect on auxin signaling-regulated plant growth and development, while only few SAUR genes have been reported in Agave species. In this study, we identified 43, 60, 24, and 21 SAUR genes with full-length coding regions in A. deserti, A. tequilana, A. H11648, and A. americana, respectively. Although phylogenetic analysis revealed that rice contained a species-specific expansion pattern of SAUR gene, no similar phenomena were observed in Agave species. The in silico expression indicated that SAUR genes had a distinct expression pattern in A. H11648 compared with other Agave species; and four SAUR genes were differentially expressed during CAM diel cycle in A. americana. Additionally, an expression analysis was conducted to estimate SAUR gene expression during different leaf developmental stages, abiotic and biotic stresses in A. H11648. Together, we first characterized the SAUR genes of Agave based on previously published transcriptome datasets and emphasized the potential functions of SAUR genes in Agave’s leaf development and stress responses. The identification of which further expands our understanding on auxin signaling-regulated plant growth and development in Agave species. Full article
(This article belongs to the Special Issue Genetics, genomics, and evolution of CAM photosynthesis)
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15 pages, 2658 KiB  
Article
Genome-Wide Identification and Characterization of Xyloglucan Endotransglycosylase/Hydrolase in Ananas comosus during Development
by Qingyun Li, Huayang Li, Chongyang Yin, Xiaotong Wang, Qing Jiang, Rui Zhang, Fangfang Ge, Yudong Chen and Long Yang
Genes 2019, 10(7), 537; https://doi.org/10.3390/genes10070537 - 16 Jul 2019
Cited by 22 | Viewed by 4651
Abstract
Xyloglucan endotransglycosylase/hydrolase (XTH) is a cell-wall-modifying enzyme participating in diverse cell morphogenetic processes and adaptation to stress. In this study, 48 XTH genes were identified from two pineapple (Ananas comosus) cultivars (‘F153’ and ‘MD2’) and designated Ac(F153)XTH1 to -24 and Ac(MD2)XTH1 [...] Read more.
Xyloglucan endotransglycosylase/hydrolase (XTH) is a cell-wall-modifying enzyme participating in diverse cell morphogenetic processes and adaptation to stress. In this study, 48 XTH genes were identified from two pineapple (Ananas comosus) cultivars (‘F153’ and ‘MD2’) and designated Ac(F153)XTH1 to -24 and Ac(MD2)XTH1 to -24 based on their orthology with Arabidopsis thaliana genes. Endoglucanase family 16 members were identified in addition to XTHs of glycoside hydrolase family 16. Phylogenetic analysis clustered the XTHs into three major groups (Group I/II, III and Ancestral Group) and Group III was subdivided into Group IIIA and Group IIIB. Similar gene structure and motif number were observed within a group. Two highly conserved domains, glycosyl hydrolase family 16 (GH16-XET) and xyloglucan endotransglycosylase C-terminus (C-XET), were detected by multiple sequences alignment of all XTHs. Segmental replication were detected in the two cultivars, with only the paralogous pair Ac(F153)XTH7-Ac(F153)XTH18 presented in ‘F153’ prior to genomic expansion. Transcriptomic analysis indicated that XTHs were involved in the regulation of fruit ripening and crassulacean acid metabolism with tissue specificity and quantitative real-time PCR analysis suggested that Ac(MD2)XTH18 was involved in root growth. The results enhance our understanding of XTHs in the plant kingdom and provide a basis for further studies of functional diversity in A. comosus. Full article
(This article belongs to the Special Issue Genetics, genomics, and evolution of CAM photosynthesis)
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11 pages, 2321 KiB  
Article
De Novo Transcriptome Assembly of Agave H11648 by Illumina Sequencing and Identification of Cellulose Synthase Genes in Agave Species
by Xing Huang, Mei Xiao, Jingen Xi, Chunping He, Jinlong Zheng, Helong Chen, Jianming Gao, Shiqing Zhang, Weihuai Wu, Yanqiong Liang, Li Xie and Kexian Yi
Genes 2019, 10(2), 103; https://doi.org/10.3390/genes10020103 - 30 Jan 2019
Cited by 25 | Viewed by 4329
Abstract
Agave plants are important crassulacean acid metabolism (CAM) plants with multiple agricultural uses, such as being used in tequila and fiber production. Agave hybrid H11648 ((A. amaniensis Trel. and Nowell × A. angustifolia Haw.) × A. amaniensis) is [...] Read more.
Agave plants are important crassulacean acid metabolism (CAM) plants with multiple agricultural uses, such as being used in tequila and fiber production. Agave hybrid H11648 ((A. amaniensis Trel. and Nowell × A. angustifolia Haw.) × A. amaniensis) is the main cultivated Agave species for fiber production in large tropical areas around the world. In this study, we conducted a transcriptome analysis of A. H11648. About 49.25 million clean reads were obtained by Illumina paired-end sequencing. De novo assembly produced 148,046 unigenes with more than 40% annotated in public databases, or matched homologs in model plants. More homologous gene pairs were found in Asparagus genome than in Arabidopsis or rice, which indicated a close evolutionary relationship between Asparagus and A. H11648. CAM-related gene families were also characterized as previously reported in A. americana. We further identified 12 cellulose synthase genes (CesA) in Asparagus genome and 38 CesA sequences from A. H11648, A. americana, A. deserti and A. tequilana. The full-length CesA genes were used as references for the cloning and assembly of their homologs in other Agave species. As a result, we obtained CesA1/3/4/5/7 genes with full-length coding region in the four Agave species. Phylogenetic and expression analysis revealed a conserved evolutionary pattern, which could not explain the distinct fiber traits in different Agave species. We inferred that transcriptional regulation might be responsible for Agave fiber development. This study represents the transcriptome of A. H11648, which would expand the number of Agave genes and benefit relevant studies of Agave fiber development. Full article
(This article belongs to the Special Issue Genetics, genomics, and evolution of CAM photosynthesis)
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