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Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics 2.0
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Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (15 April 2024) | Viewed by 7262

Special Issue Editors

Dr. Melvin J. Oliver

E-Mail Website
Guest Editor
College of Agriculture, Food & Natural Resources, University of Missouri, Columbia, MO 65211, USA
Interests: abiotic stress; desiccation tolerance; plant physiology; phylogenetics; genomics; transcriptomics; metabolomics
Special Issues, Collections and Topics in MDPI journals
Dr. Bei Gao

E-Mail Website
Guest Editor
State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
Interests: evolutionary genomics; bioinformatics; early land plants; desiccation tolerance
Special Issues, Collections and Topics in MDPI journals
Dr. Moxian Chen

E-Mail Website
Guest Editor
State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, China
Interests: proteogenomics; abiotic stress; post-transcriptional regulation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Post-transcriptional regulations, especially alternative splicing (AS) events, substantially contribute to the complexity of eukaryotic transcriptomes. With the advent of 3rd generation Iso-Seq technology, full-length transcripts could be obtained accurately and efficiently, with or without a reference genome. Investigating alternative splicing events comes to their golden age as high fidelity of Pacbio reads were achieved and the costs became more affordable. We consider that investigating and comparing AS events of genes across lineages or within phylogenetically related species would also be a very interesting topic.

Agricultural productivity has been threatened by the growing climate change problems, so investigating the molecular mechanisms underlying the various kinds of environmental stresses has become an urgent task for crop improvement. A lot of literature has revealed a linkage between AS events and plant stress tolerance. Furthermore, AS mutation has direct effect on animals and approximately 15–35% of human diseases are related to missense mutation of human genes. Thus, AS plays an important role in Kingdom Eukarya.

This Special Issue will focus on the alternative splicing events of genes and their regulation in response to abiotic stress or disease, and their evolution in different genomes. Notwithstanding, contributions on related topics aimed at understanding the biological functions of alternative splicing in plants are also welcomed, including reviews and original research articles.

Dr. Melvin J. Oliver
Dr. Bei Gao
Dr. Moxian Chen
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • alternative splicing
  • Iso-Seq
  • PacBio
  • exon skipping
  • intron retention
  • abiotic stress
  • water deficit
  • desiccation tolerance

Published Papers (5 papers)

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Research

20 pages, 4300 KiB  
Article
Identification and Alternative Splicing Profile of the Raffinose synthase Gene in Grass Species
by Junhao Xu, Xiangkai You, Yanan Leng, Youyue Li, Zeyu Lu, Yinan Huang, Moxian Chen, Jianhua Zhang, Tao Song and Tieyuan Liu
Int. J. Mol. Sci. 2023, 24(13), 11120; https://doi.org/10.3390/ijms241311120 - 05 Jul 2023
Cited by 1 | Viewed by 1181
Abstract
Raffinose synthase (Rafs) is an important enzyme in the synthesis pathway of raffinose from sucrose and galactinol in higher plants and is involved in the regulation of seed development and plant responses to abiotic stresses. In this study, we analyzed the [...] Read more.
Raffinose synthase (Rafs) is an important enzyme in the synthesis pathway of raffinose from sucrose and galactinol in higher plants and is involved in the regulation of seed development and plant responses to abiotic stresses. In this study, we analyzed the Rafs families and profiled their alternative splicing patterns at the genome-wide scale from 10 grass species representing crops and grasses. A total of 73 Rafs genes were identified from grass species such as rice, maize, foxtail millet, and switchgrass. These Rafs genes were assigned to six groups based the phylogenetic analysis. We compared the gene structures, protein domains, and expression patterns of Rafs genes, and also unraveled the alternative transcripts of them. In addition, different conserved sequences were observed at these putative splice sites among grass species. The subcellular localization of PvRafs5 suggested that the Rafs gene was expressed in the cytoplasm or cell membrane. Our findings provide comprehensive knowledge of the Rafs families in terms of genes and proteins, which will facilitate further functional characterization in grass species in response to abiotic stress. Full article
(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics 2.0)
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14 pages, 3460 KiB  
Article
Alternative Splicing Analysis Revealed the Role of Alpha-Linolenic Acid and Carotenoids in Fruit Development of Osmanthus fragrans
by Cancan Ma, Cheng Zhang, Xiaoyan Wang, Fuyuan Zhu, Xianrong Wang, Min Zhang and Yifan Duan
Int. J. Mol. Sci. 2023, 24(10), 8666; https://doi.org/10.3390/ijms24108666 - 12 May 2023
Viewed by 1093
Abstract
Alternative splicing refers to the process of producing different splicing isoforms from the same pre-mRNA through different alternative splicing events, which almost participates in all stages of plant growth and development. In order to understand its role in the fruit development of Osmanthus [...] Read more.
Alternative splicing refers to the process of producing different splicing isoforms from the same pre-mRNA through different alternative splicing events, which almost participates in all stages of plant growth and development. In order to understand its role in the fruit development of Osmanthus fragrans, transcriptome sequencing and alternative splicing analysis was carried out on three stages of O. fragrans fruit (O. fragrans “Zi Yingui”). The results showed that the proportion of skipping exon events was the highest in all three periods, followed by a retained intron, and the proportion of mutually exclusive exon events was the lowest and most of the alternative splicing events occurred in the first two periods. The results of enrichment analysis of differentially expressed genes and differentially expressed isoforms showed that alpha-Linolenic acid metabolism, flavonoid biosynthesis, carotenoid biosynthesis, photosynthesis, and photosynthetic-antenna protein pathways were significantly enriched, which may play an important role in the fruit development of O. fragrans. The results of this study lay the foundation for further study of the development and maturation of O. fragrans fruit and further ideas for controlling fruit color and improving fruit quality and appearance. Full article
(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics 2.0)
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16 pages, 3445 KiB  
Article
Identification of Photosynthesis Characteristics and Chlorophyll Metabolism in Leaves of Citrus Cultivar (Harumi) with Varying Degrees of Chlorosis
by Bo Xiong, Ling Li, Qin Li, Huiqiong Mao, Lixinyi Wang, Yuhui Bie, Xin Zeng, Ling Liao, Xun Wang, Honghong Deng, Mingfei Zhang, Guochao Sun and Zhihui Wang
Int. J. Mol. Sci. 2023, 24(9), 8394; https://doi.org/10.3390/ijms24098394 - 07 May 2023
Cited by 4 | Viewed by 1904
Abstract
In autumn and spring, citrus leaves with a Ponkan (Citrus reticulata Blanco cv. Ponkan) genetic background (Harumi, Daya, etc.) are prone to abnormal physiological chlorosis. The effects of different degrees of chlorosis (normal, mild, moderate and severe) on photosynthesis [...] Read more.
In autumn and spring, citrus leaves with a Ponkan (Citrus reticulata Blanco cv. Ponkan) genetic background (Harumi, Daya, etc.) are prone to abnormal physiological chlorosis. The effects of different degrees of chlorosis (normal, mild, moderate and severe) on photosynthesis and the chlorophyll metabolism of leaves of Citrus cultivar (Harumi) were studied via field experiment. Compared with severe chlorotic leaves, the results showed that chlorosis could break leaf metabolism balance, including reduced chlorophyll content, photosynthetic parameters, antioxidant enzyme activity and enzyme activity related to chlorophyll synthesis, increased catalase and decreased enzyme activity. In addition, the content of chlorophyll synthesis precursors showed an overall downward trend expected for uroporphyrinogen III. Furthermore, the relative expression of genes for chlorophyll synthesis (HEMA1, HEME2, HEMG1 and CHLH) was down-regulated to some extent and chlorophyll degradation (CAO, CLH, PPH, PAO and SGR) showed the opposite trend with increased chlorosis. Changes in degradation were more significant. In general, the chlorosis of Harumi leaves might be related to the blocked transformation of uroporphyrinogen III (Urogen III) to coproporphyrinogen III (Coprogen III), the weakening of antioxidant enzyme system activity, the weakening of chlorophyll synthesis and the enhancement in degradation. Full article
(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics 2.0)
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18 pages, 2927 KiB  
Article
Global Analysis of Dark- and Heat-Regulated Alternative Splicing in Arabidopsis
by Di Zhang, Mo-Xian Chen, Mehtab Muhammad Aslam, Ying-Gao Liu and Jianhua Zhang
Int. J. Mol. Sci. 2023, 24(6), 5299; https://doi.org/10.3390/ijms24065299 - 10 Mar 2023
Viewed by 1266
Abstract
Alternative splicing (AS) is one of the major post-transcriptional regulation mechanisms that contributes to plant responses to various environmental perturbations. Darkness and heat are two common abiotic factors affecting plant growth, yet the involvement and regulation of AS in the plant responses to [...] Read more.
Alternative splicing (AS) is one of the major post-transcriptional regulation mechanisms that contributes to plant responses to various environmental perturbations. Darkness and heat are two common abiotic factors affecting plant growth, yet the involvement and regulation of AS in the plant responses to these signals remain insufficiently examined. In this study, we subjected Arabidopsis seedlings to 6 h of darkness or heat stress and analyzed their transcriptome through short-read RNA sequencing. We revealed that both treatments altered the transcription and AS of a subset of genes yet with different mechanisms. Dark-regulated AS events were found enriched in photosynthesis and light signaling pathways, while heat-regulated AS events were enriched in responses to abiotic stresses but not in heat-responsive genes, which responded primarily through transcriptional regulation. The AS of splicing-related genes (SRGs) was susceptible to both treatments; while dark treatment mostly regulated the AS of these genes, heat had a strong effect on both their transcription and AS. PCR analysis showed that the AS of the Serine/Arginine-rich family gene SR30 was reversely regulated by dark and heat, and heat induced the upregulation of multiple minor SR30 isoforms with intron retention. Our results suggest that AS participates in plant responses to these two abiotic signals and reveal the regulation of splicing regulators during these processes. Full article
(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics 2.0)
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22 pages, 7615 KiB  
Article
Phylogenetic Analysis of Spliceosome SF3a2 in Different Plant Species
by Yuan Tian, Debatosh Das, Min Li, Tao Song, Jingfang Yang and Yinggao Liu
Int. J. Mol. Sci. 2023, 24(6), 5232; https://doi.org/10.3390/ijms24065232 - 09 Mar 2023
Cited by 1 | Viewed by 1234
Abstract
The formation of mature mRNA requires cutting introns and splicing exons. The occurrence of splicing involves the participation of the spliceosome. Common spliceosomes mainly include five snRNPs: U1, U2, U4/U6, and U5. SF3a2, an essential component of spliceosome U2 snRNP, participates in [...] Read more.
The formation of mature mRNA requires cutting introns and splicing exons. The occurrence of splicing involves the participation of the spliceosome. Common spliceosomes mainly include five snRNPs: U1, U2, U4/U6, and U5. SF3a2, an essential component of spliceosome U2 snRNP, participates in splicing a series of genes. There is no definition of SF3a2 in plants. The paper elaborated on SF3a2s from a series of plants through protein sequence similarity. We constructed the evolutionary relationship of SF3a2s in plants. Moreover, we analyzed the similarities and differences in gene structure, protein structure, the cis-element of the promoter, and expression pattern; we predicted their interacting proteins and constructed their collinearity. We have preliminarily analyzed SF3a2s in plants and clarified the evolutionary relationship between different species; these studies can better serve for in-depth research on the members of the spliceosome in plants. Full article
(This article belongs to the Special Issue Alternative Splicing: From Abiotic Stress Tolerance to Evolutionary Genomics 2.0)
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