Starch branching enzymes (SBEs) in banana: genome-wide identification and expression analysis reveal their involvement in fruit development, ripening and regulated responses to abiotic/biotic stresses

10.7287/peerj.preprints.27045 ◽

2018 ◽

Author(s):

Hongxia Miao ◽

Peiguang Sun ◽

Jiuhua Liu ◽

Zhiqiang Jin ◽

Biyu Xu

Keyword(s):

Fruit Development ◽

Response Patterns ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses ◽

Genome Wide ◽

Fruit Development And Ripening ◽

Branching Enzymes ◽

Salt And Drought Stress ◽

Temporal And Spatial

Starch branching enzyme (SBE), which is one of the key enzymes associated with amylopectin biosynthesis, plays important roles in variable biological processes. Despite its importance, SBE is rarely studied in the banana (Musa acuminata L.) which is a typical starchy fruit. Here, a family of ten SBE proteins (MaSBE) was firstly identified through genome-wide characterization in M. acuminata, which could be clustered into three subfamilies. Systematic transcriptome analysis revealed temporal and spatial expression variations of MaSBE genes and differential response patterns under abiotic and biotic stresses in both banana genotypes, Fen Jiao (FJ) and BaXi Jiao (BX). Moreover, MaSBE2.4 was temporally regulated during fruit development and ripening as well as in response to various abiotic/biotic stresses in both genotypes. Specifically, MaSBE2.3 expression level was higher in FJ than in BX following cold, salt, and drought stress treatments, and it was specifically induced by fungal infection in BX. Characterization of hormone- and stress-related cis-acting elements in the promoters of MaSBE genes suggests their multiple biological functions. In conclusion, our study provides new insights into the complex transcriptional characteristics of the SBE genes, and demonstrates their crucial roles in improving amylopectin biosynthesis and strengthening stress resistance in banana.

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Genome-wide identification and characterization of long noncoding RNAs involved in apple fruit development and ripening

Scientia Horticulturae ◽

10.1016/j.scienta.2022.110898 ◽

2022 ◽

Vol 295 ◽

pp. 110898

Author(s):

Shicong Wang ◽

Meimiao Guo ◽

Kexin Huang ◽

Qiaoyun Qi ◽

Wenjie Li ◽

...

Keyword(s):

Fruit Development ◽

Noncoding Rnas ◽

Apple Fruit ◽

Long Noncoding Rnas ◽

Genome Wide ◽

Fruit Development And Ripening ◽

Identification And Characterization

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Genome-wide identification and expression profiling of glutathione S-transferase family under multiple abiotic and biotic stresses in Medicago truncatula L.

PLoS ONE ◽

10.1371/journal.pone.0247170 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0247170

Author(s):

Md. Soyib Hasan ◽

Vishal Singh ◽

Shiful Islam ◽

Md. Sifatul Islam ◽

Raju Ahsan ◽

...

Keyword(s):

Medicago Truncatula ◽

Expression Profiling ◽

Developmental Stages ◽

Functional Characterization ◽

Drought Treatment ◽

Specific Expression ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses ◽

Genome Wide

Glutathione transferases (GSTs) constitute an ancient, ubiquitous, multi-functional antioxidant enzyme superfamily that has great importance on cellular detoxification against abiotic and biotic stresses as well as plant development and growth. The present study aimed to a comprehensive genome-wide identification and functional characterization of GST family in one of the economically important legume plants—Medicago truncatula. Here, we have identified a total of ninety-two putative MtGST genes that code for 120 proteins. All these members were classified into twelve classes based on their phylogenetic relationship and the presence of structural conserved domain/motif. Among them, 7 MtGST gene pairs were identified to have segmental duplication. Expression profiling of MtGST transcripts revealed their high level of organ/tissue-specific expression in most of the developmental stages and anatomical tissues. The transcripts of MtGSTU5, MtGSTU8, MtGSTU17, MtGSTU46, and MtGSTU47 showed significant up-regulation in response to various abiotic and biotic stresses. Moreover, transcripts of MtGSTU8, MtGSTU14, MtGSTU28, MtGSTU30, MtGSTU34, MtGSTU46 and MtGSTF8 were found to be highly upregulated in response to drought treatment for 24h and 48h. Among the highly stress-responsive MtGST members, MtGSTU17 showed strong affinity towards its conventional substrates reduced glutathione (GSH) and 1‐chloro‐2,4‐dinitrobenzene (CDNB) with the lowest binding energy of—5.7 kcal/mol and -6.5 kcal/mol, respectively. Furthermore, the substrate-binding site residues of MtGSTU17 were found to be highly conserved. These findings will facilitate the further functional and evolutionary characterization of GST genes in Medicago.

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Genome-wide identification and biochemical characterization of calcineurin B-like calcium sensor proteins in Chlamydomonas reinhardtii

Biochemical Journal ◽

10.1042/bcj20190960 ◽

2020 ◽

Vol 477 (10) ◽

pp. 1879-1892

Author(s):

Manoj Kumar ◽

Komal Sharma ◽

Akhilesh K. Yadav ◽

Kajal Kanchan ◽

Madhu Baghel ◽

...

Keyword(s):

Chlamydomonas Reinhardtii ◽

Biochemical Characterization ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses ◽

Physiological Processes ◽

Calcineurin B ◽

Genome Wide ◽

Dependent Protein ◽

Sensor Proteins

Calcium (Ca2+) signaling is involved in the regulation of diverse biological functions through association with several proteins that enable them to respond to abiotic and biotic stresses. Though Ca2+-dependent signaling has been implicated in the regulation of several physiological processes in Chlamydomonas reinhardtii, Ca2+ sensor proteins are not characterized completely. C. reinhardtii has diverged from land plants lineage, but shares many common genes with animals, particularly those encoding proteins of the eukaryotic flagellum (or cilium) along with the basal body. Calcineurin, a Ca2+/calmodulin-dependent protein phosphatase, is an important effector of Ca2+ signaling in animals, while calcineurin B-like proteins (CBLs) play an important role in Ca2+ sensing and signaling in plants. The present study led to the identification of 13 novel CBL-like Ca2+ sensors in C. reinhardtii genome. One of the archetypical genes of the newly identified candidate, CrCBL-like1 was characterized. The ability of CrCBL-like1 protein to sense as well as bind Ca2+ were validated using two-step Ca2+-binding kinetics. The CrCBL-like1 protein localized around the plasma membrane, basal bodies and in flagella, and interacted with voltage-gated Ca2+ channel protein present abundantly in the flagella, indicating its involvement in the regulation of the Ca2+ concentration for flagellar movement. The CrCBL-like1 transcript and protein expression were also found to respond to abiotic stresses, suggesting its involvement in diverse physiological processes. Thus, the present study identifies novel Ca2+ sensors and sheds light on key players involved in Ca2+signaling in C. reinhardtii, which could further be extrapolated to understand the evolution of Ca2+ mediated signaling in other eukaryotes.

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Characterization of Germin-like Proteins (GLPs) and Their Expression in Response to Abiotic and Biotic Stresses in Cucumber

Horticulturae ◽

10.3390/horticulturae7100412 ◽

2021 ◽

Vol 7 (10) ◽

pp. 412

Author(s):

Liting Liao ◽

Zhaoyang Hu ◽

Shiqiang Liu ◽

Yingui Yang ◽

Yong Zhou

Keyword(s):

Stress Response ◽

Expression Profiles ◽

Tissue Expression ◽

Functional Identification ◽

Abiotic And Biotic Stresses ◽

Biotic Stresses ◽

Genome Wide ◽

Growth Development ◽

Tandem Duplications

Germins and germin-like proteins (GLPs) are glycoproteins closely associated with plant development and stress response in the plant kingdom. Here, we carried out genome-wide identification and expression analysis of the GLP gene family in cucumber to study their possible functions. A total of 38 GLP genes were identified in cucumber, which could be mapped to six out of the seven cucumber chromosomes. A phylogenetic analysis of the GLP members from cucumber, Arabidopsis and rice showed that these GLPs could be divided into six groups, and cucumber GLPs in the same group had highly similar conserved motif distribution and gene structure. Gene duplication analysis revealed that six cucumber GLP genes were located in the segmental duplication regions of cucumber chromosomes, while 14 genes were associated with tandem duplications. Tissue expression profiles of cucumber GLP genes showed that many genes were preferentially expressed in specific tissues. In addition, some cucumber GLP genes were differentially expressed under salt, drought and ABA treatments, as well as under DM inoculation. Our results provide important information for the functional identification of GLP genes in the growth, development and stress response of cucumber.

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Genome-wide identification and characterization of COMT gene family during the development of blueberry fruit

BMC Plant Biology ◽

10.1186/s12870-020-02767-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yushan Liu ◽

Yizhou Wang ◽

Jiabo Pei ◽

Yadong Li ◽

Haiyue Sun

Keyword(s):

Gene Family ◽

Fruit Development ◽

Lignin Content ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Vaccinium Corymbosum ◽

Land Plant ◽

Phylogenetic Structure ◽

Genome Wide

Abstract Background Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and relationship between their expression patterns and the lignin content during fruit development have not clearly investigated by now. Results Ninety-two VcCOMTs were identified in Vaccinium corymbosum. According to phylogenetic analyses, the 92 VcCOMTs were divided into 2 groups. The gene structure and conserved motifs within groups were similar which supported the reliability of the phylogenetic structure groupings. Dispersed duplication (DSD) and whole-genome duplication (WGD) were determined to be the major forces in VcCOMTs evolution. The results showed that the results of qRT-PCR and lignin content for 22 VcCOMTs, VcCOMT40 and VcCOMT92 were related to lignin content at different stages of fruit development of blueberry. Conclusion We identified COMT gene family in blueberry, and performed comparative analyses of the phylogenetic relationships in the 15 species of land plant, and gene duplication patterns of COMT genes in 5 of the 15 species. We found 2 VcCOMTs were highly expressed and their relative contents were similar to the variation trend of lignin content during the development of blueberry fruit. These results provide a clue for further study on the roles of VcCOMTs in the development of blueberry fruit and could promisingly be foundations for breeding blueberry clutivals with higher fruit firmness and longer shelf life.

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PHYTOCHROMES B1/B2 ARE KEY REGULATORS OF EPIGENOME REPROGRAMMING DURING TOMATO FRUIT DEVELOPMENT

10.1101/2020.07.30.227447 ◽

2020 ◽

Author(s):

Ricardo Bianchetti ◽

Nicolas Bellora ◽

Luis A de Haro ◽

Rafael Zuccarelli ◽

Daniele Rosado ◽

...

Keyword(s):

Fruit Development ◽

Epigenetic Modification ◽

Tomato Fruit ◽

Dna Demethylation ◽

Temperature Perception ◽

Genome Wide ◽

Fruit Development And Ripening ◽

Histone Modifying Enzymes ◽

Level Of Understanding ◽

Agronomical Traits

AbstractPhytochrome-mediated light and temperature perception has been shown to be a major regulator of fruit development. Furthermore, chromatin remodelling via DNA demethylation has been described as a crucial mechanism behind the fruit ripening process; however, the molecular basis underlying the triggering of this epigenetic modification remains largely unknown. Here, an integrative analyses of the methylome, siRNAome and transcriptome of tomato fruits from phyA and phyB1B2 null mutants was performed, revealing that PHYB1 and PHYB2 influences genome-wide DNA methylation during fruit development and ripening. The experimental evidence indicates that PHYB1B2 signal transduction relies on a gene expression network that includes chromatin organization factors (DNA methylases/demethylases, histone-modifying enzymes and remodelling factors) and transcriptional regulators, ultimately leading to altered mRNA profile of photosynthetic and ripening-associated genes. This new level of understanding provides insights into the orchestration of epigenetic mechanisms in response to environmental cues affecting agronomical traits in fleshy fruits.

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