Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato

He, Pei-Wen; Zhang, Jingzhen; Lv, Zunfu; Cui, Peng; Xu, Xinlan; George, Melvin S.; Lu, Guoquan

doi:10.1186/s12870-023-04272-1

Cited by 8 publications

(4 citation statements)

References 60 publications

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“…Using the Ibactin gene as an internal reference, Supplementary Table S5 lists the primer sequences of the examined genes. The experiment was repeated 3 times, and the data was calculated using the 2 -△△CT method ( He et al., 2023 ).…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification of the C2H2 zinc finger gene family and expression analysis under salt stress in sweetpotato

Du,

Zhou,

Qin

et al. 2023

Front. Plant Sci.

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IntroductionThe higher plant transcription factor C2H2 zinc finger protein (C2H2-ZFP) is essential for plant growth, development, and stress response. There are limited studies on C2H2-ZFP genes in sweetpotato, despite a substantial number of C2H2-ZFP genes having been systematically found in plants.MethodsIn this work, 178 C2H2-ZFP genes were found in sweetpotato, distributed randomly on 15 chromosomes, and given new names according to where they were located. These members of the zinc finger gene family are separated into six branches, as shown by the phylogenetic tree. 24 tandem repeats of IbZFP genes and 46 fragment repeats were identified, and a homology study revealed that IbZFP genes linked more regions with wild relative species of sweetpotato as well as rhizome plants like potato and cassava. And we analyzed the expression patterns of IbZFP genes during the early development of sweetpotato storage roots (SRs) and salt stress using transcriptome data, and identified 44 IbZFP genes that exhibited differences in expression levels during the early expansion of sweetpotato SRs in different varieties, and 92 IbZFP genes that exhibited differences in expression levels under salt stress in salt tolerant and salt sensitive sweetpotato varieties. Additionally, we cloned six IbZFP genes in sweetpotato and analyzed their expression patterns in different tissues, their expression patterns under abiotic stress and hormone treatment, and subcellular localization.Results and discussionThe results showed that the IbZFP genes had tissue specificity in sweetpotato and were induced to varying degrees by drought and salt stress. ABA and GA3 treatments also affected the expression of the IbZFP genes. We selected IbZFP105, which showed significant differences in expression levels under salt stress and ABA treatment, to be heterologously expressed in Arabidopsis thaliana. We found that IbZFP105 OE lines exhibited higher tolerance to salt stress and ABA stress. This indicates that IbZFP105 can enhance the salt tolerance of plants. These results systematically identified the evolution and expression patterns of members of the C2H2-ZFP gene family in sweetpotato, providing a theoretical basis for studying the role of IbZFP genes in the development of sweetpotato SRs and in resistance to stress.

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Section: Methodsmentioning

confidence: 99%

Genome-wide identification of the C2H2 zinc finger gene family and expression analysis under salt stress in sweetpotato

Du,

Zhou,

Qin

et al. 2023

Front. Plant Sci.

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“…The direct cause of plant organ abscission is the degradation of the cell wall, which in turn is due to several associated cellulases ( Wang et al, 2023 ; Li et al, 2019 ), pectinases ( Bai et al, 2023 ), peroxidases ( Djanaguiraman et al, 2010 ), polygalacturonases ( Hu et al, 2023 ; He et al, 2023 ; Bonghi et al, 1992 ), xyloglucan endoglucan transglucosylase/hydrolyzing enzymes ( Wang et al, 2022 ; Niederhuth, Patharkar & Walker, 2013 ), and extender proteins that lead to the disruption of cell-to-cell adhesion ( Patharkar & Walker, 2018 ; Botton & Ruperti, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome differential expression analysis of defoliation of two different lemon varieties

Dong,

Yin,

Gao

et al. 2024

PeerJ

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‘Allen Eureka’ is a bud variety of Eureka lemon with excellent fruiting traits. However, it suffers from severe winter defoliation that leads to a large loss of organic nutrients and seriously affects the tree’s growth and development as well as the yield of the following year, and the mechanism of its response to defoliation is still unclear. In order to investigate the molecular regulatory mechanisms of different leaf abscission periods in lemon, two lemon cultivars (‘Allen Eureka’ and ‘Yunning No. 1’) with different defoliation traits were used as materials. The petiole abscission zone (AZ) was collected at three different defoliation stages, namely, the pre-defoliation stage (CQ), the mid-defoliation stage (CZ), and the post-defoliation stage (CH). Transcriptome sequencing was performed to analyze the gene expression differences between these two cultivars. A total of 898, 4,856, and 3,126 differentially expressed genes (DEGs) were obtained in CQ, CZ, and CH, respectively, and the number of DEGs in CZ was the largest. GO analysis revealed that the DEGs between the two cultivars were mainly enriched in processes related to oxidoreductase, hydrolase, DNA binding transcription factor, and transcription regulator activity in the defoliation stages. KEGG analysis showed that the DEGs were concentrated in CZ and involved plant hormone signal transduction, phenylpropanoid biosynthesis, glutathione metabolism, and alpha-linolenic acid metabolism. The expression trends of some DEGs suggested their roles in regulating defoliation in lemon. Eight gene families were obtained by combining DEG clustering analysis and weighted gene co-expression network analysis (WGCNA), including β-glucosidase, AUX/IAA, SAUR, GH3, POD, and WRKY, suggesting that these genes may be involved in the regulation of lemon leaf abscission. The above conclusions enrich the research related to lemon leaf abscission and provide reliable data for the screening of lemon defoliation candidate genes and analysis of defoliation pathways.

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“…It is known for its high yield, strong adaptability, and wide cultivation areas, making it a significant staple crop and industrial raw material [ 23 , 24 ]. The completion of the genome sequencing of sweet potato ( I. batatas (L.) Lam., 2n = B 1 B 1 B 2 B 2 B 2 B 2 = 6x = 90) [ 25 ] and its two diploid species, I. trifida NCNSP0306 (2n = 2x = 30) and I. triloba NCNSP0323 (2n = 2x = 30) [ 26 ], has made it possible to analyze the sweet potato gene family using bioinformatics [ 27 , 28 , 29 , 30 , 31 , 32 ]. However, the DA1-like gene family in sweet potatoes has not been reported in these whole-genome studies.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of the DA1 Gene Family in Sweet Potato and Its Two Diploid Relatives

Zhou,

Huang,

Wang

et al. 2024

IJMS

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The DA1-like gene family plays a crucial role in regulating seed and organ size in plants. The DA1 gene family has been identified in several species but has not yet been reported in sweet potatoes. In this study, nine, eleven, and seven DA1s were identified in cultivated sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid wild relatives, I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30), respectively. The DA1 genes were classified into three subgroups based on their phylogenetic relationships with Arabidopsis thaliana and Oryza sativa (rice). Their protein physiological properties, chromosomal localization, phylogenetic relationships, gene structure, promoter cis-elements, and expression patterns were systematically analyzed. The qRT-PCR results showed that the expression levels of four genes, IbDA1-1, IbDA1-3, IbDA1-6, and IbDA1-7, were higher in the sweet potato leaves than in the roots, fiber roots, and stems. In our study, we provide a comprehensive comparison and further the knowledge of DA1-like genes in sweet potatoes, and provide a theoretical basis for functional studies.

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Genome-wide identification and expression analysis of the polygalacturonase gene family in sweetpotato

Cited by 8 publications

References 60 publications

Genome-wide identification of the C2H2 zinc finger gene family and expression analysis under salt stress in sweetpotato

Genome-wide identification of the C2H2 zinc finger gene family and expression analysis under salt stress in sweetpotato

Transcriptome differential expression analysis of defoliation of two different lemon varieties

Genome-Wide Identification and Expression Analysis of the DA1 Gene Family in Sweet Potato and Its Two Diploid Relatives

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