Genome-wide identification and comparative analysis of MATE gene family in Cucurbitaceae species and their regulatory role in melon (Cucumis melo) under salt stress

Shah, Iftikhar Hussain; Manzoor, Muhammad Aamir; Sabir, Irfan Ali; Ashraf, Muhammad Arslan; Haq, Fazal; Arif, Samiah; Abdullah, Muhammad; Niu, Qingliang; Zhang, Yidong

doi:10.1007/s13580-021-00413-3

Cited by 14 publications

(12 citation statements)

References 94 publications

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“…With the in-depth development of sequencing technology and bioinformatics analysis tools, comparative genomics has been widely used in studies on species evolution and formation, ecological diffusion, habitat adaptation, and antibiotic resistance gene diffusion (Ni 2016 ; Lin et al 2018 ; Qin et al 2021 ; Shah et al 2022 ; Wang et al 2022 ; Yao et al 2022 ). The core genome is generally considered the minimum genome necessary for the survival of free-living organisms (Zafar et al 2002 ; Pandaranayaka et al 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative genomic analysis of five coprinoid mushrooms species

Wang

Zhang

Ding

et al. 2023

Funct Integr Genomics

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Although coprinoid mushrooms are widely known for the phenomenon of deliquescence and production of fungal laccases and extracellular peroxygenases, the genome structure and genetic diversity of coprinoid mushroom species have not been extensively studied. To reveal the genomic structure and diversity in coprinoid mushroom species, the genomes of five coprinoid mushroom species were compared and analyzed. A total of 24,303 orthologous gene families, including 89,462 genes, were identified in the five species. The numbers of core, softcore, dispensable, and private genes were 5617 (25.6%), 1628 (7.4%), 2083 (9.5%), and 12,574 (57.4%), respectively. Differentiation time analysis revealed that Coprinellus micaceus and Coprinellus angulatus differentiated approximately 181.0 million years ago. Coprinopsis cinerea and Coprinopsis marcescibilis differentiated approximately 131.0 million years ago, and they were differentiated from Candolleomyces aberdarensis approximately 176.0 million years ago. Gene family contraction and expansion analyses showed that 1465 genes and 532 gene families were expanded, and 95 genes and 134 gene families were contracted. Ninety-five laccase-coding genes were detected in the five species, and the distribution of the laccase-coding genes in the five species was not uniform. These data provide a reference for a deeper understanding of the genetic structure of the genomes of coprinoid mushroom species. Furthermore, this study provides a reference for follow-up studies on the genome structure of coprinoid mushroom species and the diversity of specific functional genes.

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Section: Discussionmentioning

confidence: 99%

Comparative genomic analysis of five coprinoid mushrooms species

Wang

Zhang

Ding

et al. 2023

Funct Integr Genomics

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“…The three GO terms analyzed, such as biological process, molecular function, and subcellular components, provide an important basic classes (Shah et al, 2022). GO is a standardized functional classification analysis that present information of different genes properties and their products in any organism (Balakrishnan et al, 2013).…”

Section: Discussionmentioning

confidence: 99%

Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis

Liaquat

Munis²,

Arif³

et al. 2022

Front. Plant Sci.

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One of the most diverse protein families, ATP-binding cassette (ABC) transporters, play a role in disease resistance, heavy metal tolerance, and food absorption.Differentially expressed genes contribute in the investigation of plant defense mechanisms under varying stress conditions. To elucidate the molecular mechanisms involved in Mn metal stress, we performed a transcriptomic analysis to explore the differential gene expression in Schima superba with the comparison of control. A total of 79.84 G clean data was generated and 6558 DEGs were identified in response to Mn metal stress. Differentially expressed genes were found to be involved in defense, signaling pathways, oxidative burst, transcription factors and stress responses. Genes important in metal transport were more expressive in Mn stress than control plants. The investigation of cis-acting regions in the ABC family indicated that these genes might be targeted by a large variety of trans-acting elements to control a variety of stress circumstances. Moreover, genes involved in defense responses, the mitogen-activated protein kinase (MAPK) signaling and signal transduction in S. superba were highly induced in Mn stress. Twenty ABC transporters were variably expressed on 1st, 5th, and 10th day of Mn treatment, according to the qRT PCR data. Inclusively, our findings provide an indispensable foundation for an advanced understanding of the metal resistance mechanisms. Our study will enrich the sequence information of S. superba in a public database and would provide a new understanding of the molecular mechanisms of heavy metal tolerance and detoxification.

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“…With the in-depth development of sequencing technology and bioinformatics analysis tools, comparative genomics has been widely used in studies on species evolution and formation, ecological diffusion, habitat adaptation, and antibiotic resistance gene diffusion [22][23][24][25][26][27]. The core genome is generally considered as the minimum genome necessary for the survival of free-living organisms [28,29].…”

Section: Discussionmentioning

confidence: 99%

Comparative genomic analysis of five Coprinus species

Wang

Zhang

Ding

et al. 2022

Preprint

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Background: Although Coprinus is widely known for the phenomenon of deliquescence and production of fungal laccases and extracellular peroxygenases, the genome structure and genetic diversity of Coprinus species have not been extensively studied. To reveal the genomic structure and diversity in Coprinus species, the genomes of five Coprinusspecies were compared and analyzed. Results: A total of 24,303 orthologous gene families, including 89,462 genes, were identified in the five species. The numbers of core, softcore, dispensable, and private genes were 5617 (25.6%), 1628 (7.4%), 2083 (9.5%), and 12574 (57.4%), respectively. Differentiation time analysis revealed that Coprinellus micaceus and Coprinellus angulatusdifferentiated approximately 181.0 million years ago. Coprinopsis cinerea and Coprinopsis marcescibilis differentiated approximately 131.0 million years ago, and they were differentiated from Candolleomyces aberdarensisapproximately 176.0 million years ago. Gene family contraction and expansion analyses showed that 1,465 genes and 532 gene families were expanded, and 95 genes and 134 gene families were contracted. Ninety-five laccase-coding genes were detected in the five species, and the distribution of the laccase-coding genes in the five species was not uniform. Conclusion: These data provide a reference for a deeper understanding of the genetic structure of the genomes of Coprinus species. Furthermore, this study provides a reference for follow-up studies on the genome structure of Coprinus species and the diversity of specific functional genes.

show abstract

Genome-wide identification and comparative analysis of MATE gene family in Cucurbitaceae species and their regulatory role in melon (Cucumis melo) under salt stress

Cited by 14 publications

References 94 publications

Comparative genomic analysis of five coprinoid mushrooms species

Comparative genomic analysis of five coprinoid mushrooms species

Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis

Comparative genomic analysis of five Coprinus species

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