Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton (Gossypium hirsutum L.)

Li, Yuqing; Qin, Tengfei; Dong, Na; Wei, Chunyan; Zhang, Yaxin; Sun, Rui; Dong, Tingting; Chen, Quanjia; Zhou, Ran; Wang, Qinglian

doi:10.3390/genes10120947

Cited by 18 publications

(22 citation statements)

References 89 publications

(108 reference statements)

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“…2c and d). This phenomenon has also been observed in humans, Sus scrofa, Populus and Gossypium hirsutum [30,34,[72][73][74]. In addition, in the study of maize and red clover, fusion events tended to arise inter-chromosomally rather than intra-chromosomally [22,24].…”

Section: Discussionmentioning

confidence: 64%

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Tu¹,

Shen²,

Wen³

et al. 2020

Preprint

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Background Liriodendron chinense (Hemsl.) Sarg. is an economically and ecologically important deciduous tree species that has been studied for many years. Although the complete L. chinense genome has been sequenced, the gene co-expression modules and tissue-specific genes of L. chinense remain unknown. Results Here, we used the bracts, petals, sepals, stamens, pistils, leaves, and the shoot apex of L. chinense as materials and analysed their gene co-expression modules and tissue-specific genes via hybrid sequencing. We identified 3,032 DEGs between the floral and vegetative tissues and 2,126 tissue-specific genes. By using WGCNA analysis, we identified 13 gene co-expression modules, and KEGG pathway enrichment analysis revealed that tissue-specific genes and genes from different modules were enriched in different pathways. Genes associated with plant defence were highly expressed in the bracts, genes participating in plant hormone signal transduction were highly expressed in the shoot apex, and genes participating in photosynthesis were highly expressed in the leaves, petals and sepals. Moreover, we identified 10 MIKC-type MADS-box genes that were classified as member of the AP3/PI, SVP, SEP, AG/SHP/STK, AGL12, SOC1 and TM8 subfamily. Phylogenetic analysis showed that the expression profiles of these ten genes were consistent with those reported in Arabidopsis and Populus , indicating that these genes are highly conserved evolutionarily and related to floral and vegetative tissue development. The small number of MIKC-type MADS-box genes in L. chinense was probably owing to its incomplete genome annotation. Conclusions In this work, we provided a reference transcriptome for L. chinense research by using hybrid sequencing. We identified 2,126 tissue-specific genes and 3,032 DEGs that contributed greatly to the functional differences between vegetative organs and floral organs. By using WGCNA analysis, 13 gene co-expression modules and 52 hub genes from six co-expression modules of interest were identified. Moreover, we identified 10 MIKC-type MADS-box genes that might be related to the development and growth regulation of floral and vegetative organs. These findings will improve our understanding of gene co-expression, tissue specific genes and flower development model of L. chinense .

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Section: Discussionmentioning

confidence: 64%

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Tu¹,

Shen²,

Wen³

et al. 2020

Preprint

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“…More and more studies had shown that miRNAs play key roles in host‐pathogen interactions by regulating the expression of host immune genes or viral genes, affecting viral replication (Chawla & Sokol, 2011; Kang et al, 2018; Mead & Tu, 2008; Padmanabhan et al, 2009; Simón‐Mateo & García, 2006). Studies have also confirmed that cellular miRNAs and viral miRNAs contribute to host immunity and host–pathogen interaction by regulating the expression of host or pathogen‐related genes in various organisms (Y. Li, Qin, et al, 2019; Ryan & Williams, 2019; Wu et al, 2013, 2016).…”

Section: Discussionmentioning

confidence: 92%

“…Studies have also confirmed that cellular miRNAs and viral miRNAs contribute to host immunity and host-pathogen interaction by regulating the expression of host or pathogen-related genes in various organisms (Y. Li, Qin, et al, 2019;Ryan & Williams, 2019;Wu et al, 2013Wu et al, , 2016.…”

Section: Discussionmentioning

confidence: 93%

Transcriptome of miRNA during inhibition of Bombyx mori nuclear polyhedrosis virus by geldanamycin in BmN cells

Zhao

Yin

Shen

et al. 2022

Arch Insect Biochem Physiol

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Bombyx mori nuclear polyhedrosis virus (BmNPV) is one of several viruses that cause great harm to the sericulture industry, and its pathogenic mechanism is still being explored. Geldanamycin (GA), a kind of HSP90 inhibitor, has been verified to suppress BmNPV proliferation. However, the molecular mechanism by which GA inhibits BmNPV is unclear. MicroRNAs (miRNAs) have been shown to play a key role in regulating virus proliferation and host‐pathogen interactions. In this study, BmN cells infected with BmNPV were treated by GA and DMSO for 72 h, respectively, then transcriptome analysis of miRNA was performed from the GA group and the control group. As a result, a total of 29 miRNAs were differentially expressed (DE), with 13 upregulated and 16 downregulated. Using bioinformatics analysis, it was found that the target genes of DEmiRNAs were involved in ubiquitin‐mediated proteolysis, phagosome, proteasome, endocytosis pathways, and so on. Six DEmiRNAs were verified by quantitative reverse‐transcription polymerase chain reaction. DElong noncoding RNA (DElncRNA)–DEmiRNA–messenger RNA (mRNA) regulatory networks involved in apoptosis and immune pathways were constructed in GA‐treated BmN cells, which included 12 DEmiRNA, 132 DElncRNA, and 69 mRNAs. This regulatory network enriched the functional role of miRNA in the BmNPV‐silkworm interactions and improved our understanding of the molecular mechanism of HSP90 inhibitors on BmNPV proliferation.

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“…Anther development is a multistage and complex process that determines yield and quality of most of the industrial crops. This process is controlled by a complex network of numerous genes [ 24 , 25 ]. With a plethora of plant genomes now sequenced, -omics driven technologies are playing a significant role in the study of the regulatory mechanism of anther development [ 25 , 26 ].…”

Section: Discussionmentioning

confidence: 99%

“…LncRNAs are unravelling as key regulators of plant development [ 50 ], and their role in plant sexual reproduction has been confirmed. For example, lncRNAs related to sexual reproduction have been systematically identified in Gossypium hirsutum [ 24 ], Hordeum vulgare [ 35 ] and Brassica rapa [ 15 ], but their role in the development of male buds of C. oleifera had still remained unknown. Here, we have identified a total of 414 putative lncRNAs in three different development stages of C. oleifera anthers by RNA-seq.…”

Section: Discussionmentioning

confidence: 99%

Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera

Kong

Zhuo

et al. 2022

BMC Genomics

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Background Explored the molecular science of anther development is important for improving productivity and overall yield of crops. Although the role of regulatory RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in regulating anther development has been established, their identities and functions in Camellia oleifera, an important industrial crop, have yet not been clearly explored. Here, we report the identification and characterization of genes, lncRNAs and miRNAs during three stages of the tropical C. oleifera anther development by single-molecule real-time sequencing, RNA sequencing and small RNA sequencing, respectively. Results These stages, viz. the pollen mother cells stage, tetrad stage and uninucleate pollen stage, were identified by analyzing paraffin sections of floral buds during rapid expansion periods. A total of 18,393 transcripts, 414 putative lncRNAs and 372 miRNAs were identified, of which 5,324 genes, 115 lncRNAs, and 44 miRNAs were differentially accumulated across three developmental stages. Of these, 44 and 92 genes were predicted be regulated by 37 and 30 differentially accumulated lncRNAs and miRNAs, respectively. Additionally, 42 differentially accumulated lncRNAs were predicted as targets of 27 miRNAs. Gene ontology enrichment indicated that potential target genes of lncRNAs were enriched in photosystem II, regulation of autophagy and carbohydrate phosphatase activity, which are essential for anther development. Functional annotation of genes targeted by miRNAs indicated that they are relevant to transcription and metabolic processes that play important roles in microspore development. An interaction network was built with 2 lncRNAs, 6 miRNAs and 10 mRNAs. Among these, miR396 and miR156 family were up-regulated, while their targets, genes (GROWTH REGULATING FACTORS and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes) and lncRNAs, were down-regulated. Further, the trans-regulated targets of these lncRNAs, like wall-associated kinase2 and phosphomannose isomerase1, are involved in pollen wall formation during anther development. Conclusions This study unravels lncRNAs, miRNAs and miRNA-lncRNA-mRNA networks involved in development of anthers of the tropical C. oleifera lays a theoretical foundation for further elucidation of regulatory roles of lncRNAs and miRNAs in anther development.

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Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton (Gossypium hirsutum L.)

Cited by 18 publications

References 89 publications

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

Transcriptome of miRNA during inhibition of Bombyx mori nuclear polyhedrosis virus by geldanamycin in BmN cells

Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera

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