Gene co-expression network analysis identifies trait-related modules in Arabidopsis thaliana

Liu, Wei; Lin, Liping; Zhang, Zhiyuan; Liu, Siqi; Gao, Kuan; Lv, Yuguang; Huan, Tao; He, Hongwen

doi:10.1007/s00425-019-03102-9

Cited by 32 publications

(23 citation statements)

References 58 publications

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“…Network-based approaches have been proved useful in systems biology, to mine gene function from high-throughput gene expression data. Gene co-expression analysis has become a powerful tool to build transcriptional networks of genes involved in common biological events in plants (Usadel et al, 2009; He and Maslov, 2016; Krishnan et al, 2017; Ma et al, 2018; Yu et al, 2018; Liu et al, 2019). The use of co-expression networks has uncovered candidate genes to regulate biological processes in many plants including wheat (International Wheat Genome Sequencing Consortium, 2018), rice (Aya et al, 2011; Tan et al, 2017), and Arabidopsis thaliana (Costa et al, 2015; Silva et al, 2016).…”

Section: Resultsmentioning

confidence: 99%

“…Those files can be used to investigate the relation between orthologs of MGs within a module and ranked based on the strength of the connection (weight value). Another application of co-expression networks is the identification of previously uncharacterized genes regulating biological processes (Usadel et al, 2009; Aya et al, 2011; Costa et al, 2015; Silva et al, 2016; Krishnan et al, 2017; Tan et al, 2017; International Wheat Genome Sequency Consortium, 2018; Ma et al, 2018; Yu et al, 2018; Liu et al, 2019). Cytoscape 3.7.1 software (Shannon et al, 2003) was therefore used to visualize our network and to show connections between different orthologs of MGs in meiosis-related modules.…”

Section: Resultsmentioning

confidence: 99%

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A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization

et al. 2019

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Polyploidization has played an important role in plant evolution. However, upon polyploidization, the process of meiosis must adapt to ensure the proper segregation of increased numbers of chromosomes to produce balanced gametes. It has been suggested that meiotic gene (MG) duplicates return to a single copy following whole genome duplication to stabilize the polyploid genome. Therefore, upon the polyploidization of wheat, a hexaploid species with three related (homeologous) genomes, the stabilization process may have involved rapid changes in content and expression of MGs on homeologous chromosomes (homeologs). To examine this hypothesis, sets of candidate MGs were identified in wheat using co-expression network analysis and orthology informed approaches. In total, 130 RNA-Seq samples from a range of tissues including wheat meiotic anthers were used to define co-expressed modules of genes. Three modules were significantly correlated with meiotic tissue samples but not with other tissue types. These modules were enriched for GO terms related to cell cycle, DNA replication, and chromatin modification and contained orthologs of known MGs. Overall, 74.4% of genes within these meiosis-related modules had three homeologous copies which was similar to other tissue-related modules. Amongst wheat MGs identified by orthology, rather than co-expression, the majority (93.7%) were either retained in hexaploid wheat at the same number of copies (78.4%) or increased in copy number (15.3%) compared to ancestral wheat species. Furthermore, genes within meiosis-related modules showed more balanced expression levels between homeologs than genes in non-meiosis-related modules. Taken together, our results do not support extensive gene loss nor changes in homeolog expression of MGs upon wheat polyploidization. The construction of the MG co-expression network allowed identification of hub genes and provided key targets for future studies.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization

et al. 2019

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“…We were interested not only in DEGs and tissue-speci c genes but also in co-expressed genes. Gene coexpression has an important impact on biological traits and phenotypic characteristics and has basic functions in plant growth, development, and environmental adaptability [86][87][88]. Co-expressed genes play important roles in the growth and development of moso bamboo [38].…”

Section: Discussionmentioning

confidence: 99%

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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“…As such, co-expression networks have been utilized for functional gene annotation, to identify disease driver genes, and they can be an important step towards identifying regulatory genes [26]. Understanding these networks is also valuable for understanding development and they can provide evidence for differences between cells or tissues [12,17,21].…”

Section: Introductionmentioning

confidence: 99%

The impact of sample size and tissue type on the reproducibility of gene co-expression networks

Ovens¹,

Eames²,

McQuillan³

2020

Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

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Gene co-expression network analysis identifies trait-related modules in Arabidopsis thaliana

Cited by 32 publications

References 58 publications

A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization

A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization

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

The impact of sample size and tissue type on the reproducibility of gene co-expression networks

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