Tissue-Specific Transcriptome Analysis Reveals Multiple Responses to Salt Stress in Populus euphratica Seedlings

Yu, Lejun; Ma, Jianchao; Niu, Zhimin; Bai, Xiaotao; Lei, Wenli; Shao, Xuemin; Chen, Ningning; Zhou, Fangfang; Wan, Dongshi

doi:10.3390/genes8120372

Cited by 30 publications

(25 citation statements)

References 69 publications

(83 reference statements)

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“…ABA1 has been implicated in the regulation of xylem fiber differentiation (Campbell et al ., ), but is primarily recognized as a key regulator of ABA‐mediated osmotic stress response (Chen et al ., ; Hernández‐Blanco et al ., ). We therefore investigated the expression of the ERF139 primary targets upon osmotic stress, utilizing publicly available transcriptomic datasets from Populus (Janz et al ., ; Xue et al ., ; Yu et al ., ). Expression of c .…”

Section: Resultsmentioning

confidence: 97%

An AP2/ERF transcription factor ERF139 coordinates xylem cell expansion and secondary cell wall deposition

et al. 2019

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Differentiation of xylem elements involves cell expansion, secondary cell wall (SCW) deposition and programmed cell death. Transitions between these phases require strict spatiotemporal control.The function of Populus ERF139 (Potri.013G101100) in xylem differentiation was characterized in transgenic overexpression and dominant repressor lines of ERF139 in hybrid aspen (Populus tremula 9 tremuloides). Xylem properties, SCW chemistry and downstream targets were analyzed in both types of transgenic trees using microscopy techniques, Fourier transform-infrared spectroscopy, pyrolysis-GC/MS, wet chemistry methods and RNA sequencing.Opposite phenotypes were observed in the secondary xylem vessel sizes and SCW chemistry in the two different types of transgenic trees, supporting the function of ERF139 in suppressing the radial expansion of vessel elements and stimulating accumulation of guaiacyltype lignin and possibly also xylan. Comparative transcriptomics identified genes related to SCW biosynthesis (LAC5, LBD15, MYB86) and salt and drought stress-responsive genes (ANAC002, ABA1) as potential direct targets of ERF139.The phenotypes of the transgenic trees and the stem expression profiles of ERF139 potential target genes support the role of ERF139 as a transcriptional regulator of xylem cell expansion and SCW formation, possibly in response to osmotic changes of the cells.

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Section: Resultsmentioning

confidence: 97%

An AP2/ERF transcription factor ERF139 coordinates xylem cell expansion and secondary cell wall deposition

et al. 2019

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“…Cis-acting elements that are present in the promoter region of XLOC_10 showed that XLOC_10 might be involved in lipid biosynthesis and flowering regulation. consistent for all the selected genes (Yu et al, 2017). Analysis of transcriptome dataset consisting of six major tissues dissected from mid-gestational (TS12) mouse embryos reveals 1375 DEG which are involved in the process of controlling midgestational development.…”

Section: Resultsmentioning

confidence: 99%

IDENTIFICATION OF GENES PREFERENTIALLY EXPRESSED IN MESOCARP TISSUE OF OIL PALM USING in silico ANALYSIS OF TRANSCRIPTS

Badai¹,

KuangLim²,

PekLan³

et al. 2019

JOPR

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Strong demand for palm oil creates a huge challenge for the industry to produce more palm oil on the shrinking cultivable land mass. Genetic manipulation of oil synthesis in the mesocarp tissue of oil palm offers the opportunity to improve yield and quality of palm oil on the limited land resources. However, more than one mesocarp-specific promoters are required to effectively manipulate oil synthesis to avoid epigenetic silencing caused by the sequence homology in their promoter regions. This study was aimed at identifying genes that are specifically expressed in the mesocarp tissue through in silico analysis of transcriptome datasets from different oil palm tissues. From this analysis, transcripts XLOC_10, annotated as pentatricopeptide repeat (PPR) protein was highly expressed in the mesocarp tissue. Gene expression analysis of PPR in 27 tissues of Elaeis guineensis indicated that this putative mesocarp-specific transcript was expressed in mesocarp and female inflorescence tissues only. Cis-acting elements that are present in the promoter region of PPR showed that PPR might be involved in the lipid biosynthesis and flowering regulation network in oil palm.

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“…By analysing the DEGs in the root, researchers revealed the pathway of tanshinone biosynthesis in S. miltiorrhiza [29]. Tissue-speci c genes, play important roles in plant defence, stress response, plant development and material metabolism [41,42,[80][81][82][83]. In Ferula asafetida, genes involved in terpenoid and phenylpropanoid metabolism tended to be expressed in the owers [83].…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, tissue-speci c genes play fundamental roles in tissue differentiation and maintenance [41]. Researchers have found that the divergence of tissue-speci c gene expression patterns modulates ion maintenance in tissues and improves salinity tolerance in Populus euphratica [42]. In pineapple (Ananas comosus), researchers detected 273 tissue-speci c genes, which provided a basis for the study of the genetic mechanisms that regulate fruit phenotypes [43].…”

Section: Introductionmentioning

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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Tissue-Specific Transcriptome Analysis Reveals Multiple Responses to Salt Stress in Populus euphratica Seedlings

Cited by 30 publications

References 69 publications

An AP2/ERF transcription factor ERF139 coordinates xylem cell expansion and secondary cell wall deposition

An AP2/ERF transcription factor ERF139 coordinates xylem cell expansion and secondary cell wall deposition

IDENTIFICATION OF GENES PREFERENTIALLY EXPRESSED IN MESOCARP TISSUE OF OIL PALM USING in silico ANALYSIS OF TRANSCRIPTS

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

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