Transcriptomics analyses reveal the molecular roadmap and long non‐coding <scp>RNA</scp> landscape of sperm cell lineage development

Liu, Lingtong; Lu, Yunlong; Wei, Liqin; Yu, Hua; Cao, Yinghao; Li, Yan; Song, Yongxiang; Liang, Chengzhi; Wang, Tai

doi:10.1111/tpj.14041

Cited by 17 publications

(23 citation statements)

References 86 publications

(126 reference statements)

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“…Specifically, for A. thaliana the co-expression network revealed that cluster C5 (sperm) is not well connected with other clusters (Fig. 6b), suggesting that the sperm cell transcriptome is distinctive, confirming earlier observations [58][59][60][61] . The connections between clusters followed a pattern from cluster C0…”

Section: Analysis Of Signaling Network Underpinning Male Gametophytesupporting

confidence: 86%

Comparative transcriptomic analysis reveals conserved transcriptional programs underpinning organogenesis and reproduction in land plants

Julca

Ferrari

Flores-Tornero

et al. 2020

Preprint

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The evolution of plant organs, including leaves, stems, roots, and flowers, mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. Furthermore, the fertilization products of angiosperms, seeds serve as the basis for most of our food. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes, and the development of novel regulatory programs. However, our knowledge of these events is limited, as no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we have generated gene expression atlases for various organs and gametes of 10 plant species comprising bryophytes, vascular plants, gymnosperms, and flowering plants. Comparative analysis of the atlases identified hundreds of organ- and gamete-specific gene families and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, the appearance of organ-specific gene families does not coincide with the corresponding organ's appearance, suggesting that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, suggesting that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function. To provide easy access to the expression atlases and these comparative analyses, we provide an online database, www.evorepro.plant.tools, that allows the exploration of expression profiles, organ-specific genes, phylogenetic trees, co-expression networks, and others.

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Section: Analysis Of Signaling Network Underpinning Male Gametophytesupporting

confidence: 86%

Comparative transcriptomic analysis reveals conserved transcriptional programs underpinning organogenesis and reproduction in land plants

Julca

Ferrari

Flores-Tornero

et al. 2020

Preprint

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“…The asymmetric microspore division accompanies the loss of pluripotency and leads to its daughter cells' distinct fate and identity. Our study has demonstrated that the asymmetric division is followed by global repression of genes associated with cell pluripotency and somatic development (Liu et al ., 2018). Several evidence lines have shown that decreased DNA methylation might promote the microspore's embryogenesis initiation in Brassica and triticale (Solís et al ., 2012, 2015; Nowicka et al ., 2019).…”

Section: Discussionmentioning

confidence: 99%

“…The difference in the identity of the GC and SCs is another concerning issue in reproduction biology. We revealed that the GC and SCs had nearly identical DNA methylome, which is compatible with previous transcriptome and proteome studies that showed that SCs had similar proteome and transcriptome, and almost identical histone profiles with the GC (Zhao et al ., 2013; Yang et al ., 2016; Liu et al ., 2018). These data indicate that the central landscape of molecular features in SCs may have been already established in the GC and is transmitted to SCs via GC mitosis.…”

Section: Discussionmentioning

confidence: 99%

“…Based on our previous RNA‐seq data (Liu et al ., 2018), adapter and quality‐trimmed RNA‐Seq reads were mapped to the tomato reference genome (SL3.0) using bwa (version: 0.7.17‐r1188) guided by ITAG3.2 gene models (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.2_release/ITAG3.2_gene_models.gff) and ITAG3.2_REPET_repeats_agressive.gff (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.2_release/ITAG3.2_REPET_repeats_agressive.gff), respectively. Then, the TPM (transcripts per kilobase million) of genes and TEs were calculated by using stringtie (version: 1.3.4d; Tables S11 and S12).…”

Section: Methodsmentioning

confidence: 99%

“…Based on our previous methods (Lu et al ., 2015; Liu et al ., 2018), we isolated microspores, GCs, SCs and the VC nuclei from tomato for whole‐genome bisulfite sequencing (WGBS). We found that tomato had a higher methylation level than Arabidopsis in all three contexts (CG, CHG and CHH).…”

Section: Introductionmentioning

confidence: 99%

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DNA methylation dynamics of sperm cell lineage development in tomato

Song

Liu

et al. 2020

The Plant Journal

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SUMMARY During the sexual reproduction of higher plants, DNA methylation and transcription are broadly changed to reshape a microspore into two sperm cells (SCs) and a vegetative cell (VC). However, when and how the DNA methylation of SCs is established remains not fully understood. Here we investigate the DNA methylation (5 mC) dynamics of SC lineage and the VC in tomato using whole‐genome bisulfite sequencing. We find the asymmetric division of the microspore gives its two daughter cells differential methylome. Compared with the generative cell (GC), the VC is hypomethylated at CG sites while hypermethylated at CHG and CHH sites, with the majority of differentially methylation regions targeted to transposable elements (TEs). SCs have a nearly identical DNA methylome to the GC, suggesting that the methylation landscape in SCs may be pre‐established following the asymmetric division or inherited from the GC. The random forest classifier for predicting gene and TE expression shows that methylation within the gene body is a more powerful predictor for gene expression. Among all tested samples, gene and TE expression in the microspore may be more predictable by DNA methylation. Our results depict an intact DNA methylome landscape of SC lineage in higher plants, and reveal that the impact of DNA methylation on transcription is variant in different cell types.

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