Genomics

Dataset Information

32

Transcriptomic analysis of tomato sperm cell lineage development


ABSTRACT: Sperm cell (SC) lineage development from the haploid microspore to SCs represents a unique biological process. We isolated tomato (Solanum lycopersicum) microspores, generative cells and sperm cells, and performed the genome-wide transcriptomic analysis of lncRNAs and mRNAs. SC lineage development involves global repression of genes for pluripotency, somatic development and metabolism following microspore asymmetric division and coordinated upregulation of GC/SC preferential genes. This process is accompanied by progressive loss of the active marks H3K4me3 and H3K9ac, and accumulation of the repressive marks H3K9 methylation. The SC lineage has a higher ratio of lncRNAs to mRNAs and preferentially expresses a larger percentage of lncRNAs than does the non-SC lineage. A co-expression network showed that the largest set of lncRNAs in these nodes, with more than 100 links, are GC-preferential, and a small portion of lncRNAs co-express with their neighboring genes. Single molecular FISH showed that several candidate genes may be markers distinguishing the three cell types of the SC lineage. Our findings reveal the molecular programming and potential roles of lncRNAs for SC lineage development. Overall design: Seven cell types were examined, including microspores, generative cells, sperm cells, callus, fully expanded leaves, pistil and mature pollen grain (MPG). Each cell type has three biological replicates.

INSTRUMENT(S): Illumina HiSeq 2000 (Solanum lycopersicum)

ORGANISM(S): Solanum lycopersicum  

SUBMITTER: Tai Wang  

PROVIDER: GSE117185 | GEO | 2018-07-27

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE117185_List_of_expressed_mRNAs_and_lncRNAs.txt.gz Txt
GSE117185_tomato_wlq_IGDBV1.gene.fasta.gz Fasta.gz
GSE117185_tomato_wlq_IGDBV1.gff.gz Other
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Publications

Transcriptomics analyses reveal the molecular roadmap and long non-coding RNA landscape of sperm cell lineage development.

Liu Lingtong L   Lu Yunlong Y   Wei Liqin L   Yu Hua H   Cao Yinghao Y   Li Yan Y   Yang Ning N   Song Yunyun Y   Liang Chengzhi C   Wang Tai T  

The Plant journal : for cell and molecular biology 20180827 2


Sperm cell (SC) lineage development from the haploid microspore to SCs represents a unique biological process in which the microspore generates a larger vegetative cell (VC) and a smaller generative cell (GC) enclosed in the VC, then the GC further develops to functionally specified SCs in the VC for double fertilization. Understanding the mechanisms of SC lineage development remains a critical goal in plant biology. We isolated individual cells of the three cell types, and characterized the gen  ...[more]

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