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Genome-wide analysis of PmTCP4 transcription factor binding sites by ChIP-Seq during pistil abortion in Japanese apricot

ABSTRACT: Genome-wide analysis of PmTCP4 transcription factor binding sites by ChIP-Seq during pistil abortion in Japanese apricot

PROVIDER: PRJNA549669 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9327210.fastq.gz	Fastqsanger.gz
	SRR9327220.fastq.gz	Fastqsanger.gz
	SRR9327211.fastq.gz	Fastqsanger.gz
	SRR9327221.fastq.gz	Fastqsanger.gz
	SRR9327212.fastq.gz	Fastqsanger.gz

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Genome-wide analysis of PmTCP4 transcription factor binding sites by ChIP-Seq during pistil abortion in Japanese apricot

Project description:The TCP4 transcription factor plays an important role in plant growth and development, especially in flower development. PmTCP4 is involved in the process of pistil abortion in Japanese apricot, but its molecular mechanism, particularly the DNA binding sites and co-regulatory genes, are quite unknown. Therefore, to identify the genome-wide binding sites of PmTCP4 transcription factors and their co-regulatory genes, chromatin immunoprecipitation sequencing (ChIPSeq) was carried out. ChIP-Seq data produced the maximum enriched peaks in two Japanese apricot cultivars ‘Daqiandi’ (DQD) and ‘Longyan’ (LY), which showed that the majority ofDNA-protein interactions are relevant and have a significant function in binding sites. Moreover, 720 and 251 peak-associated genes regulated by PmTCP4 were identified in DQD and LY, respectively, and most of them were involved in the flower and pistil development process. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis and oxidative phosphorylation were the most enriched pathways in both cultivars and all identified genes related to these pathways were down-regulated. This study will provide a reference for a better understanding of the PmTCP4 regulatory mechanism during pistil abortion in Japanese apricot.

2020-09-06 | GSE132994 | GEO

Comprehensive transcriptome analysis provides novel insight into pistil abortion mechanism in Japanese apricot

Project description:Flower development is a key stage in the life cycle of fruit trees and its proper development is considered its reproductive success. Pistil abortion is a widely distributed phenomenon in fruit plants and its mechanism in Japanese apricot is quite unclear. The present study was carried out to get a deep insight about the regulatory mechanism of pistil abortion in Japanese apricot using transcriptomic approach. A large number of DEGs (24,683) were identified in normal (N) and abortive pistil stages i.e. style browning (STYB), stigma browning (STIB) and ovary browning (OVB). Pair-wise comparison analysis was performed as N vs STYB, N vs STIB, N vs OVB and STIB vs OVB, and produced 9592, 8691, 8660 and 8103 transcripts, respectively. The Gene Ontology (GO) showed that different metabolic processes, plant hormones, flower development and photosystem related genes were involved in pistil abortion. The pathway analysis revealed that plant hormones signal transduction and circadian rhythm pathways were found significantly enriched. Furthermore, transcription factors such as MYB, MADS-box and NAC family remained highly expressed. Maximum number of the genes were grouped to cluster 11, and were highly expressed at OVB stage, suggesting that this stage might be critical for pistil abortion. This study provides an alternatives to be consider for further studies and understanding of pistil abortion processes in Japanese apricot, and provide a reference related to this issue for other deciduous fruit crops.

2021-06-28 | GSE141096 | GEO

Comprehensive transcriptome analysis provides novel insight into pistil abortion mechanism in Japanese apricot

Project description:Comprehensive transcriptome analysis provides novel insight into pistil abortion mechanism in Japanese apricot

| PRJNA592066 | ENA

Transcriptomic analysis reveals genes releated to pistil abortion in Prunus sibirica

Project description:Pistil development is an important developmental process that directly affects the yield of Prunus sibirica. Through transcriptome sequencing analysis of clones with abortive pistil (No. 595) and normal pistil (No. 28) of Prunus sibirica, a total of 1950 significantly differentially expressed genes were obtained, among which 1000 genes were up-regulated and 950 genes were down-regulated. The results provide a theoretical basis for further investigation of the formation mechanism of pistil abortion.

2022-07-06 | GSE192952 | GEO

Transcriptome Profile Analysis Reveals the Regulation Mechanism of Pistil Abortion in Handeliodendron bodinieri

Project description:To elucidate the molecular mechanism of pistils abortion underlying sex differentiation from transcriptomic aspects in Handeliodendron bodinieri, we use abnormal pistils before and after abortion in male flowers and normal pistils in female flowers at the same stage as control material. Key genes regulating pistil abortion was identified by using RNA-seq technique. The results show that it was abortion from the two-nucleate embryo sac to four-nucleate embryo sac at stage one (the diameters of the flower buds were 1.3–1.6 mm), at the same time, 12 genes related to ovule development, such as INO, BEL1, and CRC, 24 genes related to plant hormones, such as AHP6, ARF, ERF, and GID1, and 12 genes related the ROS, such as POD, SOD, CAT and RBOH might be involved in the regulation of pistil abortion. Therefore, this study will provide a theoretical foundation for the conservation, breeding, and application of H. bodinieri in the future.

2025-09-19 | GSE213668 | GEO

Mutation of STERILE APETALA, a transcriptional regulator, is involved in pistil abortion and organ size in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Project description:Pistil development is a complicated process in plants, and female sterile mutant is an ideal material for screening and cloning the pistil development-related genes. In our previous study, a female sterile mutant fsm (namely fsm1 here) was obtained from a Chinese cabbage DH line ‘FT’ using a combination of isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. BraA04g009730.3C was predicted as the candidate gene for mutant fsm1. BraA04g009730.3C encoded STERILE APETALA (SAP), a transcriptional regulator, which played a role in regulating floral organ development. In this study, another female sterile mutant (namely fsm2) was derived from a population combining EMS mutagenesis and germinating seeds of ‘FT’. The phenotype of mutant fsm2 was consistent with that of fsm1, exhibiting pistil abortion, and smaller floral organs. Genetic analysis indicated that the phenotype of mutant fsm2 was controlled by a single recessive nuclear gene. Allelism testing showed that the mutant genes of fsm1 and fsm2 were allelic, named as Brfsm. A single-nucleotide mutation (G-to-A) in the first exon of BraA04g009730.3C caused a missense mutation from GAA (glutamic acid) to GGA (glycine) in mutant fsm2. Comparative transcriptome analysis on the pistils of wild-type ‘FT’ and mutant fsm1 revealed that a total of 3,855 differentially expressed genes (DEGs) were obtained, among which 29 genes related to ovule development and 16 genes related to organ size were identified. Based on the validation of qRT-PCR, we proposed the possible regulatory pathways whereby SAP may mediate pistil development in the fsm mutant. The mutation of BraA04g009730.3C in fsm plants was involved in the pistil abortion and smaller floral organ in Chinese cabbage. These results lay a solid foundation for elucidating the molecular mechanism of pistil development in Chinese cabbage.

2020-03-25 | GSE147438 | GEO

Analyzing Differentially Expressed Genes and Pathways Associated with Pistil Abortion in Japanese Apricot via RNA-Seq.

Project description:Reproduction is a critical stage in the flower development process, and its failure causes serious problems affecting fruit quality and yield. Pistil abortion is one of the main factors in unsuccessful reproduction and occurs in many fruit plants. In Japanese apricot, the problem of pistil abortion is very common and affects fruit quality and plant yield; however, its molecular mechanism is not clearly understood. Therefore, in the current study, we used RNA-Seq to identify the differentially expressed genes (DEGs) and pathways actively involved in pistil abortion. A total of 3882 differentially expressed genes were found after cutoff and pairwise comparison analysis. According to KEGG pathway analysis, plant hormone signaling transduction and metabolic pathways were found most significantly enriched in this study. A total of 60 transcription factor families such as MADS-box, NAC and TCP showed their role in this process. RT-qPCR assays confirmed that the expression levels were consistent with RNA-Seq results. This study provides an alternative to be considered for further studies and understanding of pistil abortion processes in Japanese apricot, and it provides a reference related to this issue for other deciduous fruit crops.

| S-EPMC7565994 | biostudies-literature

Transcriptomic analysis reveals genes releated to pistil abortion in Prunus sibirica

Project description:Transcriptomic analysis reveals genes releated to pistil abortion in Prunus sibirica

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Identification of differentially-expressed genes associated with pistil abortion in Japanese apricot by genome-wide transcriptional analysis.

Project description:The phenomenon of pistil abortion widely occurs in Japanese apricot, and imperfect flowers with pistil abortion seriously decrease the yield in production. Although transcriptome analyses have been extensively studied in the past, a systematic study of differential gene expression has not been performed in Japanese apricot. To investigate genes related to the pistil development of Japanese apricot, high-throughput sequencing technology (Illumina) was employed to survey gene expression profiles from perfect and imperfect Japanese apricot flower buds. 3,476,249 and 3,580,677 tags were sequenced from two libraries constructed from perfect and imperfect flower buds of Japanese apricot, respectively. There were 689 significant differentially-expressed genes between the two libraries. GO annotation revealed that highly ranked genes were those implicated in small molecule metabolism, cellular component organisation or biogenesis at the cellular level and fatty acid metabolism. According to the results, we assumed that late embryogenesis abundant protein (LEA), Dicer-like 3 (DCL3) Xyloglucan endotransglucosylase/hydrolase 2 (XTH2), Pectin lyase-like superfamily protein (PPME1), Lipid transfer protein 3 (LTP3), Fatty acid biosynthesis 1 (FAB1) and Fatty acid desaturase 5 (FAD5) might have relationships with the pistil abortion in Japanese apricot. The expression patterns of 36 differentially expressed genes were confirmed by real-time (RT)-PCR. This is the first report of the Illumina RNA-seq technique being used for the analysis of differentially-expressed gene profiles related to pistil abortion that both computationally and experimentally provides valuable information for the further functional characterisation of genes associated with pistil development in woody plants.

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Transcriptome Profile Analysis Reveals the Regulation Mechanism of Pistil Abortion in Handeliodendron bodinieri

Project description:Transcriptome Profile Analysis Reveals the Regulation Mechanism of Pistil Abortion in Handeliodendron bodinieri

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