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Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii

ABSTRACT: Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii

PROVIDER: PRJNA931986 | ENA |

REPOSITORIES: ENA

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Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii [scRNA-seq]

Project description:Comprehensive utilization of cottonseeds is limited by the presence of pigment gland and its inclusion gossypol. The ideal cotton is glandless-seeds and glanded-plant, a trait found in only few Australian wild cotton species, including Gossypium bickii. Introgressing the trait to cultivated species is proved to be difficult. Understanding the biological processes towards pigment gland morphogenesis and the associated underlying molecular mechanisms will facilitate breeding cultivated cotton varieties with the trait of glandless-seeds and glanded-plant. Single-cell RNA sequencing (scRNA-seq) was performed on 12,222 protoplasts isolated from cotyledons of germinating G. bickii seeds 48-hours after imbibition. Clustered into 14 distinct clusters unsupervisedly, these cells could be grouped into eight cell populations with the assistance of known cell marker genes. The pigment gland cells were well separated from others, and could be separated into pigment gland parenchyma cells, secretory cells, and apoptotic cells. In this study, integrating pigment gland cells developmental trajectory, transcription factors regulatory networks, and core transcription factors functional validation, a relatively complete model was proposed for pigment gland formation. Light and gibberellin were verified to promote the formation of pigment glands. Besides, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11) and GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), were found to affect pigment gland formation. These findings shed new insights into pigment gland morphogenesis and lay the cornerstone for future cotton scRNA-seq investigations.

2023-04-21 | GSE224633 | GEO

Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii [bulk RNA-seq]

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Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii [scRNA-seq]

Project description:Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii [scRNA-seq]

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Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii [bulk RNA-seq]

Project description:Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii [bulk RNA-seq]

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Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-04-21 | GSE224635 | GEO

Gossypium bickii strain:G1-3 PI 530991

Project description:Gossypium bickii strain:G1-3 PI 530991 Raw sequence reads

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A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol.

Project description:The pigment gland is a morphological characteristic of Gossypium and its related genera. Gossypium bickii (G1) is characterized by delayed pigment gland morphogenesis in the cotyledons. In this study, a reference-grade genome of G1 was generated, and comparative genomics analysis showed that G1 was closest to Gossypium australe (G2), followed by A- and D-genome species. Two large fragment translocations in chromosomes 5 and 13 were detected between the G genome and other Gossypium genomes and were unique to the G1 and G2 genomes. Compared with the G2 genome, two large fragment inversions in chromosomes 12 and 13 were detected in G1. According to the phylogeny, divergence time, and similarity analysis of nuclear and chloroplast genomes, G1 was formed by hybridization between Gossypium sturtianum (C1) and a common ancestor of G2 and Gossypium nelsonii (G3). The coordinated expression patterns of pigment gland formation (GoPGF) and gossypol biosynthesis genes in G1 were verified to be consistent with its phenotype, and nine genes that were related to the process of pigment gland formation were identified. A novel gene, GbiCYP76B6, regulated by GoPGF, was found to affect gossypol biosynthesis. These findings offer insights into the origin and evolution of G1 and its mechanism of pigment gland formation and gossypol biosynthesis.

| S-EPMC9860168 | biostudies-literature

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