Dataset Information

Integrated Genomic and Transcriptomic Elucidation of Flowering in Garlic.

ABSTRACT: Commercial cultivars of garlic are sterile, and therefore efficient breeding of this crop is impossible. Recent restoration of garlic fertility has opened new options for seed production and hybridization. Transcriptome catalogs were employed as a basis for garlic genetic studies, and in 2020 the huge genome of garlic was fully sequenced. We provide conjoint genomic and transcriptome analysis of the regulatory network in flowering garlic genotypes. The genome analysis revealed phosphatidylethanolamine-binding proteins (PEBP) and LEAFY (LFY) genes that were not found at the transcriptome level. Functions of TFL-like genes were reduced and replaced by FT-like homologs, whereas homologs of MFT-like genes were not found. The discovery of three sequences of LFY-like genes in the garlic genome and confirmation of their alternative splicing suggest their role in garlic florogenesis. It is not yet clear whether AsLFY1 acts alone as the "pioneer transcription factor" or AsLFY2 also provides these functions. The presence of several orthologs of flowering genes that differ in their expression and co-expression network advocates ongoing evolution in the garlic genome and diversification of gene functions. We propose that the process of fertility deprivation in garlic cultivars is based on the loss of transcriptional functions of the specific genes.

SUBMITTER: Shemesh-Mayer E

PROVIDER: S-EPMC9698152 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Integrated Genomic and Transcriptomic Elucidation of Flowering in Garlic.

Shemesh-Mayer Einat E Faigenboim Adi A Ben Michael Tomer E TE Kamenetsky-Goldstein Rina R

International journal of molecular sciences 20221110 22

Commercial cultivars of garlic are sterile, and therefore efficient breeding of this crop is impossible. Recent restoration of garlic fertility has opened new options for seed production and hybridization. Transcriptome catalogs were employed as a basis for garlic genetic studies, and in 2020 the huge genome of garlic was fully sequenced. We provide conjoint genomic and transcriptome analysis of the regulatory network in flowering garlic genotypes. The genome analysis revealed phosphatidylethano ...[more]

PMID: 36430354

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Project description:BackgroundTreating patients with advanced sarcomas is challenging due to great histologic diversity among its subtypes. Leiomyosarcoma (LMS) and de-differentiated liposarcoma (DDLPS) are two common and aggressive subtypes of soft tissue sarcoma (STS). They differ significantly in histology and clinical behaviors. However, the molecular driving force behind the difference is unclear.MethodsWe collected 20 LMS and 12 DDLPS samples and performed whole exome sequencing (WES) to obtain their somatic mutation profiles. We also performed RNA-Seq to analyze the transcriptomes of 8 each of the LMS and DDLPS samples and obtained information about differential gene expression, pathway enrichment, immune cell infiltration in tumor microenvironment, and chromosomal rearrangement including gene fusions. Selected gene fusion events from the RNA-seq prediction were checked by RT-PCR in tandem with Sanger sequencing.ResultsWe detected loss of function mutation and deletion of tumor suppressors mostly in LMS, and oncogene amplification mostly in DDLPS. A focal amplification affecting chromosome 12q13-15 region which encodes MDM2, CDK4 and HMGA2 is notable in DDLPS. Mutations in TP53, ATRX, PTEN, and RB1 are identified in LMS but not DDLPS, while mutation of HERC2 is only identified in DDLPS but not LMS. RNA-seq revealed overexpression of MDM2, CDK4 and HMGA2 in DDLPS and down-regulation of TP53 and RB1 in LMS. It also detected more fusion events in DDLPS than LMS (4.5 vs. 1, p = 0.0195), and the ones involving chromosome 12 in DDLPS stand out. RT-PCR and Sanger sequencing verified the majority of the fusion events in DDLPS but only one event in LMS selected to be tested. The tumor microenvironmental signatures are highly correlated with histologic types. DDLPS has more endothelial cells and fibroblasts content than LMS.ConclusionsOur analysis revealed different recurrent genetic variations in LMS and DDLPS including simultaneous upregulation of gene expression and gene copy number amplification of MDM2 and CDK4. Up-regulation of tumor related genes is favored in DDLPS, while loss of suppressor function is favored in LMS. DDLPS harbors more frequent fusion events which can generate neoepitopes and potentially targeted by personalized immune treatment.

Project description:Mast flowering is synchronised highly variable flowering by a population of perennial plants over a wide geographical area. High seeding years are seen as a threat to native and endangered species due to high predator density caused by the abundance of seed. An understanding of the molecular pathways that influence masting behaviour in plants could provide better prediction of a forthcoming masting season and enable conservation strategies to be deployed. The goal of this study was to identify candidate flowering genes that might be involved in regulating mast flowering. To achieve this, high-throughput large-scale RNA-sequencing was performed on two masting plant species, Celmisia lyallii (Asteraceae), and Chionochloa pallens (Poaceae) to develop a reference transcriptome for functional and molecular analysis. An average total of 33 million 150 base-paired reads, for both species, were assembled using the Trinity pipeline, resulting in 151,803 and 348,649 transcripts respectively for C. lyallii and C. pallens. For both species, about 56% of the unigenes were annotated with gene descriptions to known proteins followed by Gene Ontology analysis, categorising them on the basis of putative biological processes, molecular function, and cellular localization. A total of 543 transcripts from C. lyallii and 470 transcripts from C. pallens were also mapped to unique flowering-time proteins identified in Arabidopsis thaliana, suggesting the conservation of the flowering network in these wild alpine plants growing in natural field conditions. Expression analysis of several selected homologous flowering-pathway genes showed seasonal and photoperiodic variations. These genes can further be analysed to understand why seasonal cues, such as the increasing photoperiod in spring, that triggers the annual flowering of most plants, are insufficient to always trigger flowering in masting plants and to uncover the molecular basis of how additional cues (such as temperature during the previous growing seasons) then determines flowering in mast years.

Dataset Information

Integrated Genomic and Transcriptomic Elucidation of Flowering in Garlic.

Publications

Integrated Genomic and Transcriptomic Elucidation of Flowering in Garlic.

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