Eragrostis curvula, a Model Species for Diplosporous Apomixis

Eragrostis curvula (Schrad.) Ness is a grass with a particular apomictic embryo sac development called Eragrostis type. Apomixis is a type of asexual reproduction that produces seeds without fertilization in which the resulting progeny is genetically identical to the mother plant and with the potential to fix the hybrid vigour from more than one generation, among other advantages. The absence of meiosis and the occurrence of only two rounds of mitosis instead of three during embryo sac development make this model unique and suitable to be transferred to economically important crops. Throughout this review, we highlight the advances in the knowledge of apomixis in E. curvula using different techniques such as cytoembryology, DNA methylation analyses, small-RNA-seq, RNA-seq, genome assembly, and genotyping by sequencing. The main bulk of evidence points out that apomixis is inherited as a single Mendelian factor, and it is regulated by genetic and epigenetic mechanisms controlled by a complex network. With all this information, we propose a model of the mechanisms involved in diplosporous apomixis in this grass. All the genetic and epigenetic resources generated in E. curvula to study the reproductive mode changed its status from an orphan to a well-characterised species.

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Cytogenetic studies in the Eragrostis curvula Complex

Bothalia ◽

10.4102/abc.v12i2.1399 ◽

1977 ◽

Vol 12 (2) ◽

pp. 215-221 ◽

Cited By ~ 9

Author(s):

T. B. Vorster

Keyword(s):

Chromosome Number ◽

Embryo Sac ◽

Plant Morphology ◽

Variable Environment ◽

Eragrostis Curvula ◽

Embryo Sac Development ◽

Transition Area ◽

Cytogenetic Studies

Cytogenetic studies were undertaken in the Eragrostis curvula Complex. Three plants were studied at each of 16 collecting points. The overall morphology and embryo sac development of all plants were evaluated, while the chromosome number and microsporogenesis of some of the plants were also studied. The collecting points were chosen so ^s to represent a variable environment extending from the bushveld to the highveld regions of the Transvaal. It was found that the embryo sac development of the plants from the bush\eld and the highveld were, for all practical purposes, obligate diplosporic apomicts, whereas the transition area contained obligate as well as facultative diplosporic apomicts. The same pattern also held as far as the plant morphology, chromosome number and microsporogenesis were concerned.

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Ultrastructural Observation on Embryo Sac Development inPhaius tankervilliae(Aiton)Bl.

Plant Science Journal ◽

10.3724/sp.j.1142.2012.20188 ◽

2012 ◽

Vol 30 (2) ◽

pp. 188 ◽

Cited By ~ 2

Author(s):

Dong-Mei LI ◽

Cheng-Hou WU ◽

Xiu-Lin YE ◽

Cheng-Ye LIANG

Keyword(s):

Embryo Sac ◽

Ultrastructural Observation ◽

Embryo Sac Development

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Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis

Diagnostics ◽

10.3390/diagnostics11060964 ◽

2021 ◽

Vol 11 (6) ◽

pp. 964

Author(s):

Sarka Benesova ◽

Mikael Kubista ◽

Lukas Valihrach

Keyword(s):

Rna Sequencing ◽

Small Rna ◽

High Sensitivity ◽

Small Rna Sequencing ◽

Rna Seq ◽

Liquid Biopsies ◽

Comprehensive Overview ◽

Rna Molecules ◽

Novel Mirna ◽

The Many

MicroRNAs (miRNAs) are a class of small RNA molecules that have an important regulatory role in multiple physiological and pathological processes. Their disease-specific profiles and presence in biofluids are properties that enable miRNAs to be employed as non-invasive biomarkers. In the past decades, several methods have been developed for miRNA analysis, including small RNA sequencing (RNA-seq). Small RNA-seq enables genome-wide profiling and analysis of known, as well as novel, miRNA variants. Moreover, its high sensitivity allows for profiling of low input samples such as liquid biopsies, which have now found applications in diagnostics and prognostics. Still, due to technical bias and the limited ability to capture the true miRNA representation, its potential remains unfulfilled. The introduction of many new small RNA-seq approaches that tried to minimize this bias, has led to the existence of the many small RNA-seq protocols seen today. Here, we review all current approaches to cDNA library construction used during the small RNA-seq workflow, with particular focus on their implementation in commercially available protocols. We provide an overview of each protocol and discuss their applicability. We also review recent benchmarking studies comparing each protocol’s performance and summarize the major conclusions that can be gathered from their usage. The result documents variable performance of the protocols and highlights their different applications in miRNA research. Taken together, our review provides a comprehensive overview of all the current small RNA-seq approaches, summarizes their strengths and weaknesses, and provides guidelines for their applications in miRNA research.

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Embryo sac development and endogenous gibberellins in pollinated and unpollinated ovaries of walnut (Juglans regia)

Physiologia Plantarum ◽

10.1111/j.1399-3054.1994.tb00656.x ◽

1994 ◽

Vol 91 (1) ◽

pp. 37-44 ◽

Cited By ~ 1

Author(s):

Francisco R. Tadeo ◽

Manuel Talon ◽

Eric Germain ◽

Francoise Dosba

Keyword(s):

Juglans Regia ◽

Embryo Sac ◽

Embryo Sac Development

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Reference transcriptome assembly and annotation for perennial ryegrass

Genome ◽

10.1139/gen-2017-0077 ◽

2017 ◽

Vol 60 (12) ◽

pp. 1086-1088 ◽

Cited By ~ 4

Author(s):

Hiroshi Shinozuka ◽

Noel O.I. Cogan ◽

German C. Spangenberg ◽

John W. Forster

Keyword(s):

Perennial Ryegrass ◽

Transcriptome Assembly ◽

Genotyping By Sequencing ◽

Whole Genome Sequence ◽

Grass Species ◽

Rna Seq ◽

Pasture Grass ◽

Tissue Samples ◽

Genome Sequence Assembly ◽

Transcriptome Resource

RNA-Seq methodology has been used to generate a comprehensive transcriptome sequence resource for perennial ryegrass, an important temperate pasture grass species. A total of 931 547 255 reads were obtained from libraries corresponding to 19 distinct tissue samples, including both vegetative and reproductive stages of development. Assembly of data generated a final filtered reference set of 48 713 contigs and scaffolds. The transcriptome resource will support whole genome sequence assembly, comparative genomics, implementation of genotyping-by-sequencing (GBS) methods based on transcript sampling, and identification of candidate genes for multiple biological functions.

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xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells

10.1101/333658 ◽

2018 ◽

Author(s):

Avi Z. Rosenberg ◽

Carrie Wright ◽

Karen Fox-Talbot ◽

Anandita Rajpurohit ◽

Courtney Williams ◽

...

Keyword(s):

Epithelial Cells ◽

Small Rna ◽

Mirna Expression ◽

Low Cost ◽

Expression Patterns ◽

Small Rna Sequencing ◽

Rna Seq ◽

Cell Type

AbstractAccurate, RNA-seq based, microRNA (miRNA) expression estimates from primary cells have recently been described. However, this in vitro data is mainly obtained from cell culture, which is known to alter cell maturity/differentiation status, significantly changing miRNA levels. What is needed is a robust method to obtain in vivo miRNA expression values directly from cells. We introduce expression microdissection miRNA small RNA sequencing (xMD-miRNA-seq), a method to isolate cells directly from formalin fixed paraffin-embedded (FFPE) tissues. xMD-miRNA-seq is a low-cost, high-throughput, immunohistochemistry-based method to capture any cell type of interest. As a proof-of-concept, we isolated colon epithelial cells from two specimens and performed low-input small RNA-seq. We generated up to 600,000 miRNA reads from the samples. Isolated epithelial cells, had abundant epithelial-enriched miRNA expression (miR-192; miR-194; miR-200b; miR-200c; miR-215; miR-375) and overall similar miRNA expression patterns to other epithelial cell populations (colonic enteroids and flow-isolated colon epithelium). xMD-derived epithelial cells were generally not contaminated by other adjacent cells of the colon as noted by t-SNE analysis. xMD-miRNA-seq allows for simple, economical, and efficient identification of cell-specific miRNA expression estimates. Further development will enhance rapid identification of cell-specific miRNA expression estimates in health and disease for nearly any cell type using archival FFPE material.

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Faculty Opinions recommendation of The Arabidopsis plastidic glucose 6-phosphate/phosphate translocator GPT1 is essential for pollen maturation and embryo sac development.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1024926.294714 ◽

2005 ◽

Author(s):

Christoph Benning

Keyword(s):

Embryo Sac ◽

Pollen Maturation ◽

Embryo Sac Development ◽

Phosphate Translocator

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Fazy rozwoju woreczka zalążkowego w zestawieniu z rozwojem pyłku u Lilium candidum [Phases of embryo sac development and pollen grains development in Lilium candidum]

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.1961.042 ◽

2015 ◽

Vol 30 (3–4) ◽

pp. 749-754 ◽

Cited By ~ 3

Author(s):

B. Rodkiewicz

Keyword(s):

Embryo Sac ◽

Pollen Grains ◽

Embryo Sac Development

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Identification and validation of miRNA reference genes in poplar under pathogen stress

10.21203/rs.3.rs-225734/v1 ◽

2021 ◽

Author(s):

Lichun Zhang ◽

Xiaoqian Yang ◽

Yiyi Yin ◽

Jinxing Wang ◽

Yanwei Wang

Keyword(s):

Gene Expression ◽

Reference Gene ◽

Small Rna ◽

Reference Genes ◽

Expression Profiles ◽

Small Rna Sequencing ◽

Rna Seq ◽

Internal Standards ◽

Qrt Pcr ◽

Canker Pathogen

Abstract Quantitative real time polymerase chain reaction (qRT-PCR) is a common method to analyze gene expression. Due to differences in RNA quantity, quality, and reverse transcription efficiency between qRT-PCR samples, reference genes are used as internal standards to normalize gene expression. However, few universal genes especially miRNAs have been identified as reference so far. Therefore, it is essential to identify reference genes that can be used across various experimental conditions, stress treatments, or tissues. In this study, 14 microRNAs (miRNAs) and 5.8S rRNA were assessed for expression stability in poplar trees infected with canker pathogen. Using three reference gene analysis programs, we found that miR156g and miR156a exhibited stable expression throughout the infection process. miR156g and miR156a were then tested as internal standards to measure the expression of miR1447 and miR171c, and the results were compared to small RNA sequencing (RNA-seq) data. We found that when miR156a was used as the reference gene, the expression of miR1447 and miR171c were consistent with the small RNA-seq expression profiles. Therefore, miR156a was the most stable miRNAs examined in this study, and could be used as a reference gene in poplar under canker pathogen stress, which should enable comprehensive comparisons of miRNAs expression and avoid the bias caused by different lenth between detected miRNAs and traditional referece genes. The present study has expanded the miRNA reference genes available for gene expression studies in trees under biotic stress.

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