Combined Transcriptome and Proteome Analysis of Anthers of AL-type Cytoplasmic Male Sterile Line and Its Maintainer Line Reveals New Insights into Mechanism of Male Sterility in Common Wheat

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Abstract

Cytoplasmic male sterility (CMS) plays an essential role in hybrid seeds production. In wheat, orf279 was reported as a CMS gene of AL-type male sterile line (AL18A), but its sterility mechanism is still unclear. Therefore, transcriptomic and proteomic analyses of the anthers of AL18A and its maintainer line (AL18B) were performed to interpret the sterility mechanism. Results showed that the electron transport chain and ROS scavenging enzyme expression levels changed in the early stages of the anther development. Biological processes, i.e., fatty acid synthesis, lipid transport, and polysaccharide metabolism, were abnormal, resulting in pollen abortion in AL18A. In addition, we identified several critical regulatory genes related to anther development through combined analysis of transcriptome and proteome. Most of the genes were enzymes or transcription factors, and 63 were partially homologous to the reported genic male sterile (GMS) genes. This study provides a new perspective of the sterility mechanism of AL18A and lays a foundation to study the functional genes of anther development.

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Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark Robinson, Davis J. McCarthy, Gordon K. Smyth (2009)

Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org). Contact: mrobinson@wehi.edu.au

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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

Jürgen Cox, Matthias Mann (2008)

Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlation analysis and graph theory, MaxQuant detects peaks, isotope clusters and stable amino acid isotope-labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space. By integrating multiple mass measurements and correcting for linear and nonlinear mass offsets, we achieve mass accuracy in the p.p.b. range, a sixfold increase over standard techniques. We increase the proportion of identified fragmentation spectra to 73% for SILAC peptide pairs via unambiguous assignment of isotope and missed-cleavage state and individual mass precision. MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.

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Contributors

Miaomiao Hao: URI : https://loop.frontiersin.org/people/1565110/overview

Wenlong Yang: URI : https://loop.frontiersin.org/people/274272/overview

Dongcheng Liu: URI : https://loop.frontiersin.org/people/421343/overview

Xin Li: URI : https://loop.frontiersin.org/people/445350/overview

Yingbin Nie: URI : https://loop.frontiersin.org/people/585925/overview

Aimin Zhang: URI : https://loop.frontiersin.org/people/436235/overview

Journal

Journal ID (nlm-ta): Front Genet

Journal ID (iso-abbrev): Front Genet

Journal ID (publisher-id): Front. Genet.

Title: Frontiers in Genetics

Publisher: Frontiers Media S.A.

ISSN (Electronic): 1664-8021

Publication date (Electronic): 17 December 2021

Publication date Collection: 2021

Volume: 12

Electronic Location Identifier: 762332

Affiliations

[ ¹ ]State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China

[ ² ]University of Chinese Academy of Sciences, Beijing, China

[ ³ ]Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China

[ ⁴ ]Institute of Crop Research, Xinjiang Academy of Agri-Reclamation Sciences, Shihezi, China

Author notes

Edited by: Karthikeyan Adhimoolam, Jeju National University, South Korea

Reviewed by: Rajeev Ranjan, Purdue University, United States

Pallavi Sinha, IRRI South Asia Hub, India

*Correspondence: Wenlong Yang, wlyang@ 123456genetics.ac.cn ; Aimin Zhang, amzhang@ 123456genetics.ac.cn

[ † ]

These authors have contributed equally to this work

This article was submitted to Plant Genomics, a section of the journal Frontiers in Genetics

Article

Publisher ID: 762332

DOI: 10.3389/fgene.2021.762332

PMC ID: 8718765

PubMed ID: 34976010

SO-VID: 8bbb6947-7f14-41a0-8393-910d9e9842b0

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This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Combined Transcriptome and Proteome Analysis of Anthers of AL-type Cytoplasmic Male Sterile Line and Its Maintainer Line Reveals New Insights into Mechanism of Male Sterility in Common Wheat

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G3: Genes|Genomes|Genetics

Most cited references 54

Trimmomatic: a flexible trimmer for Illumina sequence data

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

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