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      A decade of pollen transcriptomics

      review-article
      Author(s): ,
      Publication date (Electronic):
      Journal: Plant Reproduction
      Publisher: Springer Berlin Heidelberg
      Keywords: Pollen, Male gametophyte, Transcriptome, Gene expression, Development

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          Key message

          Overview of pollen transcriptome studies.

          Pollen development is driven by gene expression, and knowledge of the molecular events underlying this process has undergone a quantum leap in the last decade through studies of the transcriptome. Here, we outline historical evidence for male haploid gene expression and review the wealth of pollen transcriptome data now available. Knowledge of the transcriptional capacity of pollen has progressed from genetic studies to the direct analysis of RNA and from gene-by-gene studies to analyses on a genomic scale. Microarray and/or RNA-seq data can now be accessed for all phases and cell types of developing pollen encompassing 10 different angiosperms. These growing resources have accelerated research and will undoubtedly inspire new directions and the application of system-based research into the mechanisms that govern the development, function and evolution of angiosperm pollen.

          Electronic supplementary material

          The online version of this article (doi:10.1007/s00497-015-0261-7) contains supplementary material, which is available to authorized users.

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          Origins, evolution, and phenotypic impact of new genes.

          Henrik Kaessmann (2010)
          Ever since the pre-molecular era, the birth of new genes with novel functions has been considered to be a major contributor to adaptive evolutionary innovation. Here, I review the origin and evolution of new genes and their functions in eukaryotes, an area of research that has made rapid progress in the past decade thanks to the genomics revolution. Indeed, recent work has provided initial whole-genome views of the different types of new genes for a large number of different organisms. The array of mechanisms underlying the origin of new genes is compelling, extending way beyond the traditionally well-studied source of gene duplication. Thus, it was shown that novel genes also regularly arose from messenger RNAs of ancestral genes, protein-coding genes metamorphosed into new RNA genes, genomic parasites were co-opted as new genes, and that both protein and RNA genes were composed from scratch (i.e., from previously nonfunctional sequences). These mechanisms then also contributed to the formation of numerous novel chimeric gene structures. Detailed functional investigations uncovered different evolutionary pathways that led to the emergence of novel functions from these newly minted sequences and, with respect to animals, attributed a potentially important role to one specific tissue--the testis--in the process of gene birth. Remarkably, these studies also demonstrated that novel genes of the various types significantly impacted the evolution of cellular, physiological, morphological, behavioral, and reproductive phenotypic traits. Consequently, it is now firmly established that new genes have indeed been major contributors to the origin of adaptive evolutionary novelties.
          Article 0 comments Cited 353 times – based on 0 reviews     Review now
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            Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss.

            James Schnable, Nathan Springer, Michael Freeling (2011)
            Ancient tetraploidies are found throughout the eukaryotes. After duplication, one copy of each duplicate gene pair tends to be lost (fractionate). For all studied tetraploidies, the loss of duplicated genes, known as homeologs, homoeologs, ohnologs, or syntenic paralogs, is uneven between duplicate regions. In maize, a species that experienced a tetraploidy 5-12 million years ago, we show that in addition to uneven ancient gene loss, the two complete genomes contained within maize are differentiated by ongoing fractionation among diverse inbreds as well as by a pattern of overexpression of genes from the genome that has experienced less gene loss. These expression differences are consistent over a range of experiments quantifying RNA abundance in different tissues. We propose that the universal bias in gene loss between the genomes of this ancient tetraploid, and perhaps all tetraploids, is the result of selection against loss of the gene responsible for the majority of total expression for a duplicate gene pair. Although the tetraploidy of maize is ancient, biased gene loss and expression continue today and explain, at least in part, the remarkable genetic diversity found among modern maize cultivars.
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              RNA-seq differential expression studies: more sequence or more replication?

              Yuwen Liu, Jie Zhou, Kevin P. White (2014)
              RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low statistical power and inefficient use of sequencing resources. We show the explicit trade-off between more biological replicates and deeper sequencing in increasing power to detect differentially expressed (DE) genes. In the human cell line MCF7, adding more sequencing depth after 10 M reads gives diminishing returns on power to detect DE genes, whereas adding biological replicates improves power significantly regardless of sequencing depth. We also propose a cost-effectiveness metric for guiding the design of large-scale RNA-seq DE studies. Our analysis showed that sequencing less reads and performing more biological replication is an effective strategy to increase power and accuracy in large-scale differential expression RNA-seq studies, and provided new insights into efficient experiment design of RNA-seq studies. The code used in this paper is provided on: http://home.uchicago.edu/∼jiezhou/replication/. The expression data is deposited in the Gene Expression Omnibus under the accession ID GSE51403.
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                Author and article information

                Contributors
                David Twell: twe@le.ac.uk
                Journal
                Journal ID (nlm-ta): Plant Reprod
                Journal ID (iso-abbrev): Plant Reprod
                Title: Plant Reproduction
                Publisher: Springer Berlin Heidelberg (Berlin/Heidelberg )
                ISSN (Print): 2194-7953
                ISSN (Electronic): 2194-7961
                Publication date (Electronic): 12 March 2015
                Publication date PMC-release: 12 March 2015
                Publication date (Print): 2015
                Volume: 28
                Issue: 2
                Pages: 73-89
                Affiliations
                Department of Biology, University of Leicester, Leicester, LE1 7RH UK
                Author notes

                Communicated by Silvia Coimbra and Lucia Colombo.

                Article
                Publisher ID: 261
                DOI: 10.1007/s00497-015-0261-7
                PMC ID: 4432081
                PubMed ID: 25761645
                SO-VID: b75f3b34-bc4e-4595-ac54-d495f188ac43
                Copyright © © The Author(s) 2015
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.

                History
                Date received : 9 January 2015
                Date accepted : 24 February 2015
                Categories
                Subject: Review
                Custom metadata
                issue-copyright-statement © Springer-Verlag Berlin Heidelberg 2015

                Keywords: pollen,male gametophyte,transcriptome,gene expression,development
                Data availability:
                Keywords: pollen, male gametophyte, transcriptome, gene expression, development

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