The Genus Citrus

Manuel Talon, Marco Caruso, Fred G. Gmitter jr., Manuel Talon, Marco Caruso, Fred G. Gmitter, jr.

• Publisher: Woodhead Publishing
• Year: 2020
• ISBN:
  9780128122174
• Topic: Technologie et ingénierie
• Subtopic: Agriculture

The Genus Citrus presents the enormous amount of new knowledge that has been generated in recent years on nearly all topics related to citrus. Beginning with an overview of the fundamental principles and understanding of citrus biology and behavior, the book provides a comprehensive view from Citrus evolution to current market importance. Reporting on new insights supported by the elucidation of the citrus genome sequence, it presents groundbreaking theories and fills in previous knowledge gaps.

Because citrus is among the most difficult plants to improve through traditional breeding, citrus researchers, institutions and industries must quickly learn to adapt to new developments, knowledge and technologies to address the biological constraints of a unique fruit-tree such as citrus. Despite the challenges of working with citrus, tremendous progress has been made, mostly through advances in molecular biology and genomics. This book is valuable for all those involved with researching and advancing, producing, processing, and delivering citrus products.

• Includes the most current research on citrus genomic information
• Provides the first detailed description of citrus origin, a new proposal for citrus taxonomy, and a redefinition of the genus Citrus
• Details citrus challenges including climate change, global disease impacts, and plant improvement strategies

Chapter 1

The citrus genome

Frederick G. Gmitter, Jr.^a; Guohong Albert Wu^b; Daniel S. Rokhsar^b,c,d; Manuel Talon^{e a} Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, United States
^b US Department of Energy Joint Genome Institute, Walnut Creek, CA, United States
^c Department of Molecular and Cell Biology and Center for Integrative Genomics, University of California, Berkeley, Berkeley, CA, United States
^d Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
^e Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain

Abstract

The genome of any living organism is the foundation upon which every aspect of that organism’s life is built, including all physical characteristics and interactions with the environment, as well as the mechanisms by which the genome sequence content is passed to offspring. The citrus genome underlies and influences every aspect of citrus trees and fruit, and therefore nearly every chapter topic that follows in this book may best be understood when viewed through the lens of genomic comprehension. A brief history of citrus genome sequencing activities is presented in the historical context of rapidly evolving improvements in genome sequencing technologies, including a summary of de novo genome sequence assemblies. Examples of how the abundance of available citrus genome sequence information has informed studies on the nature of progenitor citrus species, and the contemporary citrus species and the admixtures represented in modern citrus cultivars. Further, the specifics of comparative genome analyses and the conclusions drawn on the evolution and domestication of mandarins are provided. Sequencing technology and associated informatics will continue to improve in the coming years, and the application of the new fundamental information to be generated will support and inform future advances in all the subject areas that follow in this book.

Keywords

DNA sequencing; Sweet orange; Illumina; Sanger sequencing; Mandarin; Pummelo; Admixture; Evolution; Domestication

1.1 Concept of genome

The genome of any living organism is indeed the foundation upon which every aspect of that organism’s life is built. The organism’s shape, size, color, mode of acquisition, and requirements for nutrients, interactions within the environment where the organism may be found, the timely and appropriate regulation of expression of fundamental coding information leading to form and function of the organism and its distinctive organs and tissues, and even the mechanisms by which the genome sequence content is passed forward to future generations—all these and many other fundamental aspects of the life of any organism are determined by the information content of the genome. The genome is the fundamental basis of all living things. Plants of the genus Citrus are certainly no exception. In this sense, the genome underlies or influences every aspect of citrus trees and fruits, and therefore certainly the next few chapters, and nearly every chapter topic that follows in this book, may best be understood when viewed through the lens of genomic comprehension. From this perspective, the editors have chosen to open the book with an introductory chapter recognizing and describing something of the foundational role of the citrus genome.

DNA sequencing and analysis seems ubiquitous in contemporary biology; however, it is worth recognizing that this technology arose in the last 25 years of the previous century. The first method of DNA sequencing, based on primers for extension that were location specific and coupled with nucleotide-specific labeling, were reported first in the early 1970s (Wu, 1972; Padmanabhan et al., 1974). These reports were followed by the classic work of Sanger et al. (1977), which remained the gold standard for genome sequencing through the first decade of the current century. The earlier methods were applied to viruses, bacteriophage, and soon to a bacterium Haemophilus influenzae, using a whole-genome shotgun (WGS) approach (Fleischmann et al., 1995). Perhaps one of the most significant developments in the earliest days of the new millennium, the first draft sequence of the human genome was published (Venter et al., 2001). Since then, sequencing technology experienced exponential growth in capacity and quality that continues unabated until today (summarized in Goodwin et al., 2016). It is as a consequence of this technological revolution that agricultural scientists, and citrus researchers specifically, have been able to make the progress and lead to incredible new insights to objectively address biological and evolutionary questions.

1.2 Citrus genomes

Within the context of the rapid evolution of genomic science and associated bioinformatics tools, the global citrus community came together in Valencia, Spain in 2003 to establish a framework for international collaboration, referred to as the International Citrus Genome Consortium (ICGC). The historical background of the ICGC as well as the fundamental principles, objectives, and goals were described previously (Talon and Gmitter, 2008; Gmitter et al., 2012). Initially, the ICGC estimated the cost of producing “the citrus genome” to be about US$16 million, and so individual research groups went to their home industries and countries to seek support for the ambitious international project. Finally, researchers from the United States, France, Italy, Spain, and Brazil acquired financial resources and engaged primarily with the US Department of Energy-Joint Genome Institute (USDOE-JGI), Genoscope in France, and Istituto Genomica Applicata (IGA) in Italy to work together for producing and making publicly available through the USDOE-JGI web portal Phytozome in January 2011, the first ever reference citrus genome sequence of a haploid clone derived from Clementine mandarin (Aleza et al., 2009; Germana et al., 2013). This was accomplished by Sanger sequencing technologies in the three institutes, coupled with a reference ge...