A significant milestone in the field of genetics came with the completion of the human genome sequencing project completed in 2001 (Fertig et al., 2012). Since then the study of genomics (organisms’ whole genomes) has been central in uncovering key information in disciplines like medical biotechnology, plant health, plant biotechnology and animal sciences. High-throughput Sequencing (NGS) has greatly increased the efficiency and speed at which genomes can be sequenced, leading to a significant increase in genomes sequenced. Interdisciplinary collaborations using information gleaned from the genome to study cell functions, pathogenesis as well as studying protein interactions and their link to diseases has informed many important advances such as the ones we highlight here.
Human medical biotechnology
Retrotransposons-related and complex diseases
Whole genome sequencing and annotating has provided the means to map complex diseases to their associated genome variants. Access to the entire genome code makes it possible to study the implications of the involvement of retrotransposons in processes that govern transcription and splicing (Elbarbary et al., 2016). Additionally, access to the entire code makes it possible to keep track of the patterns of mobility of the retrotransposons and the consequences of these activities. Kazazian and Moran (2017) provided evidence of the role played by these DNA chunks in cancer and Mendelian diseases.
DNA derived from retrotransposons serves templates for DNA recombination events that cause diseases (Kazazian and Moran, 2017). This includes unequal crossover events in the low-density lipoprotein receptor gene that is linked to familial hypercholesterolemia and other diseases (Lehrman et al., 1985; Konkel and Batzer, 2010).
Defense and disease: Staphylococcus aureus
Whole-genome mapping is a genomic tool that can be used to analyze entire bacterial genomes to align similar regions and identify deleted and inserted regions (Shukla et al., 2009). Whole-genome mapping of Staphylococcus aureus was able to identify regions (e.g. SCCmec motif and ACME) associated with methicillin resistance to characterize S. aureus as either MRSA or methicillin-sensitive(Shukla et al., 2012). Extracting relevant information on DNA seq analysis to accurately genotyping S. aureus is very important since this pathogen can attain virulence and antibiotic-resistance genes located within mobile genetic elements (Shukla et al., 2012).
Fungal Genomics and Plant Health
Many Colletotrichum species are serious pathogens of commercially important crop plants, including olive trees (Talinhas et al., 2005), and maize (O’Connell et al., 2012). For example, Colletotrichum acutatum and C. gloeosporioides are serious causal agents of olive anthracnose in Olea europaea subsp. europaea (Talinhas et al., 2005). Colletotrichum higginsianum and C. graminicola infect numerous Brassicaceae species (e.g. Arabidobsis thaliana) and maize, respectively (O’Connell et al., 2012). Their infection process includes a collection of secondary metabolites involved in host penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy) (O’Connell et al., 2012). Information on DNA seq analysis gained through comparative genomics of C. higginsianum and C. graminicola identified a large collection of pathogenicity-related genes, with the former having more families of genes responsible for proteins such as pectin-degrading enzymes and secondary metabolism enzymes (O’Connell et al., 2012).
Authors found that the infection process of C. higginsianum occurs in stages where gene expression of infection-related genes occurs first, followed by those involved in biotrophy and then those for necrotrophy, while in C. graminicola these stages likely occur simultaneously. These authors proposed that the expansive collection of infection-associated genes and the elaborate infection pathway of C. higginsianum is key to its ability to successfully infect a wider range of plants.
Food security research
Globally, honeybees (mainly Apis mellifera) are very important pollinators of crop monocultures (McGregor, 1976; Watanabe, 1994; Klein et al., 2007), and some single crops, such as coffee in Panama (Roubik, 2002). This species comprises of a wide range of subspecies that resulted from many evolutionary events (Ruttner, 1998; Chen et al., 2016). Sequencing of hundreds of honeybee genomes have provided groundbreaking insights into the evolutionary history and origin of this species (Dogantzis and Zayed, 2019). Population genomic analyses of this species (140 genomes) revealed that the subspecies of A. mellifera formed a monophyletic group, the authors posited an Asian-based origin of this species (Wallberg et al., 2014).
Information on DNA seq analysis extracted from genomes has also been used to link function with genomic regions. Studying drones revealed 44 genome regions that correspond to regions identified in royal jelly producing nurse bees (Wragg et al., 2016). Studies focused on natural honeybees have also revealed interesting insight into genetic basis of adaptation to local environments. For example, two population specific haplotype clusters were identified in a genomic comparison of highland and lowland African honey populations, most likely driving adaptation to their respective altitudes (Wallberg et al., 2017).
Genomics has facilitated the increasing realization that cross-discipline collaborations are vital to understanding the complex interactions between organisms of different classification as well as with the environment at large. Because of the shared vision of realizing the full potential of genomes, many researchers worldwide are working diligently to streamline the tools for handling genome-variant data to increase the ease of extracting information on DNA seq analysis. The study of genomes has revolutionized the field of genetic research across the board. The ability to study the genomes of human pathogens such as bacteria and fungi and the genome of the host opens up exciting avenues for understanding the interactions of host and pathogen at molecular level. This, coupled with the continued research into genome editing, promises to uncover the ability to either edit out virulence in pathogens or edit in resistance in the host genome. Improved understanding of evolutionary histories of key pathogens and their contribution to plant health will equip the plant biotechnology industry with important information for resistance breeding or reducing pathogen virulence.
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