Perspectives on Salmon Aquaculture: Current Status, Challenges and Genetic Improvement for Future Growth

With an estimated global value of US$15.6 billion, farmed salmonids represent a precious food resource, which is also the fastest increasing food producing industry with annual growth of 7% in production. A total average of 3,594,000 metric tonnes was produced in 2020, behind Chinese and Indian carps, tilapias and catfishes. Lead producers of farmed salmonids are Norway, Chile, Faroe, Canada and Scotland, stimulated by increasing global demand and market. However, over the last 2 years, production has been declining, occasioned by effects of diseases as well as rising feed costs. Over the last year, production has declined sharply due to effects of covid-19. This chapter reviews the species in culture, systems of culture, environmental footprints of salmon culture, and market trends in salmon culture. Burden of diseases, especially Infectious pancreatic Necrosis, Infectious salmon anemia and furunculosis, as well as high cost of feed formulation, key challenges curtailing growth of the salmon production industry, are discussed. A review is made of the international salmon genome sequencing effort, selective breeding for disease resistance, and the use of genomics to mitigate challenges of diseases that stifle higher production of salmonids globally.

Insights from Initial Variant Detection by Sequencing Single Sperm in Cattle

Meiotic de novo mutation (DNM) is one of the important phenomena contributing to gamete genome diversity. However, except for humans and a few model organisms, they are not well studied in livestock, including cattle. Moreover, bulk sperm samples have been routinely utilized in experiments, which include millions of single sperm cells and only report high-frequency variants. In this study, we isolated and sequenced 143 single sperms from two Holstein bulls and identified hundreds of candidate DNM events in ten sperms with deep sequencing coverage. We estimated DNM rates ranging from 1.08 × 10−8 to 3.78 × 10−8 per nucleotide per generation. We further validated 12 out of 14 selected DNM events using Sanger sequencing. To our knowledge, this is the first single sperm whole-genome sequencing effort in livestock, which provided useful information for future studies of point mutations and male fertility. Our preliminary results pointed out future research directions and highlighted the importance of uniform whole genome amplification, deep sequence coverage, and dedicated software pipelines for genetic variant detection using single-cell sequencing data.

Mitochondrial Genome Resource of a grapevine strain of Trichoderma harzianum, a potential biological control agent for fungal canker diseases

Trichoderma spp. are commonly used as bioremediation agents, biological controls, and for making biofuels. Herein, a Trichoderma harzianum strain PAR3 was isolated from grapevine roots in central California, USA. As part of a larger whole genome sequencing effort, the mitochondrial genome (mitogenome) sequence was obtained for the PAR3 strain. The mitogenome is 27,631 bp containing genes of 14 core mitochondrial proteins, 25 tRNA, and two rRNAs and a GC% content of 27.55%. BLAST search using the PAR3 mitogenome as query against GenBank sequence database showed mitogenome MUT3171 (29,791 bp) of Trichoderma lixii was the most similar (Query Coverage = 99%; Percentage Identity=100.00%) with two major deletions, 1,339 bp and 821 bp. The PAR3 mitogenome sequence will provide a useful reference for comparing different Trichoderma strains from US and around the world.

A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population

The ethnic composition of the population of a country contributes to the uniqueness of each national DNA sequencing project and, ideally, individual reference genomes are required to reduce the confounding nature of ethnic bias. This work represents a representative Whole Genome Sequencing effort of an understudied population. Specifically, high coverage consensus sequences from 120 whole genomes and 33 whole exomes were used to construct the first ever population specific major allele reference genome for the United Arab Emirates (UAE). When this was applied and compared to the archetype hg19 reference, assembly of local Emirati genomes was reduced by ∼19% (i.e., some 1 million fewer calls). In compiling the United Arab Emirates Reference Genome (UAERG), sets of annotated 23,038,090 short (novel: 1,790,171) and 137,713 structural (novel: 8,462) variants; their allele frequencies (AFs) and distribution across the genome were identified. Population-specific genetic characteristics including loss-of-function variants, admixture, and ancestral haplogroup distribution were identified and reported here. We also detect a strong correlation between FST and admixture components in the UAE. This baseline study was conceived to establish a high-quality reference genome and a genetic variations resource to enable the development of regional population specific initiatives and thus inform the application of population studies and precision medicine in the UAE.

Sucrose-phosphate phosphatase from sugarcane reveals an ancestral tandem duplication

Background Sugarcane is capable to store large amounts of sucrose in the culm at maturity hence it became a major source of sucrose for the food and the renewable energy industries. Sucrose, the main disaccharide produced by photosynthesis, is mainly stored in the vacuole of the cells of non-photosynthetic tissues. Two pathways are known to release free sucrose in plant cells, one is de novo synthesis dependent on sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (S6PP) while the other is regulatory and dependent on sucrose synthase (SuSy) activity. The molecular understanding of genes that give rise to the expression of the enzyme sucrose phosphate phosphatase, responsible for the release of sucrose in the last synthetic step lag behind the regulatory SuSy gene. Results Sugarcane genome sequencing effort disclosed the existence of a tandem duplication and the present work further support that both S6PP.1 and S6PP_2D isoforms are actively transcribed in young sugarcane plants but significantly less at maturity. Two commercial hybrids (SP80–3280 and R570) and both Saccharum spontaneum (IN84–58) and S.officinarum (BADILLA) exhibit transcriptional activity at three-month-old plants of the tandem S6PP_2D in leaves, culm, meristem and root system with a cultivar-specific distribution. Moreover, this tandem duplication is shared with other grasses and is ancestral in the group. Conclusion Detection of a new isoform of S6PP resulting from the translation of 14 exon-containing transcript (S6PP_2D) will contribute to the knowledge of sucrose metabolism in plants. In addition, expression varies along plant development and between sugarcane cultivars and parental species.

Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world

ABSTRACTBackgroundSARS-CoV-2 most likely evolved from a bat beta-coronavirus and started infecting humans in December 2019. Since then it has rapidly infected people around the world, with more than 4.5 million confirmed cases by the middle of May 2020. Early genome sequencing of the virus has enabled the development of molecular diagnostics and the commencement of therapy and vaccine development. The analysis of the early sequences showed relatively few evolutionary selection pressures. However, with the rapid worldwide expansion into diverse human populations, significant genetic variations are becoming increasingly likely. The current limitations on social movement between countries also offers the opportunity for these viral variants to become distinct strains with potential implications for diagnostics, therapies and vaccines.MethodsWe used the current sequencing archives (NCBI and GISAID) to investigate 15,487 whole genomes, looking for evidence of strain diversification and selective pressure.ResultsWe used 6,294 SNPs to build a phylogenetic tree of SARS-CoV-2 diversity and noted strong evidence for the existence of two major clades and six sub-clades, unevenly distributed across the world. We also noted that convergent evolution has potentially occurred across several locations in the genome, showing selection pressures, including on the spike glycoprotein where we noted a potentially critical mutation that could affect its binding to the ACE2 receptor. We also report on mutations that could prevent current molecular diagnostics from detecting some of the sub-clades.ConclusionThe worldwide whole genome sequencing effort is revealing the challenge of developing SARS-CoV-2 containment tools suitable for everyone and the need for data to be continually evaluated to ensure accuracy in outbreak estimations.

Effective Gene Silencing in a Microsporidian Parasite Associated with Honeybee (Apis mellifera) Colony Declines

ABSTRACT Honeybee colonies are vulnerable to parasites and pathogens ranging from viruses to vertebrates. An increasingly prevalent disease of managed honeybees is caused by the microsporidian Nosema ceranae. Microsporidia are basal fungi and obligate parasites with much-reduced genomic and cellular components. A recent genome-sequencing effort for N. ceranae indicated the presence of machinery for RNA silencing in this species, suggesting that RNA interference (RNAi) might be exploited to regulate Nosema gene expression within bee hosts. Here we used controlled laboratory experiments to show that double-stranded RNA homologous to specific N. ceranae ADP/ATP transporter genes can specifically and differentially silence transcripts encoding these proteins. This inhibition also affects Nosema levels and host physiology. Gene silencing could be mediated solely by Nosema or in concert with known systemic RNAi mechanisms in their bee hosts. These results are novel for the microsporidia and provide a possible avenue for controlling a disease agent implicated in severe honeybee colony losses. Moreover, since microsporidia are pathogenic in several known veterinary and human diseases, this advance may have broader applications in the future for disease control.

Barley Genomics: An Overview

Barley (Hordeum vulgare), first domesticated in the Near East, is a well-studied crop in terms of genetics, genomics, and breeding and qualifies as a model plant for Triticeae research. Recent advances made in barley genomics mainly include the following: (i) rapid accumulation of EST sequence data, (ii) growing number of studies on transcriptome, proteome, and metabolome, (iii) new modeling techniques, (iv) availability of genome-wide knockout collections as well as efficient transformation techniques, and (v) the recently started genome sequencing effort. These developments pave the way for a comprehensive functional analysis and understanding of gene expression networks linked to agronomically important traits. Here, we selectively review important technological developments in barley genomics and related fields and discuss the relevance for understanding genotype-phenotype relationships by using approaches such as genetical genomics and association studies. High-throughput genotyping platforms that have recently become available will allow the construction of high-density genetic maps that will further promote marker-assisted selection as well as physical map construction. Systems biology approaches will further enhance our knowledge and largely increase our abilities to design refined breeding strategies on the basis of detailed molecular physiological knowledge.