Comparative genomics and polyploid dynamics in tetraploid cotton (Gossypium)

2021 ◽  
Author(s):  
Renhai Peng ◽  
Yanchao Xu ◽  
Zhen Liu ◽  
Liyang Chen ◽  
Zhongli Zhou ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Large Scale ◽  
Crop Improvement ◽  
Tetraploid Cotton ◽  
Early Form ◽  
Chromosomal Structure ◽  
Evolutionary Forces ◽  
Genomic Landscape ◽  
Genome Level ◽  
Crop Research

Abstract Allotetraploid species of cotton (Gossypium) represent a model system for the study of plant polyploidy, molecular evolution and domestication. In this study three high-quality draft assemblies of tetraploid cottons are presented, comprising one early form of domesticated Gossypium hirsutum (AD1-genome, Gh), i.e., Gossypium hirsutum race punctatum (GhP), and two recently described wild species of tetraploid cotton, G. ekmanianum (AD6, Ge) and G. stephensii (AD7, Gs). Using comparative phylogenomics, we confirm a monophyletic origin of tetraploid Gossypium and provide a dated whole-genome level perspective for the evolution of the clade. Recombination and patterns of selection are asymmetric between the two co-resident genomes in the allopolyploid nucleus. Considerable gene structural variation occurs widely within homoeologous genomes and between heterologous genomes during evolution and domestication. Despite few large-scale chromosomal structure variations among tetraploid cotton, frequent homoeologous exchanges between subgenomes in all species have contributed to diversity and asymmetrically between subgenomes. Abiotic and biotic adaptive evolution was driven by various evolutionary forces, leading to transcriptome change and gene family expansion. Our study marks a milestone in modern polyploid crop research, completing genome sequencing for all species of polyploid Gossypium, and will facilitate a better understanding of the genomic landscape and crop improvement dynamics of polyploids.

scholarly journals Vulnerability of individual fish to capture by trawling is influenced by capacity for anaerobic metabolism

2015 ◽  
Vol 282 (1813) ◽  
pp. 20150603 ◽  
Author(s):  
Shaun S. Killen ◽  
Julie J. H. Nati ◽  
Cory D. Suski
Keyword(s):  
Large Scale ◽  
Swimming Performance ◽  
Anaerobic Capacity ◽  
Standard Metabolic Rate ◽  
Metabolic Demand ◽  
Evolutionary Forces ◽  
Individual Fish ◽  
Fundamental Information ◽  
Behavioural Phenotypes ◽  
And Function

The harvest of animals by humans may constitute one of the strongest evolutionary forces affecting wild populations. Vulnerability to harvest varies among individuals within species according to behavioural phenotypes, but we lack fundamental information regarding the physiological mechanisms underlying harvest-induced selection. It is unknown, for example, what physiological traits make some individual fish more susceptible to capture by commercial fisheries. Active fishing methods such as trawling pursue fish during harvest attempts, causing fish to use both aerobic steady-state swimming and anaerobic burst-type swimming to evade capture. Using simulated trawling procedures with schools of wild minnows Phoxinus phoxinus , we investigate two key questions to the study of fisheries-induced evolution that have been impossible to address using large-scale trawls: (i) are some individuals within a fish shoal consistently more susceptible to capture by trawling than others?; and (ii) if so, is this related to individual differences in swimming performance and metabolism? Results provide the first evidence of repeatable variation in susceptibility to trawling that is strongly related to anaerobic capacity and swimming ability. Maximum aerobic swim speed was also negatively correlated with vulnerability to trawling. Standard metabolic rate was highest among fish that were least vulnerable to trawling, but this relationship probably arose through correlations with anaerobic capacity. These results indicate that vulnerability to trawling is linked to anaerobic swimming performance and metabolic demand, drawing parallels with factors influencing susceptibility to natural predators. Selection on these traits by fisheries could induce shifts in the fundamental physiological makeup and function of descendent populations.

scholarly journals New Insights into the Evolutionary and Genomic Landscape of Molluscum Contagiosum Virus (MCV) based on Nine MCV1 and Six MCV2 Complete Genome Sequences

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 586 ◽  
Author(s):  
Tomaž Zorec ◽  
Denis Kutnjak ◽  
Lea Hošnjak ◽  
Blanka Kušar ◽  
Katarina Trčko ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Nk Cell ◽  
Molluscum Contagiosum ◽  
Molluscum Contagiosum Virus ◽  
Genome Sequences ◽  
Viral Interference ◽  
Genomic Landscape ◽  
Genetic Landscape ◽  
Common Skin

Molluscum contagiosum virus (MCV) is the sole member of the Molluscipoxvirus genus and the causative agent of molluscum contagiosum (MC), a common skin disease. Although it is an important and frequent human pathogen, its genetic landscape and evolutionary history remain largely unknown. In this study, ten novel complete MCV genome sequences of the two most common MCV genotypes were determined (five MCV1 and five MCV2 sequences) and analyzed together with all MCV complete genomes previously deposited in freely accessible sequence repositories (four MCV1 and a single MCV2). In comparison to MCV1, a higher degree of nucleotide sequence conservation was observed among MCV2 genomes. Large-scale recombination events were identified in two newly assembled MCV1 genomes and one MCV2 genome. One recombination event was located in a newly identified recombinant region of the viral genome, and all previously described recombinant regions were re-identified in at least one novel MCV genome. MCV genes comprising the identified recombinant segments have been previously associated with viral interference with host T-cell and NK-cell immune responses. In conclusion, the two most common MCV genotypes emerged along divergent evolutionary pathways from a common ancestor, and the differences in the heterogeneity of MCV1 and MCV2 populations may be attributed to the strictness of the constraints imposed by the host immune response.

scholarly journals Genetic Transformation of Apomictic Grasses: Progress and Constraints

2021 ◽  
Vol 12 ◽  
Author(s):  
Andrés M. Bellido ◽  
Eduado D. Souza Canadá ◽  
Hugo R. Permingeat ◽  
Viviana Echenique
Keyword(s):  
Genetic Transformation ◽  
Plant Transformation ◽  
Large Scale ◽  
Crop Improvement ◽  
Current Status ◽  
Grass Species ◽  
Brachiaria Brizantha ◽  
Apomictic Species ◽  
Transformation Methods

The available methods for plant transformation and expansion beyond its limits remain especially critical for crop improvement. For grass species, this is even more critical, mainly due to drawbacks in in vitro regeneration. Despite the existence of many protocols in grasses to achieve genetic transformation through Agrobacterium or biolistic gene delivery, their efficiencies are genotype-dependent and still very low due to the recalcitrance of these species to in vitro regeneration. Many plant transformation facilities for cereals and other important crops may be found around the world in universities and enterprises, but this is not the case for apomictic species, many of which are C4 grasses. Moreover, apomixis (asexual reproduction by seeds) represents an additional constraint for breeding. However, the transformation of an apomictic clone is an attractive strategy, as the transgene is immediately fixed in a highly adapted genetic background, capable of large-scale clonal propagation. With the exception of some species like Brachiaria brizantha which is planted in approximately 100 M ha in Brazil, apomixis is almost non-present in economically important crops. However, as it is sometimes present in their wild relatives, the main goal is to transfer this trait to crops to fix heterosis. Until now this has been a difficult task, mainly because many aspects of apomixis are unknown. Over the last few years, many candidate genes have been identified and attempts have been made to characterize them functionally in Arabidopsis and rice. However, functional analysis in true apomictic species lags far behind, mainly due to the complexity of its genomes, of the trait itself, and the lack of efficient genetic transformation protocols. In this study, we review the current status of the in vitro culture and genetic transformation methods focusing on apomictic grasses, and the prospects for the application of new tools assayed in other related species, with two aims: to pave the way for discovering the molecular pathways involved in apomixis and to develop new capacities for breeding purposes because many of these grasses are important forage or biofuel resources.

scholarly journals Chronic Myelomonocytic Leukemia—Hematopathology Perspective

2021 ◽  
Author(s):  
Siba El Hussein ◽  
Sa A. Wang ◽  
Naveen Pemmaraju ◽  
Joseph D. Khoury ◽  
Sanam Loghavi
Keyword(s):  
Risk Stratification ◽  
Large Scale ◽  
Chronic Myelomonocytic Leukemia ◽  
Clinical Implications ◽  
The Past ◽  
Genomic Landscape ◽  
Sequencing Studies ◽  
Myelomonocytic Leukemia ◽  
Insight Into

ABSTRACT Our understanding of chronic myelomonocytic leukemia (CMML) has evolved tremendously over the past decade. Large-scale sequencing studies have led to increased insight into the genomic landscape of CMML and clinical implications of these changes. This in turn has resulted in refined and improved risk stratification models, which to date remain versatile and subject to remodeling, as new and evolving studies continue to refine our understanding of this disease. In this article, we present an up-to-date review of CMML from a hematopathology perspective, while providing a clinically practical summary that sheds light on the constant evolution of our understanding of this disease.

scholarly journals A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

2019 ◽  
Author(s):  
Lillian K. Padgitt-Cobb ◽  
Sarah B. Kingan ◽  
Jackson Wells ◽  
Justin Elser ◽  
Brent Kronmiller ◽  
...  
Keyword(s):  
Large Scale ◽  
Humulus Lupulus ◽  
Plant Genome ◽  
Repeat Content ◽  
Haplotype Variation ◽  
Genomic Landscape ◽  
Cannabidiolic Acid ◽  
Long Read ◽  
History Of ◽  
Insight Into

AbstractHop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing, and around the world, hop has been used in traditional medicine to treat a variety of ailments. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large, repetitive, and heterozygous genome of hop. We present the first report of a haplotype-phased assembly of a large plant genome. Our assembly and annotation of the Cascade cultivar genome is the most extensive to date. PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. Previous studies estimated repeat content at around 60%. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. Our quantification of repeat content provides context for the size of the hop genome, and supports the hypothesis of whole genome duplication (WGD), rather than expansion due to LTRs. With our more complete assembly, we have identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze a phased, diploid assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

Economy and supply

2021 ◽  
pp. 191-202
Author(s):  
Dominic Perring
Keyword(s):  
Economic Impact ◽  
Large Scale ◽  
Long Distance ◽  
Early Form ◽  
Ancient Economy ◽  
Market Economies ◽  
Roman Economy ◽  
Local Taxes ◽  
Small Change

A review of the contribution that the study of London makes to our understanding of the ancient economy. It explores the economic impact of the large-scale movement of goods and supplies required to support military advance, and to meet the expectations of the unusually large garrison stationed in Britain. The underwriting of these food supplies can be treated as an early form of military annona, sharing characteristics with arrangements made for the feeding of larger cities. It is argued that London’s economy and port, revolved around the needs of annona supply embracing military and civilian consumers. The infrastructure developed to support the annona stimulated a wider trade in luxury imports, best evidenced by the pottery carried to and through London (such as Samian and amphorae). This long-distance supply is the most archaeologically evident aspect of London’s Roman economy. The use of coin is another, and this chapter reviews the use of small change within London’s internal economy and local taxes. Coin-based market economies may not have penetrated far into the surrounding countryside, where subsistence and peasant farming was allowed to persist and rent and tax could be obtained through sharecropping and other ‘in kind’ arrangements.

scholarly journals Genetic diversity assessment of sorghum (Sorghum bicolor (L.) Moench) accessions using single nucleotide polymorphism markers

2019 ◽  
Vol 17 (5) ◽  
pp. 412-420
Author(s):  
G. Afolayan ◽  
S. P. Deshpande ◽  
S. E. Aladele ◽  
A. O. Kolawole ◽  
I. Angarawai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Diversity Assessment ◽  
Crop Research ◽  
International Crop Research Institute ◽  
Private Alleles

AbstractSorghum (Sorghum bicolor (L.) Moench) is an important resource to the national economy and it is essential to assess the genetic diversity in existing sorghum germplasm for better conservation, utilization and crop improvement. The aim of this study was to evaluate the level of genetic diversity within and among sorghum germplasms collected from diverse institutes in Nigeria and Mali using Single Nucleotide Polymorphic markers. Genetic diversity among the germplasm was low with an average polymorphism information content value of 0.24. Analysis of Molecular Variation revealed 6% variation among germplasm and 94% within germplasms. Dendrogram revealed three groups of clustering which indicate variations within the germplasms. Private alleles identified in the sorghum accessions from National Center for Genetic Resources and Biotechnology, Ibadan, Nigeria and International Crop Research Institute for the Semi-Arid Tropics, Kano, Nigeria shows their prospect for sorghum improvement and discovery of new agronomic traits. The presence of private alleles and genetic variation within the germplasms indicates that the accessions are valuable resources for future breeding programs.

scholarly journals Mutation Breeding in Tomato: Advances, Applicability and Challenges

Plants ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 128 ◽  
Author(s):  
Juhi Chaudhary ◽  
Alisha Alisha ◽  
Vacha Bhatt ◽  
Sonali Chandanshive ◽  
Nirbhay Kumar ◽  
...  
Keyword(s):  
Genome Editing ◽  
Large Scale ◽  
Insertional Mutagenesis ◽  
Crop Improvement ◽  
Mutation Breeding ◽  
Tomato Crop ◽  
Technological Advances ◽  
Trait Improvement ◽  
Induced Mutagenesis ◽  
Efficient Exploration

Induced mutagenesis is one of the most effective strategies for trait improvement without altering the well-optimized genetic background of the cultivars. In this review, several currently accessible methods such as physical, chemical and insertional mutagenesis have been discussed concerning their efficient exploration for the tomato crop improvement. Similarly, challenges for the adaptation of genome-editing, a newly developed technique providing an opportunity to induce precise mutation, have been addressed. Several efforts of genome-editing have been demonstrated in tomato and other crops, exploring its effectiveness and convenience for crop improvement. Descriptive data compiled here from such efforts will be helpful for the efficient exploration of technological advances. However, uncertainty about the regulation of genome-edited crops is still a significant concern, particularly when timely trait improvement in tomato cultivars is needed. In this regard, random approaches of induced mutagenesis are still promising if efficiently explored in breeding applications. Precise identification of casual mutation is a prerequisite for the molecular understanding of the trait development as well as its utilization for the breeding program. Recent advances in sequencing techniques provide an opportunity for the precise detection of mutagenesis-induced sequence variations at a large scale in the genome. Here, we reviewed several novel next-generation sequencing based mutation mapping approaches including Mutmap, MutChromeSeq, and whole-genome sequencing-based mapping which has enormous potential to accelerate the mutation breeding in tomato. The proper utilization of the existing well-characterized tomato mutant resources combined with novel mapping approaches would inevitably lead to rapid enhancement of tomato quality and yield. This article provides an overview of the principles and applications of mutagenesis approaches in tomato and discusses the current progress and challenges involved in tomato mutagenesis research.

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