scholarly journals A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

2021 ◽  
Author(s):  
Guangwei Li ◽  
Lijian Wang ◽  
Jianping Yang ◽  
Hang He ◽  
Huaibing Jin ◽  
...  
Keyword(s):  
Cereal Crops ◽  
Comparative Genomic ◽  
Gene Duplications ◽  
Forage Crop ◽  
Genome Wide ◽  
Genomic Studies ◽  
Physical Organization ◽  
Prolamin Loci ◽  
High Quality Genome ◽  
Strong Expansion

AbstractRye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.

scholarly journals High-Quality Genome Assembly of Peronospora destructor, the Causal Agent of Onion Downy Mildew

2020 ◽  
Vol 33 (5) ◽  
pp. 718-720
Author(s):  
Karthi Natesan ◽  
Ji Yeon Park ◽  
Cheol-Woo Kim ◽  
Dong Suk Park ◽  
Young-Seok Kwon ◽  
...  
Keyword(s):  
Downy Mildew ◽  
De Novo ◽  
Gc Content ◽  
Comparative Genomic ◽  
High Quality ◽  
Sequencing Platform ◽  
Peronospora Destructor ◽  
Genomic Studies ◽  
Genome Assemblies ◽  
High Quality Genome

Peronospora destructor is an obligate biotrophic oomycete that causes downy mildew on onion (Allium cepa). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of P. destructor using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of P. destructor and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of P. destructor isolates and for comparative genomic studies of the biotrophic oomycetes.

scholarly journals Genome Sequence Resource for Elsinoë ampelina, the Causal Organism of Grapevine Anthracnose

2020 ◽  
Vol 33 (4) ◽  
pp. 576-579 ◽  
Author(s):  
Zhi Li ◽  
Yanchun Fan ◽  
Pingping Chang ◽  
Linlin Gao ◽  
Xiping Wang
Keyword(s):  
Genome Sequence ◽  
Management Strategies ◽  
Comparative Genomic ◽  
Causal Organism ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Elsinoe Ampelina ◽  
Genomic Studies ◽  
High Quality Genome ◽  
Ascomycetous Fungus

Elsinoë ampelina is an ascomycetous fungus that causes grape anthracnose, a potentially devastating disease worldwide. Here, we report a 28.29 Mb high-quality genome sequence of E. ampelina YL-1 that encodes 8,057 predicted protein-coding genes and represents the first sequenced genome assembly of E. ampelina. This study adds to the current genomic resources for the genus Elsinoë and paves the way for research on comparative genomic studies, E. ampelina–grape interactions, and improvement of management strategies.

scholarly journals Current Progress in Evolutionary Comparative Genomics of Great Apes

2021 ◽  
Vol 12 ◽  
Author(s):  
Aisha Yousaf ◽  
Junfeng Liu ◽  
Sicheng Ye ◽  
Hua Chen
Keyword(s):  
Evolutionary History ◽  
Comparative Genomic ◽  
Great Ape ◽  
Structural Variations ◽  
Genome Sequences ◽  
New Genes ◽  
Genomic Analyses ◽  
Genomic Studies ◽  
High Quality Genome ◽  
Human Specific

The availability of high-quality genome sequences of great ape species provides unprecedented opportunities for genomic analyses. Herein, we reviewed the recent progress in evolutionary comparative genomic studies of the existing great ape species, including human, chimpanzee, bonobo, gorilla, and orangutan. We elaborate discovery on evolutionary history, natural selection, structural variations, and new genes of these species, which is informative for understanding the origin of human-specific phenotypes.

scholarly journals Genome-Wide Analysis of Four Pathotypes of Wheat Rust Pathogen (Puccinia graminis) Reveals Structural Variations and Diversifying Selection

2021 ◽  
Vol 7 (9) ◽  
pp. 701
Author(s):  
Kanti Kiran ◽  
Hukam C. Rawal ◽  
Himanshu Dubey ◽  
Rajdeep Jaswal ◽  
Subhash C. Bhardwaj ◽  
...  
Keyword(s):  
Control Measures ◽  
Comparative Genomic ◽  
Puccinia Graminis ◽  
Structural Variations ◽  
Illumina Hiseq ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Genomic Studies ◽  
Paired End Sequencing ◽  
Wheat Rust

Diseases caused by Puccinia graminis are some of the most devastating diseases of wheat. Extensive genomic understanding of the pathogen has proven helpful not only in understanding host- pathogen interaction but also in finding appropriate control measures. In the present study, whole-genome sequencing of four diverse P. graminis pathotypes was performed to understand the genetic variation and evolution. An average of 63.5 Gb of data per pathotype with about 100× average genomic coverage was achieved with 100-base paired-end sequencing performed with Illumina Hiseq 1000. Genome structural annotations collectively predicted 9273 functional proteins including ~583 extracellular secreted proteins. Approximately 7.4% of the genes showed similarity with the PHI database which is suggestive of their significance in pathogenesis. Genome-wide analysis demonstrated pathotype 117-6 as likely distinct and descended through a different lineage. The 3–6% more SNPs in the regulatory regions and 154 genes under positive selection with their orthologs and under negative selection in the other three pathotypes further supported pathotype 117-6 to be highly diverse in nature. The genomic information generated in the present study could serve as an important source for comparative genomic studies across the genus Puccinia and lead to better rust management in wheat.

scholarly journals Transcription Factors of the Alx Family: Evolutionarily Conserved Regulators of Deuterostome Skeletogenesis

2020 ◽  
Vol 11 ◽  
Author(s):  
Jian Ming Khor ◽  
Charles A. Ettensohn
Keyword(s):  
Transcription Factors ◽  
Gene Family ◽  
Current Knowledge ◽  
Comparative Genomic ◽  
Gene Duplications ◽  
Evolutionarily Conserved ◽  
Genomic Studies ◽  
Gene Regulatory ◽  
Paired Class ◽  
Diverse Groups

Members of the alx gene family encode transcription factors that contain a highly conserved Paired-class, DNA-binding homeodomain, and a C-terminal OAR/Aristaless domain. Phylogenetic and comparative genomic studies have revealed complex patterns of alx gene duplications during deuterostome evolution. Remarkably, alx genes have been implicated in skeletogenesis in both echinoderms and vertebrates. In this review, we provide an overview of current knowledge concerning alx genes in deuterostomes. We highlight their evolutionarily conserved role in skeletogenesis and draw parallels and distinctions between the skeletogenic gene regulatory circuitries of diverse groups within the superphylum.

scholarly journals DNA copy number imbalances in primary cutaneous lymphomas (PCL)

2018 ◽  
Author(s):  
Georgiana Gug ◽  
Qingyao Huang ◽  
Elena Chiticariu ◽  
Caius Solovan ◽  
Michael Baudis
Keyword(s):  
Copy Number ◽  
Meta Analysis ◽  
Comparative Genomic ◽  
Specific Data ◽  
Genomic Imbalances ◽  
Genome Wide ◽  
Cutaneous Lymphomas ◽  
Number Variation ◽  
Genomic Studies ◽  
Molecular Aberrations

AbstractCutaneous lymphomas (CL) represent a clinically defined group of extranodal non-Hodgkin lymphomas harboring heterogeneous and incompletely delineated molecular aberrations. Over the past decades, molecular studies have identified several chromosomal aberrations, but the interpretation of individual genomic studies can be challenging.We conducted a meta-analysis to delineate genomic alterations for different types of PCL. Searches of PubMed and ISI Web of Knowledge for the years 1996 to 2016 identified 32 publications reporting the investigation of PCL for genome-wide copy number alterations, by means of comparative genomic hybridization techniques and whole genome and exome sequencing. For 449 samples from 22 publications, copy number variation data was accessible for sample based meta-analysis. Summary profiles for genomic imbalances, generated from case-specific data, identified complex genomic imbalances, which could discriminate between different subtypes of CL and promise a more accurate classification. The collected data presented in this study are publicly available through the “Progenetix” online repository.

scholarly journals Use of Multiple Sequencing Technologies To Produce a High-Quality Genome of the Fungus Pseudogymnoascus destructans , the Causative Agent of Bat White-Nose Syndrome

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Kevin P. Drees ◽  
Jonathan M. Palmer ◽  
Robert Sebra ◽  
Jeffrey M. Lorch ◽  
Cynthia Chen ◽  
...  
Keyword(s):  
Fungal Pathogen ◽  
Reference Genome ◽  
Comparative Genomic ◽  
Eastern North America ◽  
Pseudogymnoascus Destructans ◽  
Wildlife Diseases ◽  
White Nose Syndrome ◽  
Sequencing Technologies ◽  
Genomic Studies ◽  
High Quality Genome

White-nose syndrome has recently emerged as one of the most devastating wildlife diseases recorded, causing widespread mortality in numerous bat species throughout eastern North America. Here, we present an improved reference genome of the fungal pathogen Pseudogymnoascus destructans for use in comparative genomic studies.

scholarly journals Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora

2020 ◽  
Vol 6 (3) ◽  
pp. 39
Author(s):  
Samara M. C. Lemos ◽  
Luiz F. C. Fonçatti ◽  
Romain Guyot ◽  
Alexandre R. Paschoal ◽  
Douglas S. Domingues
Keyword(s):  
Coffea Canephora ◽  
Comparative Genomic ◽  
Pests And Diseases ◽  
Genome Regulation ◽  
Genome Wide ◽  
Genomic Studies ◽  
Non Coding Rnas ◽  
Environmental Responses ◽  
Expression Evidence

Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the C. canephora genome. This study aimed to provide a curated characterization of six ncRNA classes in the Coffea canephora genome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in the C. canephora genome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity.

Migraine: Genetic Variants and Clinical Phenotypes

2019 ◽  
Vol 26 (34) ◽  
pp. 6207-6221 ◽  
Author(s):  
Innocenzo Rainero ◽  
Alessandro Vacca ◽  
Flora Govone ◽  
Annalisa Gai ◽  
Lorenzo Pinessi ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Association Studies ◽  
Mthfr Gene ◽  
Genome Wide Association Studies ◽  
Clinical Phenotypes ◽  
Network Analyses ◽  
Genome Wide ◽  
Genomic Studies ◽  
The Common ◽  
The Relationship

Migraine is a common, chronic neurovascular disorder caused by a complex interaction between genetic and environmental risk factors. In the last two decades, molecular genetics of migraine have been intensively investigated. In a few cases, migraine is transmitted as a monogenic disorder, and the disease phenotype cosegregates with mutations in different genes like CACNA1A, ATP1A2, SCN1A, KCNK18, and NOTCH3. In the common forms of migraine, candidate genes as well as genome-wide association studies have shown that a large number of genetic variants may increase the risk of developing migraine. At present, few studies investigated the genotype-phenotype correlation in patients with migraine. The purpose of this review was to discuss recent studies investigating the relationship between different genetic variants and the clinical characteristics of migraine. Analysis of genotype-phenotype correlations in migraineurs is complicated by several confounding factors and, to date, only polymorphisms of the MTHFR gene have been shown to have an effect on migraine phenotype. Additional genomic studies and network analyses are needed to clarify the complex pathways underlying migraine and its clinical phenotypes.

scholarly journals High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata

2021 ◽  
Vol 22 (11) ◽  
pp. 5723
Author(s):  
Yuan-Yuan Xu ◽  
Sheng-Rui Liu ◽  
Zhi-Meng Gan ◽  
Ren-Fang Zeng ◽  
Jin-Zhi Zhang ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Linkage Map ◽  
Genetic Map ◽  
Expression Patterns ◽  
High Density ◽  
Poncirus Trifoliata ◽  
Leaf Abscission ◽  
Comparative Genomic ◽  
Map Comparison ◽  
Genomic Studies

A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.

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