scholarly journals Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines

2017 ◽  
Author(s):  
Alex B. Brohammer ◽  
Thomas JY. Kono ◽  
Nathan M. Springer ◽  
Suzanne E. McGaugh ◽  
Candice N. Hirsch
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Duplicate Gene ◽  
Duplication Event ◽  
Inbred Lines ◽  
Whole Genome ◽  
Ancestral State ◽  
Genome Duplication Event ◽  
Number Variation ◽  
And Function

SUMMARYMaize is a diverse paleotetraploid species with widespread presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization and differential fractionation refers to non-shared gene loss events between individuals. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole genome de novo assemblies of the inbred lines B73 and PH207. Between these two genomes, syntenic genes were highly conserved with less than 1% of syntenic genes being subject to differential fractionation. The few variable syntenic genes that were identified are unlikely to contribute to functional phenotypic variation, as there is a significant depletion of these genes in annotated gene sets. In further comparisons of 60 diverse inbred lines, non-syntenic genes were six times more likely to be variable compared to syntenic genes, suggesting that comparisons among additional genome assemblies are not likely to result in the discovery of large-scale presence/absence variation among syntenic genes.SIGNIFICANCE STATEMENTThere is a large amount of presence/absence variation for gene content in maize. One mechanism that has been hypothesized to contribute to this variation is differential fractionation between individuals following the maize whole genome duplication event. Using comparative genomics, with sorghum and rice representing the ancestral state, we observed little evidence of differential fractionation among elite inbred lines and the few differentially fractionated genes identified did not appear to confer functional significance.

scholarly journals A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event

GigaScience ◽  
2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Zheng Fan ◽  
Tao Yuan ◽  
Piao Liu ◽  
Lu-Yu Wang ◽  
Jian-Feng Jin ◽  
...  
Keyword(s):  
Whole Genome Duplication ◽  
Large Scale ◽  
Hox Genes ◽  
Genome Duplication ◽  
Duplication Event ◽  
Whole Genome ◽  
High Quality ◽  
Genome Duplication Event ◽  
Whole Genome Duplication Event ◽  
Chromosome Level

Abstract Background The spider Trichonephila antipodiana (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from ∼2 mm in length to insects larger than itself (>20‒50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it has been reported that an ancient whole-genome duplication event occurred in spiders, lack of a high-quality genome has limited characterization of this event. Results We present a chromosome-level T. antipodiana genome constructed on the basis of PacBio and Hi-C sequencing. The assembled genome is 2.29 Gb in size with a scaffold N50 of 172.89 Mb. Hi-C scaffolding assigned 98.5% of the bases to 13 pseudo-chromosomes, and BUSCO completeness analysis revealed that the assembly included 94.8% of the complete arthropod universal single-copy orthologs (n = 1,066). Repetitive elements account for 59.21% of the genome. We predicted 19,001 protein-coding genes, of which 96.78% were supported by transcriptome-based evidence and 96.32% matched protein records in the UniProt database. The genome also shows substantial expansions in several detoxification-associated gene families, including cytochrome P450 mono-oxygenases, carboxyl/cholinesterases, glutathione-S-transferases, and ATP-binding cassette transporters, reflecting the possible genomic basis of polyphagy. Further analysis of the T. antipodiana genome architecture reveals an ancient whole-genome duplication event, based on 2 lines of evidence: (i) large-scale duplications from inter-chromosome synteny analysis and (ii) duplicated clusters of Hox genes. Conclusions The high-quality T. antipodiana genome represents a valuable resource for spider research and provides insights into this species’ adaptation to the environment.

scholarly journals Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy

2018 ◽  
Author(s):  
Christine M. Gault ◽  
Karl A. Kremling ◽  
Edward S. Buckler
Keyword(s):  
Gene Expression ◽  
Gene Loss ◽  
Genome Duplication ◽  
De Novo ◽  
Gc Content ◽  
Purifying Selection ◽  
Duplicate Gene ◽  
Duplication Event ◽  
High Quality ◽  
Genome Duplication Event

AbstractPlant genomes reduce in size following a whole genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize and its sister genus, Tripsacum, share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for Tripsacum exist, it is unknown whether Tripsacum grasses and maize have maintained a similar set of genes under purifying selection. Here we present high quality de novo transcriptome assemblies for two species: Tripsacum dactyloides and Tripsacum floridanum. Genes with experimental protein evidence in maize were good candidates for genes under purifying selection in both genera because pseudogenes by definition do not produce protein. We tested whether 15,160 maize genes with protein evidence are resisting gene loss and whether their Tripsacum homologs are also resisting gene loss. Protein-encoding maize transcripts and their Tripsacum homologs have higher GC content, higher gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their Tripsacum homologs. These results indicate that gene loss is occurring in a similar fashion in both genera after a shared ancient polyploidy event. The Tripsacum transcriptome assemblies provide a high quality genomic resource that can provide insight into the evolution of maize, an highly valuable crop worldwide.Core ideasMaize genes with protein evidence have higher expression and GC contentTripsacum homologs of maize genes exhibit the same trends as in maizeMaize proteome genes have more highly correlated gene expression with TripsacumExpression dominance for homeologs occurs similarly between maize and TripsacumA similar set of genes may be decaying into pseudogenes in maize and Tripsacum

scholarly journals Insights into dispersed duplications and complex structural mutations from whole genome sequencing 706 families

2020 ◽  
Author(s):  
Christopher W. Whelan ◽  
Robert E. Handsaker ◽  
Giulio Genovese ◽  
Seva Kashin ◽  
Monkol Lek ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number Variation ◽  
Copy Number ◽  
De Novo ◽  
Whole Genome ◽  
Sequencing Data ◽  
Number Variation ◽  
Structural Mutations ◽  
Or Gene ◽  
Genomic Locations

AbstractTwo intriguing forms of genome structural variation (SV) – dispersed duplications, and de novo rearrangements of complex, multi-allelic loci – have long escaped genomic analysis. We describe a new way to find and characterize such variation by utilizing identity-by-descent (IBD) relationships between siblings together with high-precision measurements of segmental copy number. Analyzing whole-genome sequence data from 706 families, we find hundreds of “IBD-discordant” (IBDD) CNVs: loci at which siblings’ CNV measurements and IBD states are mathematically inconsistent. We found that commonly-IBDD CNVs identify dispersed duplications; we mapped 95 of these common dispersed duplications to their true genomic locations through family-based linkage and population linkage disequilibrium (LD), and found several to be in strong LD with genome-wide association (GWAS) signals for common diseases or gene expression variation at their revealed genomic locations. Other CNVs that were IBDD in a single family appear to involve de novo mutations in complex and multi-allelic loci; we identified 26 de novo structural mutations that had not been previously detected in earlier analyses of the same families by diverse SV analysis methods. These included a de novo mutation of the amylase gene locus and multiple de novo mutations at chromosome 15q14. Combining these complex mutations with more-conventional CNVs, we estimate that segmental mutations larger than 1kb arise in about one per 22 human meioses. These methods are complementary to previous techniques in that they interrogate genomic regions that are home to segmental duplication, high CNV allele frequencies, and multi-allelic CNVs.Author SummaryCopy number variation is an important form of genetic variation in which individuals differ in the number of copies of segments of their genomes. Certain aspects of copy number variation have traditionally been difficult to study using short-read sequencing data. For example, standard analyses often cannot tell whether the duplicated copies of a segment are located near the original copy or are dispersed to other regions of the genome. Another aspect of copy number variation that has been difficult to study is the detection of mutations in the copy number of DNA segments passed down from parents to their children, particularly when the mutations affect genome segments which already display common copy number variation in the population. We develop an analytical approach to solving these problems when sequencing data is available for all members of families with at least two children. This method is based on determining the number of parental haplotypes the two siblings share at each location in their genome, and using that information to determine the possible inheritance patterns that might explain the copy numbers we observe in each family member. We show that dispersed duplications and mutations can be identified by looking for copy number variants that do not follow these expected inheritance patterns. We use this approach to determine the location of 95 common duplications which are dispersed to distant regions of the genome, and demonstrate that these duplications are linked to genetic variants that affect disease risk or gene expression levels. We also identify a set of copy number mutations not detected by previous analyses of sequencing data from a large cohort of families, and show that repetitive and complex regions of the genome undergo frequent mutations in copy number.

scholarly journals Comparative Inference of Duplicated Genes Produced by Polyploidization in Soybean Genome

2013 ◽  
Vol 2013 ◽  
pp. 1-4
Author(s):  
Yanmei Yang ◽  
Jinpeng Wang ◽  
Jianyong Di
Keyword(s):  
Statistical Analysis ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Duplication Event ◽  
Plant Evolution ◽  
Soybean Genome ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Genome Duplication Event ◽  
Scientific Value

Soybean (Glycine max) is one of the most important crop plants for providing protein and oil. It is important to investigate soybean genome for its economic and scientific value. Polyploidy is a widespread and recursive phenomenon during plant evolution, and it could generate massive duplicated genes which is an important resource for genetic innovation. Improved sequence alignment criteria and statistical analysis are used to identify and characterize duplicated genes produced by polyploidization in soybean. Based on the collinearity method, duplicated genes by whole genome duplication account for 70.3% in soybean. From the statistical analysis of the molecular distances between duplicated genes, our study indicates that the whole genome duplication event occurred more than once in the genome evolution of soybean, which is often distributed near the ends of chromosomes.

scholarly journals Ethical and public policy challenges for pharmacogenomics

2014 ◽  
Vol 16 (4) ◽  
pp. 567-574 ◽  
Keyword(s):  
Psychiatric Disorders ◽  
Large Scale ◽  
Ethical Issues ◽  
De Novo ◽  
Correct Choice ◽  
Genomic Research ◽  
Drug Metabolizing Enzyme ◽  
Increased Risk ◽  
Number Variation ◽  
Metabolizing Enzyme

It is timely to consider the ethical and social questions raised by progress in pharmacogenomics, based on the current importance of pharmacogenomics for avoidance of predictable side effects of drugs, and for correct choice of medications in certain cancers. It has been proposed that the entire population be genotyped for drug-metabolizing enzyme polymorphisms, as a measure that would prevent many untoward and dangerous drug reactions. Pharmacologic treatment targeting based on genomics of disease can be expected to increase greatly in the coming years. Policy and ethical issues exist on consent for large-scale genomic pharmacogenomic data collection, public vs corporate ownership of genomic research results, testing efficacy and safety of drugs used for rare genomic indications, and accessibility of treatments based on costly research that is applicable to relatively few patients. In major psychiatric disorders and intellectual deficiency, rare and de novo deletion or duplication of chromosomal segments (copy number variation), in the aggregate, are common causes of increased risk. This implies that the policy problems of pharmacogenomics will be particularly important for the psychiatric disorders.

scholarly journals Genomic instability in an interspecific hybrid of the genus Saccharomyces: a matter of adaptability

2020 ◽  
Vol 6 (10) ◽  
Author(s):  
Miguel Morard ◽  
Clara Ibáñez ◽  
Ana C. Adam ◽  
Amparo Querol ◽  
Eladio Barrio ◽  
...  
Keyword(s):  
Genome Instability ◽  
Nuclear Genome ◽  
Duplication Event ◽  
Wine Industry ◽  
Hybrid Strain ◽  
Genome Duplication Event ◽  
Genetic Features ◽  
Number Variation ◽  
Stress Responding ◽  
Saccharomyces Kudriavzevii

Ancient events of polyploidy have been linked to huge evolutionary leaps in the tree of life, while increasing evidence shows that newly established polyploids have adaptive advantages in certain stress conditions compared to their relatives with a lower ploidy. The genus Saccharomyces is a good model for studying such events, as it contains an ancient whole-genome duplication event and many sequenced Saccharomyces cerevisiae are, evolutionary speaking, newly formed polyploids. Many polyploids have unstable genomes and go through large genome erosions; however, it is still unknown what mechanisms govern this reduction. Here, we sequenced and studied the natural S. cerevisiae × Saccharomyces kudriavzevii hybrid strain, VIN7, which was selected for its commercial use in the wine industry. The most singular observation is that its nuclear genome is highly unstable and drastic genomic alterations were observed in only a few generations, leading to a widening of its phenotypic landscape. To better understand what leads to the loss of certain chromosomes in the VIN7 cell population, we looked for genetic features of the genes, such as physical interactions, complex formation, epistatic interactions and stress responding genes, which could have beneficial or detrimental effects on the cell if their dosage is altered by a chromosomal copy number variation. The three chromosomes lost in our VIN7 population showed different patterns, indicating that multiple factors could explain the mechanisms behind the chromosomal loss. However, one common feature for two out of the three chromosomes is that they are among the smallest ones. We hypothesize that small chromosomes alter their copy numbers more frequently as a low number of genes is affected, meaning that it is a by-product of genome instability, which might be the chief driving force of the adaptability and genome architecture of this hybrid.

scholarly journals A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense

GigaScience ◽  
2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Shubo Jin ◽  
Chao Bian ◽  
Sufei Jiang ◽  
Kai Han ◽  
Yiwei Xiong ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Evolutionary Biology ◽  
Sex Differentiation ◽  
Duplication Event ◽  
Whole Genome ◽  
Genome Duplication Event ◽  
Protein Coding ◽  
Macrobrachium Nipponense ◽  
Oriental River Prawn ◽  
Chromosome Level

Abstract Background The oriental river prawn, Macrobrachium nipponense, is an economically important shrimp in China. Male prawns have higher commercial value than females because the former grow faster and reach larger sizes. It is therefore important to reveal sex-differentiation and development mechanisms of the oriental river prawn to enable genetic improvement. Results We sequenced 293.3 Gb of raw Illumina short reads and 405.7 Gb of Pacific Biosciences long reads. The final whole-genome assembly of the Oriental river prawn was ∼4.5 Gb in size, with predictions of 44,086 protein-coding genes. A total of 49 chromosomes were determined, with an anchor ratio of 94.7% and a scaffold N50 of 86.8 Mb. A whole-genome duplication event was deduced to have happened 109.8 million years ago. By integration of genome and transcriptome data, 21 genes were predicted as sex-related candidate genes. Conclusion The first high-quality chromosome-level genome assembly of the oriental river prawn was obtained. These genomic data, along with transcriptome sequences, are essential for understanding sex-differentiation and development mechanisms in the oriental river prawn, as well as providing genetic resources for in-depth studies on developmental and evolutionary biology in arthropods.

scholarly journals The de novo genome of the “Spanish” slug Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Panpulmonata): massive expansion of transposable elements in a major pest species

2020 ◽  
Author(s):  
Zeyuan Chen ◽  
Özgül Doğan ◽  
Nadège Guiglielmoni ◽  
Anne Guichard ◽  
Michael Schrödl
Keyword(s):  
Transposable Elements ◽  
Genome Assembly ◽  
De Novo ◽  
Repetitive Sequences ◽  
Land Snails ◽  
Whole Genome ◽  
Pest Species ◽  
High Quality ◽  
Genome Duplication Event ◽  
Arion Vulgaris

AbstractBackgroundThe “Spanish” slug, Arion vulgaris Moquin-Tandon, 1855, is considered to be among the 100 worst pest species in Europe. It is common and invasive to at least northern and eastern parts of Europe, probably benefitting from climate change and the modern human lifestyle. The origin and expansion of this species, the mechanisms behind its outstanding adaptive success and ability to outcompete other land slugs are worth to be explored on a genomic level. However, a high-quality chromosome-level genome is still lacking.FindingsThe final assembly of A. vulgaris was obtained by combining short reads, linked reads, Nanopore long reads, and Hi-C data. The genome assembly size is 1.54 Gb with a contig N50 length of 8.6 Mb. We found a recent expansion of transposable elements (TEs) which results in repetitive sequences accounting for more than 75% of the A. vulgaris genome, which is the highest among all known gastropod species. We identified 32,518 protein coding genes, and 2,763 species specific genes were functionally enriched in response to stimuli, nervous system and reproduction. With 1,237 single-copy orthologs from A. vulgaris and other related mollusks with whole-genome data available, we reconstructed the phylogenetic relationships of gastropods and estimated the divergence time of stylommatophoran land snails (Achatina) and Arion slugs at around 126 million years ago, and confirmed the whole genome duplication event shared by them.ConclusionsTo our knowledge, the A. vulgaris genome is the first land slug genome assembly published to date. The high-quality genomic data will provide valuable genetic resources for further phylogeographic studies of A. vulgaris origin and expansion, invasiveness, as well as molluscan aquatic-land transition and shell formation.

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