A Genome-Wide Identification Study Reveals That HmoCYP76AD1, HmoDODAα1 and HmocDOPA5GT Involved in Betalain Biosynthesis in Hylocereus

Betalains are water-soluble nitrogen-containing pigments with multiple bioactivities. Pitayas are the only at large-scale commercially grown fruit containing abundant betalains for consumers. Currently, the key genes involved in betalain biosynthesis remain to be fully elucidated. Moreover, genome-wide analyses of these genes in betalain biosynthesis are not available in betalain-producing plant species. In this study, totally 53 genes related to betalain biosynthesis were identified from the genome data of Hylocereus undatus. Four candidate genes i.e., one cytochrome P-450 R gene (HmoCYP76AD1), two L-DOPA 4,5-dioxygenase genes (HmoDODAα1 and HmoDODAα2), and one cyclo-DOPA 5-O glucosyltransferase gene (HmocDOPA5GT) were initially screened according to bioinformatics and qRT-PCR analyses. Silencing HmoCYP76AD1, HmoDODAα1, HmoDODAα2 or HmocDOPA5GT resulted in loss of red pigment. HmoDODAα1 displayed a high level of L-DOPA 4,5-dioxygenase activity to produce betalamic acid and formed yellow betaxanthin. Co-expression of HmoCYP76AD1, HmoDODAα1 and HmocDOPA5GT in Nicotiana benthamiana and yeast resulted in high abundance of betalain pigments with a red color. These results suggested that HmoCYP76AD1, HmoDODAα1, and HmocDOPA5GT play key roles in betalain biosynthesis in Hylocereus. The results of the present study provide novel genes for molecular breeding programs of pitaya.

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Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽

10.1093/genetics/159.4.1765 ◽

2001 ◽

Vol 159 (4) ◽

pp. 1765-1778

Author(s):

Gregory J Budziszewski ◽

Sharon Potter Lewis ◽

Lyn Wegrich Glover ◽

Jennifer Reineke ◽

Gary Jones ◽

...

Keyword(s):

Large Scale ◽

Protein Translocation ◽

Gene Families ◽

Mutant Phenotype ◽

Lethal Mutant ◽

A Genome ◽

Genes Encoding ◽

High Level ◽

Mutant Lines ◽

Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

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Phenotypic Screen and Transcriptomics Approach Complement Each Other in Functional Genomics of Defensive Stink Gland Physiology

10.21203/rs.3.rs-1117784/v1 ◽

2021 ◽

Author(s):

Sabrina Lehmann ◽

Bibi Atika ◽

Daniela Grossmann ◽

Christian Schmitt-Engel ◽

Nadi Strohlein ◽

...

Keyword(s):

Functional Genomics ◽

Large Scale ◽

Reverse Genetics ◽

Expression Profiles ◽

Forward Genetics ◽

Large Set ◽

Knock Down ◽

Genome Wide ◽

Phenotypic Screen ◽

A Genome

Abstract Background Functional genomics uses unbiased systematic genome-wide gene disruption or analyzes natural variations such as gene expression profiles of different tissues from multicellular organisms to link gene functions to particular phenotypes. Functional genomics approaches are of particular importance to identify large sets of genes that are specifically important for a particular biological process beyond known candidate genes, or when the process has not been studied with genetic methods before. Results Here, we present a large set of genes whose disruption interferes with the function of the odoriferous defensive stink glands of the red flour beetle Tribolium castaneum. This gene set is the result of a large-scale systematic phenotypic screen using a reverse genetics strategy based on RNA interference applied in a genome-wide forward genetics manner. In this first-pass screen, 130 genes were identified, of which 69 genes could be confirmed to cause knock-down gland phenotypes, which vary from necrotic tissue and irregular reservoir size to irregular color or separation of the secreted gland compounds. The knock-down of 13 genes caused specifically a strong reduction of para-benzoquinones, suggesting a specific function in the synthesis of these toxic compounds. Only 14 of the 69 confirmed gland genes are differentially overexpressed in stink gland tissue and thus could have been detected in a transcriptome-based analysis. Moreover, of the 29 previously transcriptomics-identified genes causing a gland phenotype, only one gene was recognized by this phenotypic screen despite the fact that 13 of them were covered by the screen. Conclusion Our results indicate the importance of combining diverse and independent methodologies to identify genes necessary for the function of a certain biological tissue, as the different approaches do not deliver redundant results but rather complement each other. The presented phenotypic screen together with a transcriptomics approach are now providing a set of close to hundred genes important for odoriferous defensive stink gland physiology in beetles.

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Epigenomic changes after acupuncture treatment in patients suffering from burnout

Complementary Medicine Research ◽

10.1159/000521347 ◽

2021 ◽

Author(s):

Marc Petitpierre ◽

Ludwig Stenz ◽

Ariane Paoloni-Giacobino

Keyword(s):

Acupuncture Treatment ◽

Maslach Burnout Inventory ◽

Personal Accomplishment ◽

Steroid Synthesis ◽

Genome Wide ◽

A Genome ◽

Before And After ◽

High Level ◽

The Brain

Introduction: The effects of acupuncture treatment in patients suffering from burnout may imply an epigenetic control mediated by DNA methylation changes. In this observational study, a genome-wide characterization of epigenetic changes in blood DNA, before and after acupuncture treatment, was performed in a cohort of 11 patients suffering from burnout. Methods: Burnout was assessed using the Maslach Burnout Inventory (MBI) and DNA was extracted from blood samples and analyzed by Illumina EPIC BeadChip. Results: Before acupuncture, all patients suffered of emotional exhaustion (EE) (MBI-EE score, 44±6), 81% suffered of depersonalization (DP) (MBI-DP score, 16±6), and 72% of low feelings of personal accomplishment (PA) (MBI-PA score, 29±9). After acupuncture, all MBI dimensions improved significantly (EE, 16±11 [p=1.5*10-4]; DP, 4±5 [p=5.3*10-4]; and PA, 40±6 [p=4.1*10-3]). For each patient, both methylomes obtained before and after acupuncture co-clustered in the multidimensional scaling plot, indicating a high level of similarity. Genes corresponding to the 10 most differentially methylated CpGs showed enrichment in the brain dopaminergic signalling, steroid synthesis and in the insulin sensitivity pathways. Conclusion: Acupuncture treatment was found to be highly effective on all burnout dimensions and the epigenetic targets identified were involved in some major disturbances of this syndrome.

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A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy

Microorganisms ◽

10.3390/microorganisms7060161 ◽

2019 ◽

Vol 7 (6) ◽

pp. 161 ◽

Cited By ~ 1

Author(s):

Ming-Hsin Tsai ◽

Yen-Yi Liu ◽

Von-Wun Soo ◽

Chih-Chieh Chen

Keyword(s):

Microbial Diversity ◽

Large Scale ◽

Gene Selection ◽

Marker Gene ◽

Genome Comparison ◽

Marker Genes ◽

Species Classification ◽

Genome Wide ◽

A Genome ◽

Comparison Approach

Microbial diversity has always presented taxonomic challenges. With the popularity of next-generation sequencing technology, more unculturable bacteria have been sequenced, facilitating the discovery of additional new species and complicated current microbial classification. The major challenge is to assign appropriate taxonomic names. Hence, assessing the consistency between taxonomy and genomic relatedness is critical. We proposed and applied a genome comparison approach to a large-scale survey to investigate the distribution of genomic differences among microorganisms. The approach applies a genome-wide criterion, homologous coverage ratio (HCR), for describing the homology between species. The survey included 7861 microbial genomes that excluded plasmids, and 1220 pairs of genera exhibited ambiguous classification. In this study, we also compared the performance of HCR and average nucleotide identity (ANI). The results indicated that HCR and ANI analyses yield comparable results, but a few examples suggested that HCR has a superior clustering effect. In addition, we used the Genome Taxonomy Database (GTDB), the gold standard for taxonomy, to validate our analysis. The GTDB offers 120 ubiquitous single-copy proteins as marker genes for species classification. We determined that the analysis of the GTDB still results in classification boundary blur between some genera and that the marker gene-based approach has limitations. Although the choice of marker genes has been quite rigorous, the bias of marker gene selection remains unavoidable. Therefore, methods based on genomic alignment should be considered for use for species classification in order to avoid the bias of marker gene selection. On the basis of our observations of microbial diversity, microbial classification should be re-examined using genome-wide comparisons.

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A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns

Genome Biology and Evolution ◽

10.1093/gbe/evz142 ◽

2019 ◽

Vol 11 (8) ◽

pp. 2078-2098 ◽

Cited By ~ 8

Author(s):

Shu-Ye Jiang ◽

Jingjing Jin ◽

Rajani Sarojam ◽

Srinivasan Ramachandran

Keyword(s):

Gene Family ◽

Large Scale ◽

Family Members ◽

Terpene Synthase ◽

Limited Information ◽

Terpene Synthases ◽

Genome Wide ◽

A Genome ◽

Family Expansion ◽

Insight Into

Abstract Terpenes are organic compounds and play important roles in plant growth and development as well as in mediating interactions of plants with the environment. Terpene synthases (TPSs) are the key enzymes responsible for the biosynthesis of terpenes. Although some species were employed for the genome-wide identification and characterization of the TPS family, limited information is available regarding the evolution, expansion, and retention mechanisms occurring in this gene family. We performed a genome-wide identification of the TPS family members in 50 sequenced genomes. Additionally, we also characterized the TPS family from aromatic spearmint and basil plants using RNA-Seq data. No TPSs were identified in algae genomes but the remaining plant species encoded various numbers of the family members ranging from 2 to 79 full-length TPSs. Some species showed lineage-specific expansion of certain subfamilies, which might have contributed toward species or ecotype divergence or environmental adaptation. A large-scale family expansion was observed mainly in dicot and monocot plants, which was accompanied by frequent domain loss. Both tandem and segmental duplication significantly contributed toward family expansion and expression divergence and played important roles in the survival of these expanded genes. Our data provide new insight into the TPS family expansion and evolution and suggest that TPSs might have originated from isoprenyl diphosphate synthase genes.

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Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior

Science ◽

10.1126/science.aat7693 ◽

2019 ◽

Vol 365 (6456) ◽

pp. eaat7693 ◽

Cited By ~ 53

Author(s):

Andrea Ganna ◽

Karin J. H. Verweij ◽

Michel G. Nivard ◽

Robert Maier ◽

Robbee Wedow ◽

...

Keyword(s):

Sexual Behavior ◽

Genetic Architecture ◽

Large Scale ◽

Genome Wide Association Study ◽

Same Sex ◽

Genome Wide ◽

A Genome ◽

Number Of Sexual Partners ◽

Opposite Sex ◽

Males And Females

Twin and family studies have shown that same-sex sexual behavior is partly genetically influenced, but previous searches for specific genes involved have been underpowered. We performed a genome-wide association study (GWAS) on 477,522 individuals, revealing five loci significantly associated with same-sex sexual behavior. In aggregate, all tested genetic variants accounted for 8 to 25% of variation in same-sex sexual behavior, only partially overlapped between males and females, and do not allow meaningful prediction of an individual’s sexual behavior. Comparing these GWAS results with those for the proportion of same-sex to total number of sexual partners among nonheterosexuals suggests that there is no single continuum from opposite-sex to same-sex sexual behavior. Overall, our findings provide insights into the genetics underlying same-sex sexual behavior and underscore the complexity of sexuality.

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A critical evaluation of results from genome-wide association studies of micronutrient status and their utility in the practice of precision nutrition

British Journal Of Nutrition ◽

10.1017/s0007114519001119 ◽

2019 ◽

Vol 122 (2) ◽

pp. 121-130 ◽

Cited By ~ 2

Author(s):

Marie-Joe Dib ◽

Ruan Elliott ◽

Kourosh R. Ahmadi

Keyword(s):

Large Scale ◽

Association Studies ◽

Critical Evaluation ◽

Water Soluble ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Micronutrient Deficiencies ◽

Micronutrient Status ◽

Genome Wide ◽

Fat Soluble Vitamins

AbstractRapid advances in ‘omics’ technologies have paved the way forward to an era where more ‘precise’ approaches – ‘precision’ nutrition – which leverage data on genetic variability alongside the traditional indices, have been put forth as the state-of-the-art solution to redress the effects of malnutrition across the life course. We purport that this inference is premature and that it is imperative to first review and critique the existing evidence from large-scale epidemiological findings. We set out to provide a critical evaluation of findings from genome-wide association studies (GWAS) in the roadmap to precision nutrition, focusing on GWAS of micronutrient disposition. We found that a large number of loci associated with biomarkers of micronutrient status have been identified. Mean estimates of heritability of micronutrient status ranged between 20 and 35 % for minerals, 56–59 % for water-soluble and 30–70 % for fat-soluble vitamins. With some exceptions, the majority of the identified genetic variants explained little of the overall variance in status for each micronutrient, ranging between 1·3 and 8 % (minerals), <0·1–12 % (water-soluble) and 1·7–2·3 % for (fat-soluble) vitamins. However, GWAS have provided some novel insight into mechanisms that underpin variability in micronutrient status. Our findings highlight obvious gaps that need to be addressed if the full scope of precision nutrition is ever to be realised, including research aimed at (i) dissecting the genetic basis of micronutrient deficiencies or ‘response’ to intake/supplementation (ii) identifying trans-ethnic and ethnic-specific effects (iii) identifying gene–nutrient interactions for the purpose of unravelling molecular ‘behaviour’ in a range of environmental contexts.

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A panel of elite accessions of durum wheat (Triticum durum Desf.) suitable for association mapping studies

Plant Genetic Resources ◽

10.1079/pgr2006117 ◽

2006 ◽

Vol 4 (1) ◽

pp. 79-85 ◽

Cited By ~ 44

Author(s):

Marco Maccaferri ◽

Maria Corinna Sanguineti ◽

Vincenzo Natoli ◽

José Luis Araus Ortega ◽

Moncef Ben Salem ◽

...

Keyword(s):

Association Mapping ◽

Durum Wheat ◽

Gene Pools ◽

Breeding Lines ◽

Genome Wide ◽

A Genome ◽

High Heritability ◽

Diverse Origin ◽

Triticum Durum Desf ◽

High Level

The effectiveness of association mapping (AM) based on linkage disequilibrium (LD) is currently being tested in a number of crops. An important prerequisite for the application of AM is the availability of collections of accessions with a suitable level of genetic variation for target traits and with limited spurious LD due to the presence of population structure. Herein, the results of a genome-wide molecular characterization of a collection of elite durum wheat accessions well-adapted to Mediterranean environments are presented. Ninety-seven highly polymorphic simple sequence repeats and 166 amplified fragment length polymorphism markers were used to characterize 189 durum accessions, mainly cultivars and advanced breeding lines. Genome-wide significant and sizeable LD indices at a centimorgan scale were observed, while LD mainly decayed within 10 cM. On the other hand, effects due to spurious LD were notably lower than those previously observed in a durum wheat collection sampling durum gene pools of more diverse origin. These results, coupled with the high level of genetic variability detected for a number of important morpho-physiological traits and their high heritability, indicate the suitability of this collection for AM studies targeting agronomically important traits.

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Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1808833115 ◽

2018 ◽

Vol 116 (3) ◽

pp. 900-908 ◽

Cited By ~ 4

Author(s):

Hamutal Arbel ◽

Sumanta Basu ◽

William W. Fisher ◽

Ann S. Hammonds ◽

Kenneth H. Wan ◽

...

Keyword(s):

Large Scale ◽

Scale Validation ◽

Expression Patterns ◽

Prediction Method ◽

High Accuracy ◽

Genome Wide ◽

Rank List ◽

A Genome ◽

Improved Accuracy ◽

Genome Wide Scan

Identifying functional enhancer elements in metazoan systems is a major challenge. Large-scale validation of enhancers predicted by ENCODE reveal false-positive rates of at least 70%. We used the pregrastrula-patterning network of Drosophila melanogaster to demonstrate that loss in accuracy in held-out data results from heterogeneity of functional signatures in enhancer elements. We show that at least two classes of enhancers are active during early Drosophila embryogenesis and that by focusing on a single, relatively homogeneous class of elements, greater than 98% prediction accuracy can be achieved in a balanced, completely held-out test set. The class of well-predicted elements is composed predominantly of enhancers driving multistage segmentation patterns, which we designate segmentation driving enhancers (SDE). Prediction is driven by the DNA occupancy of early developmental transcription factors, with almost no additional power derived from histone modifications. We further show that improved accuracy is not a property of a particular prediction method: after conditioning on the SDE set, naïve Bayes and logistic regression perform as well as more sophisticated tools. Applying this method to a genome-wide scan, we predict 1,640 SDEs that cover 1.6% of the genome. An analysis of 32 SDEs using whole-mount embryonic imaging of stably integrated reporter constructs chosen throughout our prediction rank-list showed >90% drove expression patterns. We achieved 86.7% precision on a genome-wide scan, with an estimated recall of at least 98%, indicating high accuracy and completeness in annotating this class of functional elements.

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Genome-wide identification of SSR markers in the Brassica A genome and their utility in breeding

Canadian Journal of Plant Science ◽

10.1139/cjps-2015-0250 ◽

2016 ◽

Vol 96 (5) ◽

pp. 808-818 ◽

Cited By ~ 4

Author(s):

Neil Hobson ◽

Habibur Rahman

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Low Cost ◽

Pak Choi ◽

Genome Wide ◽

A Genome ◽

Wide Range ◽

Genetic Pools ◽

High Level ◽

Simple Sequence

Simple sequence repeat (SSR) markers can be applied to genotyping projects at low cost with inexpensive equipment. The objective of this study was to develop SSR markers from the publically-available genome sequence of Brassica rapa and provide the physical position of these markers on the chromosomes for use in breeding and research. To assess the utility of these new markers, a subset of 60 markers were used to genotype 43 accessions of B. rapa. Fifty-five markers from the 10 chromosome scaffolds produced a total of 730 amplicons, which were then used to perform a phylogenetic analysis of the accessions, illustrating their utility in distinguishing between a wide range of germplasm. In agreement with similar studies of genetic diversity, our markers separated accessions into distinct genetic pools including Chinese cabbage, Chinese winter oilseed, European winter oilseed, Canadian spring oilseed, pak-choi, turnip, and yellow sarson. The results further illustrate the presence of a high level of genetic diversity in B. rapa, and demonstrate the potential of these SSR markers for use in breeding and research.

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