Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

2020 ◽  
Author(s):  
Xin Wang ◽  
Lei Gao ◽  
Chen Jiao ◽  
Stefanos Stravoravdis ◽  
Prashant S. Hosmani ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Regulatory Networks ◽  
Fruit Weight ◽  
Genome Comparison ◽  
Future Research ◽  
Eqtl Analysis ◽  
Structural Variants ◽  
Solanum Pimpinellifolium ◽  
Modern Cultivar ◽  
Modern Breeding

AbstractSolanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern breeding of tomato. Here we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 high-confidence structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions unravels alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous novel SVs underlying genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and novel SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.

scholarly journals Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xin Wang ◽  
Lei Gao ◽  
Chen Jiao ◽  
Stefanos Stravoravdis ◽  
Prashant S. Hosmani ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Regulatory Networks ◽  
Fruit Weight ◽  
Genome Comparison ◽  
Future Research ◽  
Eqtl Analysis ◽  
Structural Variants ◽  
Solanum Pimpinellifolium ◽  
Modern Cultivar ◽  
Tomato Breeding

AbstractSolanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern tomato breeding. Here, we present a high-quality chromosome-scale genome sequence of SP LA2093. Genome comparison identifies more than 92,000 structural variants (SVs) between LA2093 and the modern cultivar, Heinz 1706. Genotyping these SVs in ~600 representative tomato accessions identifies alleles under selection during tomato domestication, improvement and modern breeding, and discovers numerous SVs overlapping genes known to regulate important breeding traits such as fruit weight and lycopene content. Expression quantitative trait locus (eQTL) analysis detects hotspots harboring master regulators controlling important fruit quality traits, including cuticular wax accumulation and flavonoid biosynthesis, and SVs contributing to these complex regulatory networks. The LA2093 genome sequence and the identified SVs provide rich resources for future research and biodiversity-based breeding.

scholarly journals A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons

2021 ◽  
Vol 118 (23) ◽  
pp. e2101486118
Author(s):  
Susanne S. Renner ◽  
Shan Wu ◽  
Oscar A. Pérez-Escobar ◽  
Martina V. Silber ◽  
Zhangjun Fei ◽  
...  
Keyword(s):  
Citrullus Lanatus ◽  
Wild Relatives ◽  
Nile Valley ◽  
Structural Variants ◽  
Flesh Color ◽  
Genetic Changes ◽  
Modern Cultivar ◽  
Melon Genome ◽  
Modern Breeding ◽  
Chromosome Level

Wild relatives or progenitors of crops are important resources for breeding and for understanding domestication. Identifying them, however, is difficult because of extinction, hybridization, and the challenge of distinguishing them from feral forms. Here, we use collection-based systematics, iconography, and resequenced accessions of Citrullus lanatus and other species of Citrullus to search for the potential progenitor of the domesticated watermelon. A Sudanese form with nonbitter whitish pulp, known as the Kordofan melon (C. lanatus subsp. cordophanus), appears to be the closest relative of domesticated watermelons and a possible progenitor, consistent with newly interpreted Egyptian tomb paintings that suggest that the watermelon may have been consumed in the Nile Valley as a dessert by 4360 BP. To gain insights into the genetic changes that occurred from the progenitor to the domesticated watermelon, we assembled and annotated the genome of a Kordofan melon at the chromosome level, using a combination of Pacific Biosciences and Illumina sequencing as well as Hi-C mapping technologies. The genetic signature of bitterness loss is present in the Kordofan melon genome, but the red fruit flesh color only became fixed in the domesticated watermelon. We detected 15,824 genome structural variants (SVs) between the Kordofan melon and a typical modern cultivar, “97103,” and mapping the SVs in over 400 Citrullus accessions revealed shifts in allelic frequencies, suggesting that fruit sweetness has gradually increased over the course of watermelon domestication. That a likely progenitor of the watermelon still exists in Sudan has implications for targeted modern breeding efforts.

scholarly journals A Classification of Basic Helix-Loop-Helix Transcription Factors of Soybean

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Karen A. Hudson ◽  
Matthew E. Hudson
Keyword(s):  
Transcription Factors ◽  
Genome Sequence ◽  
Search Algorithm ◽  
Soybean Genome ◽  
Binding Potential ◽  
Future Research ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Bhlh Genes ◽  
Wide Range

The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH) family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281) of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.

scholarly journals Analysis of the complete genome sequence of a marine-derived strainStreptomycessp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6122 ◽  
Author(s):  
Liang-Yu Chen ◽  
Hao-Tian Cui ◽  
Chun Su ◽  
Feng-Wu Bai ◽  
Xin-Qing Zhao
Keyword(s):  
Bioactive Compounds ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Dna Hybridization ◽  
Complete Genome ◽  
System Analysis ◽  
Genome Mining ◽  
Biosynthetic Gene Cluster ◽  
Genome Comparison ◽  
Genome Sequences

Genome sequences of marine streptomycetes are valuable for the discovery of useful enzymes and bioactive compounds by genome mining. However, publicly available complete genome sequences of marine streptomycetes are still limited. Here, we present the complete genome sequence of a marine streptomyceteStreptomycessp. S063 CGMCC 14582. Species delineation based on the pairwise digital DNA-DNA hybridization and genome comparison ANI (average nucleotide identity) value showed thatStreptomycessp. S063 CGMCC 14582 possesses a unique genome that is clearly different from all of the other available genomes. Bioactivity tests showed thatStreptomycessp. S063 CGMCC 14582 produces metabolites with anti-complement activities, which are useful for treatment of numerous diseases that arise from inappropriate activation of the human complement system. Analysis of the genome reveals no biosynthetic gene cluster (BGC) which shows even low similarity to that of the known anti-complement agents was detected in the genome, indicating thatStreptomycessp. S063 CGMCC 14582 may produce novel anti-complement agents of microbial origin. Four BGCs which are potentially involved in biosynthesis of non-ribosomal peptides were disrupted, but no decrease of anti-complement activities was observed, suggesting that these four BGCs are not involved in biosynthesis of the anti-complement agents. In addition, LC-MS/MS analysis and subsequent alignment through the Global Natural Products Social Molecular Networking (GNPS) platform led to the detection of novel peptides produced by the strain.Streptomycessp. S063 CGMCC 14582 grows rapidly and is salt tolerant, which benefits efficient secondary metabolite production via seawater-based fermentation. Our results indicate thatStreptomycessp. S063 has great potential to produce novel bioactive compounds, and also is a good host for heterologous production of useful secondary metabolites for drug discovery.

scholarly journals De Novo Genome Assembly of a Foxtail Millet Cultivar Huagu11 Uncovered the Genetic Difference to the Cultivar Yugu1, and the Genetic Mechanism of Imazethapyr Tolerance

2021 ◽  
Author(s):  
Jie Wang ◽  
Shiming Li ◽  
Lei Lan ◽  
Mushan Xie ◽  
Shu Cheng ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Reference Genome ◽  
Foxtail Millet ◽  
Setaria Italica ◽  
Genome Comparison ◽  
Sequencing Technology ◽  
High Quality ◽  
Next Generation Sequencing Technology ◽  
Generation Sequencing

Abstract Background: Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. Results: Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97% and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. Conclusions: A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was found that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.

scholarly journals Molecular Evolution of Calcium Signaling and Transport in Plant Adaptation to Abiotic Stress

2021 ◽  
Vol 22 (22) ◽  
pp. 12308
Author(s):  
Tao Tong ◽  
Qi Li ◽  
Wei Jiang ◽  
Guang Chen ◽  
Dawei Xue ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Calcium Signaling ◽  
Stress Responses ◽  
Evolutionary Biology ◽  
Regulatory Networks ◽  
Cascade Reactions ◽  
Future Research ◽  
Spatiotemporal Pattern ◽  
Green Plants ◽  
Signaling Components

Adaptation to unfavorable abiotic stresses is one of the key processes in the evolution of plants. Calcium (Ca2+) signaling is characterized by the spatiotemporal pattern of Ca2+ distribution and the activities of multi-domain proteins in integrating environmental stimuli and cellular responses, which are crucial early events in abiotic stress responses in plants. However, a comprehensive summary and explanation for evolutionary and functional synergies in Ca2+ signaling remains elusive in green plants. We review mechanisms of Ca2+ membrane transporters and intracellular Ca2+ sensors with evolutionary imprinting and structural clues. These may provide molecular and bioinformatics insights for the functional analysis of some non-model species in the evolutionarily important green plant lineages. We summarize the chronological order, spatial location, and characteristics of Ca2+ functional proteins. Furthermore, we highlight the integral functions of calcium-signaling components in various nodes of the Ca2+ signaling pathway through conserved or variant evolutionary processes. These ultimately bridge the Ca2+ cascade reactions into regulatory networks, particularly in the hormonal signaling pathways. In summary, this review provides new perspectives towards a better understanding of the evolution, interaction and integration of Ca2+ signaling components in green plants, which is likely to benefit future research in agriculture, evolutionary biology, ecology and the environment.

In Silico Recognition of Protein-Protein Interaction

2011 ◽  
pp. 248-268
Author(s):  
Byung-Hoon Park ◽  
Phuongan Dam ◽  
Chongle Pan ◽  
Ying Xu ◽  
Al Geist ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Regulatory Networks ◽  
Machine Learning Techniques ◽  
Translation Regulation ◽  
Future Research ◽  
Protein Protein Interactions ◽  
Protein Protein Interaction ◽  
Protein Levels ◽  
Protein Functions ◽  
Model Protein

Protein-protein interactions are fundamental to cellular processes. They are responsible for phenomena like DNA replication, gene transcription, protein translation, regulation of metabolic pathways, immunologic recognition, signal transduction, etc. The identification of interacting proteins is therefore an important prerequisite step in understanding their physiological functions. Due to the invaluable importance to various biophysical activities, reliable computational methods to infer protein-protein interactions from either structural or genome sequences are in heavy demand lately. Successful predictions, for instance, will facilitate a drug design process and the reconstruction of metabolic or regulatory networks. In this chapter, we review: (a) high-throughput experimental methods for identification of protein-protein interactions, (b) existing databases of protein-protein interactions, (c) computational approaches to predicting protein-protein interactions at both residue and protein levels, (d) various statistical and machine learning techniques to model protein-protein interactions, and (e) applications of protein-protein interactions in predicting protein functions. We also discuss intrinsic drawbacks of the existing approaches and future research directions.

scholarly journals Genome Sequence Data of the Soybean Pathogen Stagonosporopsis vannaccii: A Resource for Studies on Didymellaceae Evolution

2020 ◽  
Vol 33 (8) ◽  
pp. 1022-1024
Author(s):  
Giovanni Cafà ◽  
Thaís Regina Boufleur ◽  
Renata Rebellato Linhares de Castro ◽  
Nelson Sidnei Massola ◽  
Riccardo Baroncelli
Keyword(s):  
Comparative Genomics ◽  
Genome Sequence ◽  
Plant Pathogens ◽  
Sequence Data ◽  
Gene Prediction ◽  
Whole Genome Sequence ◽  
Future Research ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Associated Species

The genus Stagonosporopsis is classified within the Didymellaceae family and has around 40 associated species. Among them, several species are important plant pathogens responsible for significant losses in economically important crops worldwide. Stagonosporopsis vannaccii is a newly described species pathogenic to soybean. Here, we present the draft whole-genome sequence, gene prediction, and annotation of S. vannaccii isolate LFN0148 (also known as IMI 507030). To our knowledge, this is the first genome sequenced of this species and represents a new useful source for future research on fungal comparative genomics studies.

scholarly journals Role of ATF3 as a prognostic biomarker and correlation of ATF3 expression with macrophage infiltration in hepatocellular carcinoma

2020 ◽  
Author(s):  
Lijuan Li ◽  
Shaohua Song ◽  
Xuailin Fang ◽  
Donglin Cao
Keyword(s):  
Hepatocellular Carcinoma ◽  
Transcription Factors ◽  
Regulatory Networks ◽  
Macrophage Infiltration ◽  
Future Research ◽  
Activating Transcription Factor 3 ◽  
Poor Overall Survival ◽  
Basic Leucine Zipper ◽  
Atf3 Expression

Abstract Background: The abnormal expression of activating transcription factor 3 (ATF3), a member of the basic leucine zipper (bZIP) family of transcription factors, is associated with carcinogenesis. However, the expression pattern and exact role of ATF3 in the development and progression of hepatocellular carcinoma (HCC) remain unclear. Methods: We used UALCAN, ONCOMINE, Kaplan-Meier plotter, and cBioPortal databases to investigate the prognostic value of ATF3 expression in HCC. Results: ATF3 was found to be expressed at low levels in multiple HCC tumor tissues. Moreover, low ATF3 expression was significantly associated with clinical cancer stage and pathological tumor grade in patients with HCC. Therefore, low expression of ATF3 was significantly associated with poor overall survival in patients with HCC. Functional network analysis showed that ATF3 regulates cytokine receptors and signaling pathways via various cancer-related kinases, miRNAs, and transcription factors. ATF3 expression was found to be correlated with macrophage infiltration levels and with macrophage immune marker sets in HCC patients. Conclusions: Using data mining methods, we clarified the role of ATF3 expression and related regulatory networks in HCC, laying a foundation for further functional research. Future research will validate our findings and establish clinical applications of ATF3 in the diagnosis and treatment of HCC.

scholarly journals Complete Genome Sequence of Bacillus coagulans BC01, a Promising Human Probiotic Strain Isolated from Thick Broad Bean Sauce

2021 ◽  
Vol 10 (19) ◽  
Author(s):  
Yang Yu ◽  
Xueping Yu ◽  
Jialiang Ouyang ◽  
Xin Ma
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Broad Bean ◽  
Bacillus Coagulans ◽  
Probiotic Strain ◽  
Whole Genome Sequence ◽  
Future Research ◽  
Content Type ◽  
Molecular Information

We report the whole-genome sequence of a promising human probiotic, Bacillus coagulans BC01, isolated from thick broad-bean sauce. B. coagulans BC01 is widely used in China, where it is considered a treatment for diarrhea, constipation, and allergies and an immunity booster. The complete genome sequence of B. coagulans BC01 will help future research to provide more molecular information about its features and safety.

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