scholarly journals European maize genomes unveil pan-genomic dynamics of repeats and genes

2019 ◽  
Author(s):  
G. Haberer ◽  
E. Bauer ◽  
N. Kamal ◽  
H. Gundlach ◽  
I. Fischer ◽  
...  
Keyword(s):  
De Novo ◽  
Long Terminal Repeat Retrotransposons ◽  
Hybrid Breeding ◽  
Corn Belt ◽  
Genome Sequences ◽  
High Quality ◽  
A Genome ◽  
Modern Maize ◽  
European Maize ◽  
Genome Scale

AbstractThe exceptional diversity of maize (Zea mays) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today’s highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report high quality de novo genome sequences of the four European flint lines EP1, F7, DK105 and PE0075 assembled to pseudomolecules with scaffold N50 ranging between 6.1 to 10.4 Mb. Comparative analyses with the two US Corn Belt genomes B73 and PH207 elucidates the pronounced differences between both germplasm groups. While overall syntenic order and consolidated gene annotations reveal only moderate pan-genomic differences, whole genome alignments delineating the core and dispensable genome, and the analysis of repeat structures, heterochromatic knobs and orthologous long terminal repeat retrotransposons (LTRs) unveil the extreme dynamics of the maize genome. Haplotypes derived from core genome SNPs demonstrate the tessellation of modern maize resulting from a complex breeding history. The high quality genome sequences of the flint pool are a crucial complement to the maize pan-genome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding.

scholarly journals Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

2021 ◽  
Author(s):  
Xinxin Yi ◽  
Jing Liu ◽  
Shengcai Chen ◽  
Hao Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Wide ◽  
A Genome ◽  
Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

scholarly journals Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences

2014 ◽  
Vol 30 (19) ◽  
pp. 2709-2716 ◽  
Author(s):  
Sagar M. Utturkar ◽  
Dawn M. Klingeman ◽  
Miriam L. Land ◽  
Christopher W. Schadt ◽  
Mitchel J. Doktycz ◽  
...  
Keyword(s):  
De Novo ◽  
Hybrid Assembly ◽  
Genome Sequences ◽  
High Quality ◽  
High Quality Genome

scholarly journals A high-quality de novo genome assembly from a single parasitoid wasp

2020 ◽  
Author(s):  
Xinhai Ye ◽  
Yi Yang ◽  
Zhaoyang Tian ◽  
Le Xu ◽  
Kaili Yu ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Parasitoid Wasp ◽  
Genome Comparison ◽  
Single Individual ◽  
High Quality ◽  
De Novo Genome Assembly ◽  
Low Input ◽  
A Genome ◽  
High Level

AbstractSequencing and assembling a genome with a single individual have several advantages, such as lower heterozygosity and easier sample preparation. However, the amount of genomic DNA of some small sized organisms might not meet the standard DNA input requirement for current sequencing pipelines. Although few studies sequenced a single small insect with about 100 ng DNA as input, it may still be challenging for many small organisms to obtain such amount of DNA from a single individual. Here, we use 20 ng DNA as input, and present a high-quality genome assembly for a single haploid male parasitoid wasp (Habrobracon hebetor) using Nanopore and Illumina. Because of the low input DNA, a whole genome amplification (WGA) method is used before sequencing. The assembled genome size is 131.6 Mb with a contig N50 of 1.63 Mb. A total of 99% Benchmarking Universal Single-Copy Orthologs are detected, suggesting the high level of completeness of the genome assembly. Genome comparison between H. hebetor and its relative Bracon brevicornis shows a high-level genome synteny, indicating the genome of H. hebetor is highly accurate and contiguous. Our study provides an example for de novo assembling a genome from ultra-low input DNA, and will be used for sequencing projects of small sized species and rare samples, haploid genomics as well as population genetics of small sized species.

scholarly journals De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri

2019 ◽  
Vol 9 (10) ◽  
pp. 3079-3085 ◽  
Author(s):  
Joshua A. Udall ◽  
Evan Long ◽  
Chris Hanson ◽  
Daojun Yuan ◽  
Thiruvarangan Ramaraj ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo ◽  
Close Relative ◽  
Sequencing Data ◽  
Genome Sequences ◽  
D Genome ◽  
Cotton Species ◽  
A Genome ◽  
Long Read ◽  
Gossypium Raimondii

Cotton is an agriculturally important crop. Because of its importance, a genome sequence of a diploid cotton species (Gossypium raimondii, D-genome) was first assembled using Sanger sequencing data in 2012. Improvements to DNA sequencing technology have improved accuracy and correctness of assembled genome sequences. Here we report a new de novo genome assembly of G. raimondii and its close relative G. turneri. The two genomes were assembled to a chromosome level using PacBio long-read technology, HiC, and Bionano optical mapping. This report corrects some minor assembly errors found in the Sanger assembly of G. raimondii. We also compare the genome sequences of these two species for gene composition, repetitive element composition, and collinearity. Most of the identified structural rearrangements between these two species are due to intra-chromosomal inversions. More inversions were found in the G. turneri genome sequence than the G. raimondii genome sequence. These findings and updates to the D-genome sequence will improve accuracy and translation of genomics to cotton breeding and genetics.

scholarly journals Reconstruction of a Genome-Scale Metabolic Model of Streptomyces albus J1074: Improved Engineering Strategies in Natural Product Synthesis

Metabolites ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 304
Author(s):  
Cheewin Kittikunapong ◽  
Suhui Ye ◽  
Patricia Magadán-Corpas ◽  
Álvaro Pérez-Valero ◽  
Claudio J. Villar ◽  
...  
Keyword(s):  
Natural Products ◽  
De Novo ◽  
Streptomyces Coelicolor ◽  
Metabolic Model ◽  
Streptomyces Species ◽  
Model Driven ◽  
A Genome ◽  
Streptomyces Albus ◽  
Genome Scale ◽  
Streptomyces Albus J1074

Streptomyces albus J1074 is recognized as an effective host for heterologous production of natural products. Its fast growth and efficient genetic toolbox due to a naturally minimized genome have contributed towards its advantage in expressing biosynthetic pathways for a diverse repertoire of products such as antibiotics and flavonoids. In order to develop precise model-driven engineering strategies for de novo production of natural products, a genome-scale metabolic model (GEM) was reconstructed for the microorganism based on protein homology to model species Streptomyces coelicolor while drawing annotated data from databases and literature for further curation. To demonstrate its capabilities, the Salb-GEM was used to predict overexpression targets for desirable compounds using flux scanning with enforced objective function (FSEOF). Salb-GEM was also utilized to investigate the effect of a minimized genome on metabolic gene essentialities in comparison to another Streptomyces species, S. coelicolor.

scholarly journals Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible FungusPleurotus ostreatus

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Jibin Qu ◽  
Mengran Zhao ◽  
Tom Hsiang ◽  
Xiaoxing Feng ◽  
Jinxia Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Noncoding Rnas ◽  
Genome Sequences ◽  
Small Noncoding Rnas ◽  
Basidiomycetous Fungus ◽  
A Genome ◽  
Genome Assemblies ◽  
Genome Scale ◽  
Identification And Characterization

Noncoding RNAs (ncRNAs) have been identified in many fungi. However, no genome-scale identification of ncRNAs has been inventoried for basidiomycetes. In this research, we detected 254 small noncoding RNAs (sncRNAs) in a genome assembly of an isolate (CCEF00389) ofPleurotus ostreatus, which is a widely cultivated edible basidiomycetous fungus worldwide. The identified sncRNAs include snRNAs, snoRNAs, tRNAs, and miRNAs. SnRNA U1 was not found in CCEF00389 genome assembly and some other basidiomycetous genomes by BLASTn. This implies that if snRNA U1 of basidiomycetes exists, it has a sequence that varies significantly from other organisms. By analyzing the distribution of sncRNA loci, we found that snRNAs and most tRNAs (88.6%) were located in pseudo-UTR regions, while miRNAs are commonly found in introns. To analyze the evolutionary conservation of the sncRNAs inP. ostreatus, we aligned all 254 sncRNAs to the genome assemblies of some other Agaricomycotina fungi. The results suggest that most sncRNAs (77.56%) were highly conserved inP. ostreatus, and 20% were conserved in Agaricomycotina fungi. These findings indicate that most sncRNAs ofP. ostreatuswere not conserved across Agaricomycotina fungi.

scholarly journals Draft Genome Sequences of Bifidobacterium Strains N4G05 and N5G01, Isolated from the Human Vaginal Microbiome

2018 ◽  
Vol 6 (2) ◽  
Author(s):  
Aline C. Freitas ◽  
Janet E. Hill
Keyword(s):  
De Novo ◽  
Draft Genome ◽  
Nucleotide Identity ◽  
Vaginal Microbiome ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
High Quality

ABSTRACT We report here the draft genome sequences of Bifidobacterium strains N4G05 and N5G01, isolated from the human vaginal microbiome. Genome sequences were obtained by de novo assembly from high-quality reads. Both strains were closely related to Bifidobacterium kashiwanohense based on barcode marker sequences and average nucleotide identity analysis.

scholarly journals Genome Report: Whole Genome Sequence and Annotation of the Parasitoid Jewel Wasp Nasonia giraulti Laboratory Strain RV2X[u]

2020 ◽  
Vol 10 (8) ◽  
pp. 2565-2572 ◽  
Author(s):  
Xiaozhu Wang ◽  
Yogeshwar D. Kelkar ◽  
Xiao Xiong ◽  
Ellen O. Martinson ◽  
Jeremy Lynch ◽  
...  
Keyword(s):  
De Novo ◽  
Rapid Development ◽  
Laboratory Strain ◽  
Whole Genome Sequence ◽  
High Quality ◽  
Important Species ◽  
A Genome ◽  
Behavioral Expression ◽  
Genomic Studies ◽  
Low Coverage

Jewel wasps in the genus of Nasonia are parasitoids with haplodiploidy sex determination, rapid development and are easy to culture in the laboratory. They are excellent models for insect genetics, genomics, epigenetics, development, and evolution. Nasonia vitripennis (Nv) and N. giraulti (Ng) are closely-related species that can be intercrossed, particularly after removal of the intracellular bacterium Wolbachia, which serve as a powerful tool to map and positionally clone morphological, behavioral, expression and methylation phenotypes. The Nv reference genome was assembled using Sanger, PacBio and Nanopore approaches and annotated with extensive RNA-seq data. In contrast, Ng genome is only available through low coverage resequencing. Therefore, de novo Ng assembly is in urgent need to advance this system. In this study, we report a high-quality Ng assembly using 10X Genomics linked-reads with 670X sequencing depth. The current assembly has a genome size of 259,040,977 bp in 3,160 scaffolds with 38.05% G-C and a 98.6% BUSCO completeness score. 97% of the RNA reads are perfectly aligned to the genome, indicating high quality in contiguity and completeness. A total of 14,777 genes are annotated in the Ng genome, and 72% of the annotated genes have a one-to-one ortholog in the Nv genome. We reported 5 million Ng-Nv SNPs which will facility mapping and population genomic studies in Nasonia. In addition, 42 Ng-specific genes were identified by comparing with Nv genome and annotation. This is the first de novo assembly for this important species in the Nasonia model system, providing a useful new genomic toolkit.

scholarly journals Genome Survey Sequencing of Acer truncatum Bunge to Identify Genomic Information, Simple Sequence Repeat (SSR) Markers and Complete Chloroplast Genome

Forests ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 87 ◽  
Author(s):  
Rongkai Wang ◽  
Jinshuan Fan ◽  
Pan Chang ◽  
Ling Zhu ◽  
Mengran Zhao ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Ssr Markers ◽  
Genome Sequence ◽  
De Novo ◽  
Quality Data ◽  
Nervonic Acid ◽  
High Quality ◽  
Genome Survey ◽  
A Genome ◽  
Genome Survey Sequencing

The Acer truncatum Bunge is a particular forest tree species found in the north of China. Due to the recent discovery that its seeds contain a considerable amount of nervonic acid, this species has received more and more attention. However, there have been no reports of the genome in this species. In this study, we report on the Acer truncatum genome sequence produced by genome survey sequencing. In total, we obtained 61.90 Gbp of high-quality data, representing approximately 116x coverage of the Acer truncatum genome. The genomic characteristics of Acer truncatum include a genome size of 529.88 Mbp, a heterozygosis rate of 1.06% and a repeat rate of 48.8%. A total of 392,961 high-quality genomic SSR markers were developed and a graphical map of the annotated circular chloroplast genome was generated. Thus far, this is the first report of de novo whole genome sequencing and assembly of Acer truncatum. We believe that this genome sequence dataset may provide a new resource for future genomic analysis and molecular breeding studies of Acer truncatum.

scholarly journals First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies

Metabolites ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 232
Author(s):  
Alina Renz ◽  
Lina Widerspick ◽  
Andreas Dräger
Keyword(s):  
Minimal Medium ◽  
Laboratory Experiments ◽  
Carbon Sources ◽  
Metabolic Model ◽  
High Quality ◽  
High Importance ◽  
Manual Curation ◽  
A Genome ◽  
Severe Infections ◽  
Genome Scale

Dolosigranulum pigrum is a quite recently discovered Gram-positive coccus. It has gained increasing attention due to its negative correlation with Staphylococcus aureus, which is one of the most successful modern pathogens causing severe infections with tremendous morbidity and mortality due to its multiple resistances. As the possible mechanisms behind its inhibition of S. aureus remain unclear, a genome-scale metabolic model (GEM) is of enormous interest and high importance to better study its role in this fight. This article presents the first GEM of D. pigrum, which was curated using automated reconstruction tools and extensive manual curation steps to yield a high-quality GEM. It was evaluated and validated using all currently available experimental data of D. pigrum. With this model, already predicted auxotrophies and biosynthetic pathways could be verified. The model was used to define a minimal medium for further laboratory experiments and to predict various carbon sources’ growth capacities. This model will pave the way to better understand D. pigrum’s role in the fight against S. aureus.

Sign in / Sign up

Export Citation Format

Share Document