scholarly journals A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Michiharu Nakano ◽  
Hideki Hirakawa ◽  
Eigo Fukai ◽  
Atsushi Toyoda ◽  
Rei Kajitani ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Positional Cloning ◽  
Pure Line ◽  
Cut Flowers ◽  
Retrotransposon Family ◽  
Line Breeding ◽  
Large Genome Size ◽  
Interspersed Repeats ◽  
Modern Breeding ◽  
Chromosome Level

AbstractChrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspersed repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to arelatively large genome size. Furthermore, we identified a retrotransposon family, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.

scholarly journals A chromosome-level genome sequence of a model chrysanthemum: evolution and 1 reference for hexaploid cultivated chrysanthemum

2021 ◽  
Author(s):  
Michiharu Nakano ◽  
Hideki Hirakawa ◽  
Eigo Fukai ◽  
Atsushi Toyoda ◽  
Rei Kajitani ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Positional Cloning ◽  
Pure Line ◽  
Cut Flowers ◽  
Line Breeding ◽  
Large Genome Size ◽  
Modern Breeding ◽  
Model Strain ◽  
Recent Segmental Duplication ◽  
Chromosome Level

Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspread repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to a relatively large genome size. Furthermore, we identified aretrotransposon, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.

scholarly journals The chromosome‐level genome sequence and karyotypic evolution of Megadenia pygmaea (Brassicaceae)

2020 ◽  
Author(s):  
Wenjie Yang ◽  
Lei Zhang ◽  
Terezie Mandáková ◽  
Li Huang ◽  
Ting Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Karyotypic Evolution ◽  
Chromosome Level

scholarly journals Chromosome-Level Genome Sequence of Aspergillus chevalieri M1, Isolated from Katsuobushi

2021 ◽  
Vol 10 (37) ◽  
Author(s):  
Chihiro Kadooka ◽  
Kazuki Mori ◽  
Kayu Okutsu ◽  
Yumiko Yoshizaki ◽  
Kazunori Takamine ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Significant Role ◽  
Filamentous Fungus ◽  
Sequence Data ◽  
Genomic Research ◽  
Content Type ◽  
Ripening Process ◽  
Chromosome Level

In this study, we report the chromosome-level genome sequence of the osmophilic filamentous fungus Aspergillus chevalieri M1, which was isolated from a dried bonito, katsuobushi. This fungus plays a significant role in the fermentation and ripening process. Thus, elucidating the sequence data for this fungus will aid in subsequent genomic research on the fungi involved in katsuobushi production.

scholarly journals The chromosome‐level genome sequence of the camphor tree provides insights into Lauraceae evolution and terpene biosynthesis

2021 ◽  
Author(s):  
Tengfei Shen ◽  
Haoran Qi ◽  
Xiaoyue Luan ◽  
Wenlin Xu ◽  
Faxin Yu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Terpene Biosynthesis ◽  
Camphor Tree ◽  
Chromosome Level

scholarly journals Chromosome-scale genome sequence of Alternaria alternata causing Alternaria brown spot of citrus

2021 ◽  
Author(s):  
Yunpeng Gai ◽  
Haijie Ma ◽  
Yanan Chen ◽  
Lei Li ◽  
Yingze Cao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Alternaria Alternata ◽  
Draft Genome ◽  
Gc Content ◽  
Brown Spot ◽  
Toxin Gene ◽  
Alternaria Brown Spot ◽  
Alternaria Species ◽  
Chromosome Level

Alternaria brown spot (ABS) caused by Alternaria alternata is an economically important fungal disease of citrus worldwide. The ABS pathogen A. alternata tangerine pathotype can produce a host-specific ACT toxin, which is regulated by ACT toxin gene cluster located in the conditionally dispensable chromosome (CDC). Previously, we have assembled a draft genome of A. alternata tangerine pathotype strain Z7, which comprises 165 contigs. In this study, we report a chromosome-level genome assembly of A. alternata Z7 through the combination of Oxford nanopore sequencing and Illumina sequencing technologies. The assembly of A. alternata Z7 had a total size of 34.28 Mb, with a GC content of 51.01% and contig N50 of Mb. The genome is encompassed 12067 protein-coding genes, 34 rRNAs, and 107 tRNAs. Interestingly, A. alternata Z7 is composed of 10 essential chromosomes (ECs) and 2 conditionally dispensable chromosomes (CDCs), which is consistent with the experimental evidences of pulsed-field gel electrophoresis (PFGE). To our best knowledge, this is the first chromosome-level genome assembly of A. alternata. In addition, a database for citrus-related Alternaria genomes has been established to provide public resources for the sequences, annotation and comparative genomics data of Alternaria species. The improved genome sequence and annotation at the chromosome level is a significant step toward a better understanding of the pathogenicity of A. alternata. The database will be updated regularly whenever the genomes of newly isolated Alternaria species are available. The citrus-related Alternaria genomes database is open accessible through http://www.zjudata.com/alternaria/blast.php.

scholarly journals Development of a sequence-based reference physical map of pea (Pisum sativum L.)

2019 ◽  
Author(s):  
Krishna Kishore Gali ◽  
Bunyamin Tar’an ◽  
Mohammed-Amin Madoui ◽  
Edwin van der Vossen ◽  
Jan van Oeveren ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Positional Cloning ◽  
Physical Map ◽  
Repetitive Sequences ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Bac Clones ◽  
Pooled Dna ◽  
Mapping Technology ◽  
Generation Sequencing

AbstractWhole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. To address the challenges of accurate assembly of the pea genome (~4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. These WGP tags were used to assemble 220,013 BACs into contigs. Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. The average contig size is 0.33 Mbp and the N50 contig size is 0.62 Mbp. WGPTM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. This sequence-based physical map will be useful to assemble the genome sequence of pea. Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest.

scholarly journals Chromosome-Level Genome Sequence of Leishmania (Leishmania) tropica Strain CDC216-162, Isolated from an Afghanistan Clinical Case

2021 ◽  
Vol 10 (20) ◽  
Author(s):  
Yvette Unoarumhi ◽  
Dhwani Batra ◽  
Mili Sheth ◽  
Vidhya Narayanan ◽  
Wuling Lin ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Clinical Case ◽  
Illumina Miseq ◽  
Considerable Improvement ◽  
Genomic Sequencing ◽  
Leishmania Tropica ◽  
Genome Sequences ◽  
Content Type ◽  
Chromosome Level

ABSTRACT PacBio and Illumina MiSeq platforms were used for genomic sequencing of a Leishmania (Leishmania) tropica strain isolated from a patient infected in Pakistan. PacBio assemblies were generated using Flye v2.4 and polished with MiSeq data. The results represent a considerable improvement of the currently available genome sequences in the GenBank database.

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.

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.

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