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 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 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 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 The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads

2021 ◽  
Author(s):  
Thomas W Woehner ◽  
Ofere Francis Emeriewen ◽  
Alexander Wittenberg ◽  
Harrie Schneiders ◽  
Ilse Vrijenhoek ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Sour Cherry ◽  
Evolutionary Analysis ◽  
Protein Coding ◽  
Draft Genome Assembly ◽  
Repeat Content ◽  
Long Read ◽  
Chromosome Level

Background: Cherries are stone fruits and belong to the economically important plant family of Rosaceae with worldwide cultivation of different species. The ground cherry, Prunus fruticosa Pall. is one ancestor of cultivated sour cherry, an important tetraploid cherry species. Here, we present a long read chromosome-level draft genome assembly and related plastid sequences using the Oxford Nanopore Technology PromethION platform and R10.3 pore type. Finding: The final assemblies obtained from 117.3 Gb cleaned reads representing 97x coverage of expected 1.2 Gb tetraploid (2n=4x=32) and 0.3 Gb haploid (1n=8) genome sequence of P. fruticosa were calculated. The N50 contig length ranged between 0.3 and 0.5 Mb with the longest contig being ~6 Mb. BUSCO estimated a completeness between 98.7 % for the 4n and 96.1 % for the 1n datasets. Using a homology and reference based scaffolding method, we generated a final consensus genome sequence of 366 Mb comprising eight chromosomes. The N50 scaffold was ~44 Mb with the longest chromosome being 66.5 Mb. The repeat content was estimated to ~190 Mb (52 %) and 58,880 protein-coding genes were annotated. The chloroplast and mitochondrial genomes were 158,217 bp and 383,281 bp long, which is in accordance with previously published plastid sequences. Conclusion: This is the first report of the genome of ground cherry (P. fruticosa) sequenced by long read technology only. The datasets obtained from this study provide a foundation for future breeding, molecular and evolutionary analysis in Prunus studies.

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 Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Muyou Can ◽  
Wei Wei ◽  
Hailing Zi ◽  
Magaweng Bai ◽  
Yunfei Liu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
The Family ◽  
Chromosome Level

scholarly journals Genomic analysis based on chromosome-level genome assembly reveals an expansion of terpene biosynthesis of Azadirachta indica

2021 ◽  
Author(s):  
Yuhui Du ◽  
Wei Song ◽  
Zhiqiu Yin ◽  
shengbo wu ◽  
jiaheng liu ◽  
...  
Keyword(s):  
Azadirachta Indica ◽  
Genome Assembly ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genomic Research ◽  
Comparative Genomic ◽  
Terpene Biosynthesis ◽  
Chromosome 13 ◽  
Duplication Events ◽  
Chromosome Level

Azadirachta indica (neem), an evergreen tree of the Meliaceae family, is a source of the potent biopesticide azadirachtin. The lack of a chromosome-level assembly impedes the understanding of in-depth genomic architecture and the comparative genomic analysis of A. indica. Here, a high-quality genome assembly of A. indica was constructed using a combination of data from Illumina, PacBio, and Hi-C technology, which is the first chromosome-scale genome assembly of A. indica. The genome size of A. indica is 281 Mb anchored to 14 chromosomes (contig N50=6 Mb and scaffold N50=19 Mb). The genome assembly contained 115 Mb repetitive elements and 25,767 protein-coding genes. Evolutional analysis revealed that A. indica did not experience any whole-genome duplication (WGD) event after the core eudicot γ event, but some genes and genome segment might undergo recent duplications. The secondary metabolite clusters, TPS genes, and CYP genes were also identified. Comparative genomic analysis revealed that most of the A. indica-specific TPS genes and CYP genes were located on the terpene-related clusters on chromosome 13. It is suggested that chromosome 13 may play an important role in the specific terpene biosynthesis of A. indica. And the gene duplication events may be responsible for the terpene biosynthesis expansion in A. indica. This will shed light on terpene biosynthesis in A. indica and facilitate comparative genomic research of the family Meliaceae.

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

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

The Chromosome-Level Genome Sequence of the Autotetraploid Alfalfa and Resequencing of Core Germplasms Provide Genomic Resources for Alfalfa Research

2020 ◽  
Vol 13 (9) ◽  
pp. 1250-1261
Author(s):  
Chen Shen ◽  
Huilong Du ◽  
Zhuo Chen ◽  
Hongwei Lu ◽  
Fugui Zhu ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genomic Resources ◽  
Chromosome Level
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