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

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.

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

Plant Biotechnology Journal ◽

10.1111/pbi.13749 ◽

2021 ◽

Author(s):

Tengfei Shen ◽

Haoran Qi ◽

Xiaoyue Luan ◽

Wenlin Xu ◽

Faxin Yu ◽

...

Keyword(s):

Genome Sequence ◽

Terpene Biosynthesis ◽

Camphor Tree ◽

Chromosome Level

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

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-10-20-0278-sc ◽

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.

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

Microbiology Resource Announcements ◽

10.1128/mra.00842-20 ◽

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.

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

10.1101/2021.06.01.446499 ◽

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.

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

10.1101/2021.06.28.450068 ◽

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.

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

Scientific Data ◽

10.1038/s41597-020-0518-3 ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Muyou Can ◽

Wei Wei ◽

Hailing Zi ◽

Magaweng Bai ◽

Yunfei Liu ◽

...

Keyword(s):

Genome Sequence ◽

The Family ◽

Chromosome Level

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

Molecular Plant ◽

10.1016/j.molp.2020.07.003 ◽

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

Communications Biology ◽

10.1038/s42003-021-02704-y ◽

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.

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