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 Draft Genome Sequence of Alternaria alternata Isolated from Onion Leaves in South Africa

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Wubetu Bihon ◽  
Michele Cloete ◽  
Abe Shegro Gerrano ◽  
Dean Oelofse ◽  
Patrick Adebola
Keyword(s):  
South Africa ◽  
Genome Sequence ◽  
Alternaria Alternata ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Whole Genome ◽  
Coding Sequences

Alternaria alternata (Fr.) Keissler strain PPRI 21032 was isolated from onion leaves collected in Roodeplaat, Pretoria, South Africa. The whole genome of this strain was sequenced and produced a total of 33.12 Mb with a GC content of 50.9%. The whole genome comprises 11,701 predicted coding sequences.

scholarly journals Draft Genome Sequence of Branchiibius sp. NY16-3462-2, Isolated from a Mixed Clinical Sample

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Pascal Lapierre ◽  
Tanya A. Halse ◽  
Joseph Shea ◽  
Vincent E. Escuyer ◽  
Kimberlee A. Musser
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Clinical Sample ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Gram Positive ◽  
Draft Genome Assembly ◽  
Gram Positive Cocci

Here, we report the release of a draft genome assembly of a Gram-positive cocci Branchiibius sp. NY16-3462-2 with a high-GC content, sequenced from a mixed clinical sample containing Mycobacterium tuberculosis . This genome is the first publicly available sequence from a representative of the genus Branchiibius .

scholarly journals Draft Genome Sequence of a Sporulating and Motile Strain of Lachnotalea glycerini Isolated from Water in Québec City, Canada

2017 ◽  
Vol 5 (42) ◽  
Author(s):  
Andrée F. Maheux ◽  
Dominique K. Boudreau ◽  
Ève Bérubé ◽  
Maurice Boissinot ◽  
Frédéric Raymond ◽  
...  
Keyword(s):  
Water Sample ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Quebec City ◽  
Content Type

ABSTRACT Lachnotalea glycerini CCRI-19302 belongs to the genus Lachnotalea. The strain was isolated from a water sample harvested in Québec City, Canada. The genome assembly comprised 4,694,231 bp, with 34.6% GC content. This is the first documentation to report the genome sequence of a sporulating and motile strain of L. glycerini.

scholarly journals First Draft Genome Sequence of Staphylococcus condimenti F-2 T

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Beiwen Zheng ◽  
Xinjun Hu ◽  
Xiawei Jiang ◽  
Ang Li ◽  
Jian Yao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Starter Culture ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome

This report describes the draft genome sequence of S. condimenti strain F-2 T (DSM 11674), a potential starter culture. The genome assembly comprised 2,616,174 bp with 34.6% GC content. To the best of our knowledge, this is the first documentation that reports the whole-genome sequence of S. condimenti.

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 An Isolate of Alternaria alternata That Is Pathogenic to Both Tangerines and Rough Lemon and Produces Two Host-Selective Toxins, ACT- and ACR-Toxins

2005 ◽  
Vol 95 (3) ◽  
pp. 241-247 ◽  
Author(s):  
A. Masunaka ◽  
K. Ohtani ◽  
T. L. Peever ◽  
L. W. Timmer ◽  
T. Tsuge ◽  
...  
Keyword(s):  
Alternaria Alternata ◽  
Leaf Spot ◽  
The Other ◽  
Brown Spot ◽  
Parasexual Cycle ◽  
Rough Lemon ◽  
Alternaria Brown Spot ◽  
Alternaria Species ◽  
Genomic Regions ◽  
Toxin Producers

Two different pathotypes of Alternaria alternata cause Alternaria brown spot of tangerines and Alternaria leaf spot of rough lemon. The former produces the host-selective ACT-toxin and the latter produces ACR-toxin. Both pathogens induce similar symptoms on leaves or young fruits of their respective hosts, but the host ranges of these pathogens are distinct and one pathogen can be easily distinguished from another by comparing host ranges. We isolated strain BC3-5-1-OS2A from a leaf spot on rough lemon in Florida, and this isolate is pathogenic on both cv. Iyokan tangor and rough lemon and also produces both ACT-toxin and ACR-toxin. Isolate BC3-5-1-OS2A carries both genomic regions, one of which was known only to be present in ACT-toxin producers and the other was known to exist only in ACR-toxin producers. Each of the genomic regions is present on distinct small chromosomes, one of 1.05 Mb and the other of 2.0 Mb. Alternaria species have no known sexual or parasexual cycle in nature and populations of A. alternata on citrus are clonal. Therefore, the ability to produce both toxins was not likely acquired through meiotic or mitotic recombination. We hypothesize that a dispensable chromosome carrying the gene cluster controlling biosynthesis of one of the host-selective toxins was transferred horizontally and rearranged by duplication or translocation in another isolate of the fungus carrying genes for biosynthesis of the other host-selective toxin.

scholarly journals Draft Genome Sequence of the Fungus Paraphoma sp. B47-9, a Producer of a Biodegradable Plastic–Degrading Enzyme

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Yuka Sameshima-Yamashita ◽  
Hideaki Koike ◽  
Motoo Koitabashi ◽  
Azusa Saika ◽  
Tomotake Morita ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gc Content ◽  
Biodegradable Plastic ◽  
Draft Genome Sequence ◽  
Degrading Enzyme ◽  
Draft Genome Assembly

Paraphoma sp. B47-9 is a producer of a biodegradable plastic–degrading enzyme. Here, we report the draft genome sequence of this strain. The draft genome assembly has a size of 39.3 Mb with a GC content of 52.4% and consists of 185 scaffolds.

scholarly journals Draft Genome Sequence of Fusarium oxysporum f. sp. albedinis Strain Foa 133, the Causal Agent of Bayoud Disease on Date Palm

2020 ◽  
Vol 9 (29) ◽  
Author(s):  
Slimane Khayi ◽  
Siham Khoulassa ◽  
Fatima Gaboun ◽  
Rabha Abdelwahd ◽  
Ghizlane Diria ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Date Palm ◽  
Draft Genome ◽  
Gc Content ◽  
Causal Agent ◽  
Vascular Wilt ◽  
Content Type ◽  
Bayoud Disease

ABSTRACT Fusarium oxysporum f. sp. albedinis is the causal agent of vascular wilt of date palm. Here, we report the genome assembly of the Foa 133 strain, which consists of 3,325 contigs with a total length of 56,228,901 bp, a GC content of 47.42%, an N50 value of 131,587 bp, and 3,684 predicted genes.

scholarly journals Draft Genome Sequence of Romboutsia weinsteinii sp. nov. Strain CCRI-19649T Isolated from Surface Water

2017 ◽  
Vol 5 (40) ◽  
Author(s):  
Andrée F. Maheux ◽  
Dominique K. Boudreau ◽  
Ève Bérubé ◽  
Maurice Boissinot ◽  
Philippe Cantin ◽  
...  
Keyword(s):  
Surface Water ◽  
Water Sample ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Quebec City

ABSTRACT Romboutsia weinsteinii sp. nov. CCRI-19649T belongs to the genus Romboutsia. The strain was isolated from a water sample harvested in Québec City, Québec, Canada. The genome assembly comprised 4,134,593 bp with a 29.3% GC content. This is the first documentation that reports the genome sequence of R. weinsteinii.

scholarly journals Genome Sequence of Pseudomonas sp. Strain LAP_36, A Rhizosphere Bacterium Isolated from King George Island, Antarctica

2021 ◽  
Vol 10 (48) ◽  
Author(s):  
Sarah Mederos da Silveira ◽  
Sheila da Silva ◽  
Andrew Macrae ◽  
Rommel T. J. Ramos ◽  
Fabrício A. Araújo ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
South Shetland Islands ◽  
Deschampsia Antarctica ◽  
King George Island ◽  
Protein Coding ◽  
Content Type ◽  
Shetland Islands ◽  
Rhizosphere Bacterium

Pseudomonas sp. strain LAP_36 was isolated from rhizosphere soil from Deschampsia antarctica on King George Island, South Shetland Islands, Antarctica. Here, we report on its draft genome sequence, which consists of 8,794,771 bp with 60.0% GC content and 8,011 protein-coding genes.

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