scholarly journals Comparative analysis using the draft genome sequence of California poppy (Eschscholzia californica) for exploring the candidate genes involved in benzylisoquinoline alkaloid biosynthesis

2021 ◽  
Vol 85 (4) ◽  
pp. 851-859
Author(s):  
Yasuyuki Yamada ◽  
Hideki Hirakawa ◽  
Kentaro Hori ◽  
Yohei Minakuchi ◽  
Atsushi Toyoda ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Plant Species ◽  
Genome Sequence ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Rrna Genes ◽  
Eschscholzia Californica ◽  
California Poppy ◽  
Genes Encoding

ABSTRACT Genome characterization of California poppy (Eschscholzia californica cv. “Hitoezaki”), which produces pharmaceutically important benzylisoquinoline alkaloids (BIAs), was carried out using the draft genome sequence. The numbers of tRNA and rRNA genes were close to those of the other plant species tested, whereas the frequency of repetitive sequences was distinct from those species. Comparison of the predicted genes with those of Amborella trichopoda, Nelumbo nucifera, Solanum lycopersicum, and Arabidopsis thaliana, and analyses of gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway indicated that the enzyme genes involved in BIA biosynthesis were highly enriched in the California poppy genome. Further comparative analysis using the genome information of Papaver somniferum and Aquilegia coerulea, both BIA-producing plants, revealed that many genes encoding BIA biosynthetic enzymes, transcription factors, transporters, and candidate proteins, possibly related to BIA biosynthesis, were specifically distributed in these plant species.

scholarly journals Draft Genome Sequence of Limisphaera ngatamarikiensis NGM72.4T, a Moderately Alkaliphilic Thermophile Belonging to the Class Verrucomicrobiae

2020 ◽  
Vol 9 (18) ◽  
Author(s):  
Carlo R. Carere ◽  
Jason A. Steen ◽  
Philip Hugenholtz ◽  
Matthew B. Stott
Keyword(s):  
New Zealand ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Coding Sequences ◽  
Content Type ◽  
Aotearoa New Zealand

Limisphaera ngatamarikiensis NGM72.4T is a thermophilic representative of the class Verrucomicrobiae. Isolated from geothermally heated subaqueous clay sediments from a Ngatamariki hotspring in Aotearoa New Zealand, the 3,908,748-bp genome was sequenced using the Illumina HiSeq 2500 platform. Annotation revealed 3,083 coding sequences, including 3,031 proteins, 3 rRNA genes, and 46 tRNA genes.

scholarly journals Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 03-8664 Isolated from a Human Throat

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Luis C. Guimarães ◽  
Marcus V. C. Viana ◽  
Leandro J. Benevides ◽  
Diego C. B. Mariano ◽  
Adonney A. O. Veras ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Rrna Genes ◽  
Coding Sequences ◽  
Domesticated Animals ◽  
Zoonotic Infections ◽  
Corynebacterium Ulcerans ◽  
Emergent Pathogen

Corynebacterium ulcerans is an emergent pathogen infecting wild and domesticated animals worldwide that may serve as reservoirs for zoonotic infections. In this study, we present the draft genome of C. ulcerans strain 03-8664. The draft genome has 2,428,683 bp, 2,262 coding sequences, and 12 rRNA genes.

scholarly journals Draft Genome Sequence of Shewanella sp. Strain ISO12, a Candidate Probiotic Isolated from the Intestine of Fundulus heteroclitus

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Harold J. Schreier
Keyword(s):  
Genome Sequence ◽  
Fundulus Heteroclitus ◽  
Draft Genome ◽  
Bioinformatic Analysis ◽  
Draft Genome Sequence ◽  
Genes Encoding ◽  
Probiotic Activity

ABSTRACT The genome of Shewanella sp. strain ISO12, which was isolated from the intestine of wild-caught Fundulus heteroclitus, was sequenced and is reported here. Bioinformatic analysis revealed genes encoding the bacteriocin marinocine and those potentially associated with probiotic activity. The genome sequence will assist in further identifying probiotic and other antibacterial processes.

scholarly journals Draft Genome Sequence of the Extremely Desiccation-Tolerant Cyanobacterium Gloeocapsopsis sp. Strain AAB1

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
Fernando Puente-Sánchez ◽  
Carlos González-Silva ◽  
Victor Parro ◽  
Javier Tamames ◽  
Armando Azua-Bustos
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Draft Genome ◽  
Atacama Desert ◽  
Draft Genome Sequence ◽  
Rrna Genes ◽  
Trna Genes ◽  
Content Type

ABSTRACT Gloeocapsopsis sp. strain AAB1 is an extremely desiccation-tolerant cyanobacterium isolated from translucent quartz stones from the Atacama Desert (Chile). Here, we report its draft genome sequence, which consists of 137 contigs with an ∼5.4-Mb genome size. The annotation revealed 5,641 coding DNA sequences, 38 tRNA genes, and 5 rRNA genes.

scholarly journals Draft Genome Sequence of Bacillus pacificus KVCMST-8A-12, Isolated from a Marine Sediment Sample from the Kanyakumari Coast, India

2021 ◽  
Vol 10 (50) ◽  
Author(s):  
Asha Santhi ◽  
Venkatesh Subramanian ◽  
Krishnaveni Muthan
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Content Type ◽  
Marine Sediment Sample

A DNase-producing Bacillus pacificus strain was isolated, and the whole-genome sequence is reported in this paper. The draft genome sequence of Bacillus pacificus KVCMST-8A-12 constitutes 2.4 Gbp of raw reads, with a GC content of 35.24%. In total, 5,661 protein-coding genes, 64 tRNA genes, and 4 rRNA genes were predicted.

scholarly journals Draft Genome Sequence of an Environmental trh + Vibrio parahaemolyticus K23 Strain Isolated from Kerala, India

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Divya Meparambu Prabhakaran ◽  
Goutam Chowdhury ◽  
Gururaja Perumal Pazhani ◽  
Thandavarayan Ramamurthy ◽  
Sabu Thomas
Keyword(s):  
Comparative Analysis ◽  
Genome Sequence ◽  
Vibrio Parahaemolyticus ◽  
Draft Genome ◽  
Clinical Isolates ◽  
Draft Genome Sequence

Vibrio parahaemolyticus is the leading cause of seafood-related gastroenteritis. Here, we report the draft genome sequence of a trh + strain, V. parahaemolyticus K23, isolated from seafood. The sequence will be useful for comparative analysis between environmental and clinical isolates of V. parahaemolyticus .

scholarly journals Draft Genome Sequence of Modestobacter sp. strain VKM Ac-2676 from soil in the area of sharply continental climate

2017 ◽  
Author(s):  
Oleg V. Vasilenko ◽  
Sergey V. Tarlachkov ◽  
Irina P. Starodumova ◽  
Elena V. Ariskina ◽  
Kseniya I. Ariskina ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Ion Torrent ◽  
Sequencing Technology ◽  
Climate Zone ◽  
Genes Encoding ◽  
Ion Torrent Sequencing ◽  
Continental Climate

A draft genome sequence of a novel actinobacterium, Modestobacter sp. strain VKM Ac-2676, was derived using Ion Torrent sequencing technology. The genome size is 3.88 Mb with average G+C content of 73.40%. The genes encoding properties relevant to adaptability of this bacterium to a sharply continental climate zone were revealed.

scholarly journals Draft Genome Sequence of Lignin-Degrading Agrobacterium sp. Strain S2, Isolated from a Decaying Oil Palm Empty Fruit Bunch

2021 ◽  
Vol 10 (19) ◽  
Author(s):  
Ummu Habibah Faisal ◽  
Nurul Syazwani Ahmad Sabri ◽  
Nurtasbiyah Yusof ◽  
Analhuda Abdullah Tahir ◽  
Nuurul Nadrah Mohd Said ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Oil Palm ◽  
Lignin Degradation ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Empty Fruit Bunch ◽  
Genes Encoding

ABSTRACT We report the draft genome sequence of Agrobacterium sp. strain S2, isolated from a decaying oil palm empty fruit bunch (OPEFB) in Negeri Sembilan, Malaysia, which yields potential genes encoding lignin degradation enzymes. This genome of 9,722,071 bp exhibited 58.9% GC content, 10,416 coding genes, and 12 RNAs.

scholarly journals Draft Genome Sequence of Klebsiella pneumoniae AWD5

2017 ◽  
Vol 5 (5) ◽  
Author(s):  
Jina Rajkumari ◽  
L. Paikhomba Singha ◽  
Piyush Pandey
Keyword(s):  
Klebsiella Pneumoniae ◽  
Genome Sequence ◽  
De Novo ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Rrna Genes ◽  
Polyaromatic Hydrocarbon ◽  
Coding Sequences ◽  
Content Type ◽  
Benzoate Degradation

ABSTRACT Here, we report the draft genome sequence of Klebsiella pneumoniae strain AWD5, isolated from an automobile workshop in India. The de novo assembly resulted in a 4,807,409 bp genome containing 25 rRNA genes, 81 tRNAs, and 4,636 coding sequences (CDS). It carries important genes for polyaromatic hydrocarbon degradation and benzoate degradation.

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