scholarly journals Phased genome sequence of an interspecific hybrid flowering cherry, Somei-Yoshino (Cerasus × yedoensis)

2019 ◽  
Author(s):  
Kenta Shirasawa ◽  
Tomoya Esumi ◽  
Hideki Hirakawa ◽  
Hideyuki Tanaka ◽  
Akihiro Itai ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Interspecific Hybrid ◽  
Allelic Variation ◽  
Transcriptome Data ◽  
Sequencing Technology ◽  
Eukaryotic Genes ◽  
Flowering Cherry ◽  
Whole Genome Resequencing ◽  
Floral Bud

AbstractWe report the phased genome sequence of an interspecific hybrid, the flowering cherry Somei-Yoshino (Cerasus × yedoensis). The sequence was determined by single-molecule real-time sequencing technology and assembled using a trio-binning strategy in which allelic variation was resolved to obtain phased sequences. The resultant assembly consisting of two haplotype genomes spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, we established a pair of eight pseudomolecule sequences, with highly conserved structures between two genome sequences with 2.4 million sequence variants. A whole genome resequencing analysis of flowering cherry varieties suggested that Somei-Yoshino is derived from a cross between C. spachiana and either C. speciose or its derivative. Transcriptome data for flowering date revealed comprehensive changes in gene expression in floral bud development toward flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.

scholarly journals Phased genome sequence of an interspecific hybrid flowering cherry, ‘Somei-Yoshino’ (Cerasus × yedoensis)

DNA Research ◽  
2019 ◽  
Vol 26 (5) ◽  
pp. 379-389 ◽  
Author(s):  
Kenta Shirasawa ◽  
Tomoya Esumi ◽  
Hideki Hirakawa ◽  
Hideyuki Tanaka ◽  
Akihiro Itai ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Interspecific Hybrid ◽  
Time Course ◽  
Sequence Data ◽  
Eukaryotic Genes ◽  
Flowering Cherry ◽  
Whole Genome Resequencing ◽  
Floral Bud ◽  
Genome Information

Abstract We report the phased genome sequence of an interspecific hybrid, the flowering cherry ‘Somei-Yoshino’ (Cerasus × yedoensis). The sequence data were obtained by single-molecule real-time sequencing technology, split into two subsets based on genome information of the two probable ancestors, and assembled to obtain two haplotype phased genome sequences of the interspecific hybrid. The resultant genome assembly consisting of the two haplotype sequences spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, we established a pair of eight pseudomolecule sequences, with highly conserved structures between the two haplotype sequences with 2.4 million sequence variants. A whole genome resequencing analysis of flowering cherries suggested that ‘Somei-Yoshino’ might be derived from a cross between C. spachiana and either C. speciosa or its relatives. A time-course transcriptome analysis of floral buds and flowers suggested comprehensive changes in gene expression in floral bud development towards flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.

scholarly journals Whole-Genome Sequence of Mycoplasma bovis Strain Ningxia-1

2018 ◽  
Vol 6 (4) ◽  
Author(s):  
Peng Sun ◽  
Haifeng Luo ◽  
Xin Zhang ◽  
Jingyi Xu ◽  
Yanan Guo ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Whole Genome Sequence ◽  
Mycoplasma Bovis ◽  
Sequencing Technology ◽  
Circular Chromosome ◽  
A Genome ◽  
Variable Surface ◽  
Integrative Conjugative Elements ◽  
Single Circular Chromosome

ABSTRACT A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology. The strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia, China. The single circular chromosome of 1,033,629 bp shows differences between complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins (VSPs), pathogenicity islands (PAIs), etc.

scholarly journals Draft Genome Sequence of the Wood-Decaying Fungus Xylaria sp. BCC 1067

2019 ◽  
Vol 8 (25) ◽  
Author(s):  
Sawannee Sutheeworapong ◽  
Nuthatai Suteerapongpan ◽  
Prasobsook Paenkaew ◽  
Peerada Prommeenate ◽  
Supapon Cheevadhanarak ◽  
...  
Keyword(s):  
Real Time ◽  
Genome Sequence ◽  
Single Molecule ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Lignocellulolytic Enzymes ◽  
Sequencing Technology ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Technology Analysis

Xylaria sp. BCC 1067 is a wood-decaying fungus which is capable of producing lignocellulolytic enzymes. Based on the results of a single-molecule real-time sequencing technology analysis, we present the first draft genome of Xylaria sp. BCC 1067, comprising 54.1 Mb with 12,112 protein-coding genes.

scholarly journals Complete Genome Sequence of Lactobacillus fermentum MTCC 25067 (Formerly TDS030603), a Viscous Exopolysaccharide-Producing Strain Isolated from Indian Fermented Milk

2017 ◽  
Vol 5 (13) ◽  
Author(s):  
Ni Putu Desy Aryantini ◽  
Jashbhai B. Prajapati ◽  
Tadasu Urashima ◽  
Kenji Fukuda
Keyword(s):  
Real Time ◽  
Genome Sequence ◽  
Single Molecule ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Fermented Milk ◽  
Lactobacillus Fermentum ◽  
Sequencing Technology ◽  
Content Type

ABSTRACT Lactobacillus fermentum MTCC 25067 (formerly TDS030603) is capable of producing a highly viscous slime exopolysaccharide. We report here the complete genome sequence of the strain, which was deciphered by using PacBio single-molecule real-time sequencing technology.

scholarly journals Complete Genome Sequence ofPaenibacillussp. Strain IHBB 10380 Using PacBio Single-Molecule Real-Time Sequencing Technology

2015 ◽  
Vol 3 (2) ◽  
Author(s):  
Mohinder Pal ◽  
Mohit K. Swarnkar ◽  
Rishu Thakur ◽  
Shashi Kiran ◽  
Sanjay Chhibber ◽  
...  
Keyword(s):  
Real Time ◽  
Genome Sequence ◽  
Single Molecule ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Sequencing Technology

scholarly journals Genome sequence analysis of a giant-rooted ‘Sakurajima daikon’ radish (Raphanus sativus)

2020 ◽  
Author(s):  
Kenta Shirasawa ◽  
Hideki Hirakawa ◽  
Nobuko Fukino ◽  
Hiroyasu Kitashiba ◽  
Sachiko Isobe
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Raphanus Sativus ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Genetic Maps ◽  
Complex Nature ◽  
Eukaryotic Genes ◽  
Long Read ◽  
Large Round

AbstractDaikon radish (Raphanus sativus) roots vary in size and shape between cultivars. This study reports the genome sequence assembly of a giant-rooted ‘Sakurajima daikon’ radish variety, ‘Okute-Sakurajima’, which produces extremely large round roots. Radish genome assembly is hampered by the repetitive and complex nature of the genome. To address this, single-molecule real-time technology was used to obtain long-read sequences at 60× genome coverage. De novo assembly of the long reads generated 504.5 Mb contig sequences consisting of 1,437 sequences with contig N50 length of 1.2 Mb, including 94.1% of the core eukaryotic genes. Nine pseudomolecule sequences, comprising 69.3% of the assembled contig length, were generated with high-density SNP genetic maps. The chromosome-level sequences revealed structure variations and rearrangements among Brassicaceae genomes. In total, 89,915 genes were predicted in the ‘Okute-Sakurajima’ genome, 30,033 of which were unique to the assembly in this study. The improved genome information generated in this study will not only form a new baseline resource for radish genomics, but will also provide insights into the molecular mechanisms underlying formation of giant radish roots.

scholarly journals Genome sequencing and analysis of two early-flowering cherry (Cerasus × kanzakura) varieties, ‘Kawazu-zakura’ and ‘Atami-zakura’

2021 ◽  
Author(s):  
Kenta Shirasawa ◽  
Akihiro Itai ◽  
Sachiko Isobe
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Early Flowering ◽  
Gene Clustering ◽  
Sequence Information ◽  
Genome Sequences ◽  
Cherry Tree ◽  
Fundamental Information ◽  
Flowering Cherry ◽  
Early Flowering Phenotype

AbstractTo gain genetic insights into the early-flowering phenotype of ornamental cherry, also known as sakura, we determined the genome sequences of two early-flowering cherry (Cerasus × kanzakura) varieties, ‘Kawazu-zakura’ and ‘Atami-zakura’. Since the two varieties are interspecific hybrids, likely derived from crosses between Cerasus campanulata (early-flowering species) and Cerasus speciosa, we employed the haplotype-resolved sequence assembly strategy. Genome sequence reads obtained from each variety by single molecule real-time sequencing (SMRT) were split into two subsets, based on the genome sequence information of the two probable ancestors, and assembled to obtain haplotype-phased genome sequences. The resultant genome assembly of ‘Kawazu-zakura’ spanned 519.8 Mb with 1,544 contigs and an N50 value of 1,220.5 kb, while that of ‘Atami-zakura’ totaled 509.6 Mb with 2,180 contigs and an N50 value of 709.1 kb. A total of 72,702 and 72,528 potential protein-coding genes were predicted in the genome assemblies of ‘Kawazu-zakura’ and ‘Atami-zakura’, respectively. Gene clustering analysis identified 2,634 clusters uniquely presented in the C. campanulata haplotype sequences, which might contribute to its early-flowering phenotype. Genome sequences determined in this study provide fundamental information for elucidating the molecular and genetic mechanisms underlying the early-flowering phenotype of ornamental cherry tree varieties and their relatives.

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