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.

scholarly journals Complete Genome Sequences of Two Mutacin-Producing Streptococcus mutans Strains, T8 and UA140

2020 ◽  
Vol 9 (24) ◽  
Author(s):  
Indranil Biswas
Keyword(s):  
Antimicrobial Peptides ◽  
Streptococcus Mutans ◽  
Genome Sequence ◽  
Complete Genome ◽  
Clinical Isolates ◽  
Sequence Information ◽  
Genome Sequences ◽  
Content Type ◽  
Genome Sequence Information

ABSTRACT Streptococcus mutans is known to produce various antimicrobial peptides called mutacins. Two clinical isolates, T8 and UA140, are well characterized regarding their mutacin production, but genome sequence information was previously unavailable. Complete genome sequences of these two mutacin-producing strains are reported here.

scholarly journals Draft Genome Sequences of Two Novel Sub-Antarctic Williamsia Species

2017 ◽  
Vol 5 (41) ◽  
Author(s):  
Akhikun Nahar ◽  
Anthony L. Baker ◽  
Michael A. Charleston ◽  
John P. Bowman ◽  
Margaret L. Britz
Keyword(s):  
Genome Sequence ◽  
Metabolic Pathways ◽  
Draft Genome ◽  
Illumina Miseq ◽  
Shotgun Sequencing ◽  
Sequence Information ◽  
Sequencing Technology ◽  
Genome Sequences ◽  
Cold Tolerant ◽  
Genome Sequence Information

ABSTRACT Illumina MiSeq shotgun sequencing technology was used to sequence the genomes of two novel sub-Antarctic Williamsia species, designated strains 1135 and 1138. The estimated genome sizes for strains 1135 and 1138 are 5.99 Mb and 6.08 Mb, respectively. This genome sequence information will aid in understanding the lipid metabolic pathways of cold-tolerant Williamsia species.

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 Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype

DNA Research ◽  
2020 ◽  
Author(s):  
Kenji Nashima ◽  
Kenta Shirasawa ◽  
Andrea Ghelfi ◽  
Hideki Hirakawa ◽  
Sachiko Isobe ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Dna Markers ◽  
Sequence Data ◽  
Sequence Information ◽  
Sequencing Data ◽  
Double Flower ◽  
Causative Gene ◽  
Hydrangea Macrophylla ◽  
Genome Sequence Information

Abstract Owing to its high ornamental value, the double flower phenotype of hydrangea (Hydrangea macrophylla) is one of its most important traits. In this study, genome sequence information was obtained to explore effective DNA markers and the causative genes for double flower production in hydrangea. Single-molecule real-time sequencing data followed by a Hi-C analysis were employed. Two haplotype-phased sequences were obtained from the heterozygous genome of hydrangea. One assembly consisted of 3,779 scaffolds (2.256 Gb in length and N50 of 1.5 Mb), the other also contained 3,779 scaffolds (2.227 Gb in length, and N50 of 1.4 Mb). A total of 36,930 genes were predicted in the sequences, of which 32,205 and 32,222 were found in each haplotype. A pair of 18 pseudomolecules was constructed along with a high-density single-nucleotide polymorphism (SNP) genetic linkage map. Using the genome sequence data, and two F2 populations, the SNPs linked to double flower loci (djo and dsu) were discovered. DNA markers linked to djo and dsu were developed, and these could distinguish the recessive double flower allele for each locus, respectively. The LEAFY gene is a very likely candidate as the causative gene for dsu, since frameshift was specifically observed in the double flower accession with dsu.

scholarly journals Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense

2021 ◽  
Author(s):  
Kenta Shirasawa ◽  
Nobuo Kobayashi ◽  
Akira Nakatsuka ◽  
Hideya Ohta ◽  
Sachiko Isobe
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Sequence Information ◽  
Whole Genome ◽  
Closely Related Species ◽  
Chiba Prefecture ◽  
Genome Sequence Assembly ◽  
Genome Sequence Information ◽  
Relationship Of ◽  
Long Fragment Read

To enhance the genomics and genetics of azalea, the whole-genome sequences of two species of Rhododendron were determined and analyzed in this study: Rhododendron ripense, the cytoplasmic donor and ancestral species of large-flowered and evergreen azalea cultivars, respectively; and Rhododendron kiyosumense, a native of Chiba prefecture (Japan) seldomly bred and cultivated. A chromosome-level genome sequence assembly of R. ripense was constructed by single-molecule real-time (SMRT) sequencing and genetic mapping, while the genome sequence of R. kiyosumense was assembled using the single-tube long fragment read (stLFR) sequencing technology. The R. ripense genome assembly contained 319 contigs (506.7 Mb; N50 length: 2.5 Mb) and was assigned to the genetic map to establish 13 pseudomolecule sequences. On the other hand, the genome of R. kiyosumense was assembled into 32,308 contigs (601.9 Mb; N50 length: 245.7 kb). A total of 34,606 genes were predicted in the R. ripense genome, while 35,785 flower and 48,041 leaf transcript isoforms were identified in R. kiyosumense through Iso-Seq analysis. Overall, the genome sequence information generated in this study enhances our understanding of genome evolution in the Ericales and reveals the phylogenetic relationship of closely-related species. This information will also facilitate the development of phenotypically attractive azalea cultivars.

scholarly journals Improved Complete Genome Sequence of the Extremely Radioresistant Bacterium Deinococcus radiodurans R1 Obtained Using PacBio Single-Molecule Sequencing

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Xiaoting Hua ◽  
Yuejin Hua
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Deinococcus Radiodurans ◽  
Nucleotide Polymorphisms ◽  
Genome Sequences ◽  
Single Nucleotide ◽  
Single Molecule Sequencing ◽  
Deinococcus Radiodurans R1

The genome sequence of Deinococcus radiodurans R1 was published in 1999. We resequenced D. radiodurans R1 using PacBio and compared the sequence with the published one. Large insertions and single nucleotide polymorphisms (SNPs) were observed among the genome sequences. A more accurate genome sequence will be helpful to studies of D. radiodurans.

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 Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype

2020 ◽  
Author(s):  
K Nashima ◽  
K Shirasawa ◽  
A Ghelfi ◽  
H Hirakawa ◽  
S Isobe ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Single Molecule ◽  
Dna Markers ◽  
Sequence Data ◽  
Sequence Information ◽  
Sequencing Data ◽  
Double Flower ◽  
Causative Gene ◽  
Hydrangea Macrophylla ◽  
Wide Range

AbstractOwing to its high ornamental value, the double flower phenotype of hydrangea (Hydrangea macrophylla) is one of its most important traits. In this study, genome sequence information was obtained to explore effective DNA markers and the causative genes for double flower production in hydrangea. Single molecule real-time sequencing data followed by a HiC analysis was employed. The resultant haplotype-phased sequences consisted of 3,779 sequences (2.256 Gb in length and N50 of 1.5 Mb), and 18 pseudomolecules comprising 1.08 Gb scaffold sequences along with a high-density SNP genetic linkage map. Using the genome sequence data obtained from two breeding populations, the SNPs linked to double flower loci (Djo and Dsu), were discovered for each breeding population. DNA markers J01 linked to Djo and S01 linked to Dsu were developed, and these could be used successfully to distinguish the recessive double flower allele for each locus respectively. The LEAFY gene was suggested as the causative gene for Dsu, since frameshift was specifically observed in double flower accession with dsu. The genome information obtained in this study will facilitate a wide range of genomic studies on hydrangea in the future.

scholarly journals Identification and characterization of regulatory pathways involved in early flowering in the new leaves of alfalfa (Medicago sativa L.) by transcriptome analysis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dongmei Ma ◽  
Bei Liu ◽  
Lingqiao Ge ◽  
Yinyin Weng ◽  
Xiaohui Cao ◽  
...  
Keyword(s):  
Medicago Sativa ◽  
Secondary Metabolism ◽  
Flowering Time ◽  
Degradation Pathway ◽  
Early Flowering ◽  
Receptor Kinase ◽  
Leucine Rich Repeat ◽  
Kinase Family ◽  
Pathogenesis Related ◽  
Early Flowering Phenotype

Abstract Background Alfalfa (Medicago sativa L.) is a perennial legume extensively planted throughout the world as a high nutritive value livestock forage. Flowering time is an important agronomic trait that contributes to the production of alfalfa hay and seeds. However, the underlying molecular mechanisms of flowering time regulation in alfalfa are not well understood. Results In this study, an early-flowering alfalfa genotype 80 and a late-flowering alfalfa genotype 195 were characterized for the flowering phenotype. Our analysis revealed that the lower jasmonate (JA) content in new leaves and the downregulation of JA biosynthetic genes (i.e. lipoxygenase, the 12-oxophytodienoate reductase-like protein, and salicylic acid carboxyl methyltransferase) may play essential roles in the early-flowering phenotype of genotype 80. Further research indicated that genes encode pathogenesis-related proteins [e.g. leucine rich repeat (LRR) family proteins, receptor-like proteins, and toll-interleukin-like receptor (TIR)-nucleotide-binding site (NBS)-LRR class proteins] and members of the signaling receptor kinase family [LRR proteins, kinases domain of unknown function 26 (DUF26) and wheat leucine-rich repeat receptor-like kinase10 (LRK10)-like kinases] are related to early flowering in alfalfa. Additionally, those involved in secondary metabolism (2-oxoglutarate/Fe (II)-dependent dioxygenases and UDP-glycosyltransferase) and the proteasome degradation pathway [really interesting new gene (RING)/U-box superfamily proteins and F-box family proteins] are also related to early flowering in alfalfa. Conclusions Integrated phenotypical, physiological, and transcriptomic analyses demonstrate that hormone biosynthesis and signaling pathways, pathogenesis-related genes, signaling receptor kinase family genes, secondary metabolism genes, and proteasome degradation pathway genes are responsible for the early flowering phenotype in alfalfa. This will provide new insights into future studies of flowering time in alfalfa and inform genetic improvement strategies for optimizing this important trait.

scholarly journals Draft Genome Sequences of Fungus Aspergillus calidoustus

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Fabian Horn ◽  
Jörg Linde ◽  
Derek J. Mattern ◽  
Grit Walther ◽  
Reinhard Guthke ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Genome Sequence ◽  
Functional Annotation ◽  
Draft Genome ◽  
Genome Mining ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Genome Sequences

Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504) . The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining.

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