Biology subjects

Isobe, S.

Publications and source records attributed to Isobe, S..

52 records · Page 3Linked to original sources

bioRxiv2021

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

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.

genomics↗

bioRxiv2021

Genome features of common vetch (Vicia sativa) in natural habitats

Wild plants are often tolerant to biotic and abiotic stresses in their natural environments, whereas domesticated plants such as crops frequently lack such resilience. This difference is thought to be due to the high levels of genome heterozygosity in wild plant populations and the low levels of heterozygosity in domesticated crop species. In this study, common vetch (Vicia sativa) was used as a model to examine this hypothesis. The common vetch genome (2n = 14) was estimated as 1.8 Gb in size. Genome sequencing produced a reference assembly that spanned 1.5 Gb, from which 31,146 genes were predicted. Using this sequence as a reference, 24,118 single nucleotide polymorphisms were discovered in 1,243 plants from 12 natural common vetch populations in Japan. Common vetch genomes exhibited high heterozygosity at the population level, with lower levels of heterozygosity observed at specific genome regions. Such patterns of heterozygosity are thought to be essential for adaptation to different environments. These findings suggest that high heterozygosity at the population level would be required for wild plants to survive under natural conditions while allowing important gene loci to be fixed to adapt the conditions. The resources generated in this study will provide insights into de novo domestication of wild plants and agricultural enhancement. HighlightSequence analysis of the common vetch (Vicia sativa) genome and SNP genotyping across natural populations revealed nucleotide diversity levels associated with native population environments.

genomics↗

bioRxiv2021

Whole-genome sequence analysis of mutations in rice plants regenerated from zygotes, mature embryos, and immature embryos

Somaclonal variation was studied by whole-genome sequencing in rice plants (Oryza sativa L., Nipponbare) regenerated from the zygotes, mature embryos, and immature embryos of a single mother plant. The mother plant and its seed-propagated progeny were also sequenced. A total of 338 variants of the mother plant sequence were detected in the progeny, and mean values ranged from 9.0 of the seed-propagated plants to 37.4 of regenerants from mature embryos. The ratio of single nucleotide variants among the variants was 74.3%, and the natural mutation rate calculated using the variants in the seed-propagated plants was 1.2 x 10-8. The percentage and the mutation rate were consistent with the values reported previously. Plants regenerated from mature embryos had significantly more variants than different progeny types. Therefore, using zygotes and immature embryos can reduce somaclonal variation during the genetic manipulation of rice.

plant biology↗

bioRxiv2021

A Chromosome-scale draft genome sequence of horsegram (Macrotyloma uniflorum)

Horsegram [Macrotyloma uniflorum (Lam.) Verdc.] is an underutilized warm season diploid legume (2n=20, 22), It is consumed as a food legume in India, and animal feed and fodder in Africa and Australia. Because of its ability to grow under water-deficient and marginal soil conditions, horsegram is a preferred choice in the era of the global climatic change. In recognition of its potential as a crop species, we generated and analyzed a draft genome sequence for HPK-4. The genome sequences of HPK-4 were generated by Illumina platform. Ten chromosome-scale pseudomolecules were created by aligning scaffold sequences onto a linkage map. The total length of the ten pseudomolecules were 259.2 Mb, covering 89% of the total length of the assembled sequences. A total of 36,105 genes were predicted on the assembled sequences, and 14,736 were considered to be horsegram specific genes by comparative analysis with Phaseolus. vulgaris, Vigna. angularis, Lotus. japonicus and Arabidopsis. thaliana. The results of macrosynteny analysis suggested that the genome structure of V. angularis is more similar to horsegram than that of P. vulgaris. Diversity analysis in the 91 accessions of horsegram with dd-RAD-Seq analysis indicated narrow genetic diversity among the horsegram accessions. This is the first attempt to generate a draft genome sequence in horsegram and will provide a reference for sequence-based analysis of the horsegram germplasm to elucidate the genetic basis of important traits.

genomics↗

bioRxiv2021

Endogenous Retroviral Elements Generate Pathologic Neutrophils and Elastase Rich Exosomes in Pulmonary Arterial Hypertension

Neutrophil elastase (NE) is implicated in pulmonary arterial hypertension (PAH) but the role of neutrophils in the pathogenesis of PAH is unclear. Here we show that neutrophils from PAH vs. control subjects produce and release increased NE associated with enhanced extracellular trap formation. PAH neutrophils are highly adherent and show decreased migration consistent with increased vinculin, identified on proteomic analysis and previously linked to an antiviral response. This was substantiated by a transcriptomic interferon signature in PAH neutrophils and an increase in human endogenous retrovirus (HERV-K) envelope protein. NE and interferon genes are induced by HERV-K envelope and vinculin is increased by HERV-K dUTPase that is elevated in PAH plasma. Neutrophil exosomes from PAH plasma contain increased NE and HERV-K envelope and induce pulmonary hypertension in mice, that is mitigated by the NE inhibitor and antiviral agent, elafin. Thus, elevated HERVs explain pathological neutrophils linked to PAH induction and progression.

immunology↗

bioRxiv2020

Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety 'Nijisseiki

AimThe Japanese pear (P. pyrifolia) variety Nijisseiki is valued for its superior flesh texture, which has led to its use as a breeding parent for most Japanese pear cultivars. However, in the absence of genomic resources for Japanese pear, the parents of the Nijisseiki cultivar remain unknown, as does the genetic basis of its favorable texture. The genomes of pear and related species are complex due to ancestral whole genome duplication and high heterozygosity, and long-sequencing technology was used to address this. Methods and ResultsDe novo assembly of long sequence reads covered 136x of the Japanese pear genome and generated 503.9 Mb contigs consisting of 114 sequences with an N50 value of 7.6{square}Mb. Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences. In total, 44,876 protein-encoding genes were predicted, 84.3% of which were supported by predicted genes and transcriptome data from Japanese pear relatives. As expected, evidence of whole genome duplication was observed, consistent with related species. Conclusion and PerspectiveThis is the first genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.

genomics↗

bioRxiv2020

KusakiDB v1.0: a novel approach for validation and completeness of protein orthologous groups

Plants have quite a low coverage in the major protein databases despite their roughly 350,000 species. Moreover, the agricultural sector is one of the main categories in bioeconomy. In order to manipulate and/or engineer plant-based products, it is important to understand the essential fabric of an organism, its proteins. Therefore, we created KusakiDB, which is a database of orthologous proteins, in plants, that correlates three major databases, OrthoDB, UniProt and RefSeq. KusakiDB has an orthologs assessment and management tools in order to compare orthologous groups, which can provide insights not only under an evolutionary point of view but also evaluate structural gene prediction quality and completeness among plant species. KusakiDB could be a new approach to reduce error propagation of functional annotation in plant species. Additionally, this method could, potentially, bring to light some orthologs unique to a few species or families that could have evolved at a high evolutionary rate or could have been a result of a horizontal gene transfer. Availability and ImplementationThe software is implemented in R. It is available at http://pgdbjsnp.kazusa.or.jp/app/kusakidb and at https://hub.docker.com/r/ghelfi/kusakidb under the MIT license. Contactandreaghelfi@kazusa.or.jp Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2020

Genomic region associated with pod color variation in pea (Pisum sativum)

Pea (Pisum sativum) was chosen as the research material by Gregor Mendel to discover the laws of inheritance. Out of seven traits studied by Mendel, genes controlling three traits including pod shape, pod color, and flower position have not been identified to date. With the aim to identify the genomic region controlling pod color, we determined the genome sequence of a pea line with yellow pods. Genome sequence reads obtained using a nanopore sequencing technology were assembled into 117,981 contigs that spanned 3.3 Gb in length and showed an N50 value of 51.2 kb. Using single nucleotide polymorphisms (SNPs) detected in a pea mapping population, these contigs were genetically anchored to the publicly available pseudomolecule sequences of the pea genome. Subsequent genetic and association analyses identified a genomic region responsible for pea pod color. At this genomic location, genes encoding 3 exoribonucleases were selected as potential candidates controlling pod color, based on DNA sequencing and transcriptome analysis of green and yellow pod lines. The results presented in this study are expected to accelerate pan-genome studies in pea and facilitate the identification of the gene controlling one of the traits studied by Mendel.

genomics↗

bioRxiv2020

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

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 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.

genomics↗

bioRxiv2020

AnAms1.0: A high-quality chromosome-scale assembly of a domestic cat Felis catus of American Shorthair breed

The domestic cat (Felis catus) is one of the most popular companion animals in the world. Comprehensive genomic resources will aid the development and application of veterinary medicine including to improve feline health, in particular, to enable precision medicine which is promising in human application. However, currently available cat genome assemblies were mostly built based on the Abyssinian cat breed which is highly inbred and has limited power in representing the vast diversity of the cat population. Moreover, the current reference assembly remains fragmented with sequences contained in thousands of scaffolds. We constructed a reference-grade chromosome-scale genome assembly of a domestic cat, Felis catus genome of American Shorthair breed, Anicom American shorthair 1.0 (AnAms1.0) with high contiguity (scaffold N50 > 120 Mb), by combining multiple advanced genomic technologies, including PacBio long-read sequencing as well as sequence scaffolding by long-range genomic information obtained from Hi-C and optical mapping data. Homology-based and ab initio gene annotation was performed with the Iso-Seq data. Analyzed data is be publicly accessible on Cats genome informatics (Cats-I, https://cat.annotation.jp/), a cat genome database established as a platform to facilitate the accumulation and sharing of genomic resources to improve veterinary care.

genomics↗

bioRxiv2020

Genome sequence analysis of a giant-rooted 'Sakurajima daikon' radish (Raphanus sativus)

Daikon 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 60x 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.

genomics↗

bioRxiv2019

Genetic Mapping in Autohexaploid Sweet Potato with Low-coverage NGS-based Genotyping Data

Next-generation sequencing (NGS)-based genotyping methods can generate numerous genetic markers in a single experiment and have contributed to plant genetic mapping. However, the benefits of NGS-based methods are limited in autopolyploids as their genetic segregation mode is complex. Moreover, autopolyploids have large genomes and require abundant sequencing data to obtain sufficient genetic markers. There are several methods for genetic mapping in autopolyploids. These approaches may be impractical for plant genetic studies as they require large amounts of data and are not cost-effective. In the present study, we propose a simple strategy for genetic mapping of polyploids in a cost-effective manner. The allele dosage probabilities calculated from NGS read counts were used in association analyses to detect loci associated with specific phenotypes. This approach is superior to conventional methods of determining allele dosage, which usually result in the filtering of many genetic markers with low read depth. The validity of the strategy was demonstrated using real phenotype data from autohexaploid sweet potato populations to detect genetic loci for both qualitative and quantitative traits, the latter of which required the use of allele dosage probabilities for the detection of loci. We demonstrate that this proposed method is useful with reasonable NGS read counts.

genetics↗

bioRxiv2019

The Ficus erecta genome to identify the Ceratocystis canker resistance gene for breeding programs in common fig (F. carica)

Ficus erecta, a wild relative of common fig (F. carica), is a donor of Ceratocystis canker resistance in fig breeding programs. Interspecific hybridization followed by recurrent backcrossing is an effective method to transfer the resistance trait from wild to cultivated fig; however, this is time consuming and labor-intensive for trees, especially for gynodioecious plants such as fig. In this study, genome resources were developed for F. erecta to facilitate fig breeding programs. The genome sequence of F. erecta was determined using single-molecule real-time sequencing technology. The resultant assembly spanned 331.6 Mb with 538 contigs and an N50 length of 1.9 Mb, from which 51,806 high-confidence genes were predicted. Pseudomolecule sequences corresponding to the chromosomes of F. erecta were established with a genetic map based on single nucleotide polymorphisms from double-digest restriction-site associated DNA sequencing. Subsequent linkage analysis and whole genome resequencing identified a candidate gene for the Ceratocystis canker resistance trait. Genome-wide genotyping analysis enabled selection of female lines that possessed resistance and effective elimination of donor genome from progeny. The genome resources provided in this study will accelerate and enhance disease resistance breeding programs in fig.

genomics↗

bioRxiv2019

De novo whole-genome assembly in interspecific hybrid table grape, ‘Shine Muscat’

This study presents the first genome sequence of an interspecific grape hybrid, Shine Muscat (Vitis labruscana x V. vinifera), an elite table grape cultivar bred in Japan. The complexity of the genome structure, arising from the interspecific hybridization, necessitated the use of a sophisticated genome assembly pipeline with short-read genome sequence data. The resultant genome assemblies consisted of two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a \"haploid\" genome. The unphased sequences spanned 490.1 Mb in length, 99.4% of the estimated genome size, with 8,696 scaffold sequences with an N50 length of 13.2 Mb. The phased sequences had 15,650 scaffolds spanning 1.0 Gb with N50 of 4.2 Mb. The two sequences comprised 94.7% and 96.3% of the core eukaryotic genes, indicating that the entire genome of Shine Muscat was represented. Examination of genome structures revealed possible genome rearrangements between the genomes of Shine Muscat and a V. vinifera line. Furthermore, full-length transcriptome sequencing analysis revealed 13,947 gene loci on the Shine Muscat genome, from which 26,199 transcript isoforms were transcribed. These genome resources provide new insights that could help cultivation and breeding strategies produce more high-quality table grapes such as Shine Muscat.

genomics↗

bioRxiv2019

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

We report the phased genome sequence of an interspecific hybrid, the flowering cherry Somei-Yoshino (Cerasus x 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.

genomics↗

bioRxiv2018

Hayai-Annotation Plants: an ultra-fast and comprehensive gene annotation system in plants

Hayai-Annotation Plants is a browser-based interface for an ultra-fast and accurate gene annotation system for plant species using R. The pipeline combines the sequence-similarity searches, using USEARCH against UniProtKB (taxonomy Embryophyta), with a functional annotation step. Hayai-Annotation Plants provides five layers of annotation: 1) gene name; 2) gene ontology terms consisting of its three main domains (Biological Process, Molecular Function, and Cellular Component); 3) enzyme commission number; 4) protein existence level; 5) and evidence type. In regard to speed and accuracy, Hayai-Annotation Plants annotated Arabidopsis thaliana (Araport11, representative peptide sequences) within five minutes with an accuracy of 96.4 %.\n\nAvailability and ImplementationThe software is implemented in R and runs on Macintosh and Linux systems. It is freely available at https://github.com/kdri-genomics/Hayai-Annotation-Plants under the GPLv3 license.

bioinformatics↗