Article
Entomology
John H. Boyle, Pasi M. A. Rastas, Xin Huang, Austin G. Garner, Indra Vythilingam, Peter A. Armbruster
Summary: This study constructed a high-density linkage map for the Asian tiger mosquito, reassembled its genome into AalbF3 with improvements over AalbF2, and demonstrated the utility of AalbF3 for comparative genomics analysis. The AalbF3 assembly is smaller with a higher proportion of complete genes and more aligned RNAseq reads compared to AalbF2. The study identified candidate SNPs associated with photoperiodic diapause, an important ecological adaptation for the rapid range expansion and climatic adaptation of Aedes albopictus.
Article
Biotechnology & Applied Microbiology
Xueyan Shen, Yong Chao Niu, Joseph Angelo V. Uichanco, Norman Phua, Pranjali Bhandare, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, Laszlo Orban
Summary: For Asian seabass cultured in sea cages, aquatic pathogens, environmental factors, and stress are major causes of disease, resulting in substantial economic losses. Researchers identified a genomic region associated with increased robustness in response to pathogen-infected marine environments. This finding has potential applications in selecting robust Asian seabass lines for breeding programs.
Article
Genetics & Heredity
Yue Shi, Baohua Chen, Shengnan Kong, Qingmin Zeng, Leibin Li, Bo Liu, Fei Pu, Peng Xu
Summary: This study updated the chromosome-level genome of Takifugu bimaculatus, improving its contiguity and correctness. A new criterion for evaluating assembly differences and a novel method for integrating multiple assembly information were developed. The research provided profound insights into genetic recombination and effective genome assembly.
Article
Agronomy
Cheng Pan, Xueyi He, Shiyue Song, Liping Zou, Mengxin Wang, Baoyu Han
Summary: In this study, nine CmPEBP genes were identified for the first time in the Hangzhou White Chrysanthemum, and their biological role in flowering was preliminarily studied. The CmPEBP genes were classified into three subfamilies and showed tissue-specific expression patterns. Their expression patterns also varied under different temperatures and hormone stressors. This research is important for understanding the flowering and floral organ development of the Hangzhou White Chrysanthemum, especially in response to exogenous hormone spraying.
Article
Plant Sciences
Hirotomo Murai, Tomofumi Mochizuki
Summary: In this study, the tomato aspermy virus (TAV) vector was optimized for virus-induced gene silencing (VIGS) in Chrysanthemum seticuspe, making it useful as a model chrysanthemum plant. Vacuum infiltration into sprouts successfully infected the plant without symptoms. This report is the first of VIGS in chrysanthemums.
Article
Virology
Jie Chen, Yafeng Dong, Hui Wang, Jie Zhang, Changnian Ma, Liangliang Cao, Leiding Shen, Kuirong Cao, Xudong Fan
Summary: The complete genome sequence of a putative novel member of the genus Sadwavirus, tentatively named chrysanthemum sadwavirus (ChSV), was determined by high-throughput sequencing of a chrysanthemum from an orchard in Tongxiang, Zhejiang province. Phylogenetic analysis showed that ChSV clustered with members of the subgenus Stramovirus (genus Sadwavirus).
ARCHIVES OF VIROLOGY
(2023)
Article
Plant Sciences
Li Zhang, Xiangsheng Li, Lichun Chang, Tianpeng Wang, Jianli Liang, Runmao Lin, Jian Wu, Xiaowu Wang
Summary: This study successfully increased the genetic diversity of Brassica juncea by introgressing the A genome of Brassica rapa. New B. juncea germplasm with expanded phenotypic variations was developed, and the introgression of B. rapa segments was tracked using SNP markers. The results showed that the introgression of the B. rapa genome significantly increased the genetic diversity of B. juncea.
HORTICULTURE RESEARCH
(2022)
Article
Multidisciplinary Sciences
Mohamed Awad, Xiangchao Gan
Summary: This paper introduces GALA, a computational framework for chromosome-based sequencing data separation and gap-free de novo assembly. It allows integration of different data sources and addresses the challenge of achieving gap-free chromosome-scale assemblies using current workflows for long-read platforms. The method is demonstrated through the assembly of various genomes.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Dong-ru Kang, Yi Zhu, Shuai-lei Li, Peng-hui Ai, Muhammad Ayoub Khan, Hong-xu Ding, Ying Wang, Zi-cheng Wang
Summary: This study investigates the effect of MET1 gene silencing on gene expression profile in Chrysanthemum x morifolium 'Zijingling', revealing significant changes in differentially expressed genes related to essential plant biological processes. While a sufficient number of candidate genes associated with flowering were identified, the overall number of genes with significant differences between transgenic and control lines was relatively low. This study sheds light on the transcriptional level interference of CmMET1 on chrysanthemum growth and development, providing a basis for further research on epigenetic regulation mechanisms in flower induction and development.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
Article
Plant Sciences
Hualin Nie, Moonkyo Kim, Sanghee Lee, Sohee Lim, Mi Sun Lee, Ju Hyeok Kim, Sol Ji Noh, Seong Won Park, Sang-Tae Kim, Ah-Young Shin, Yi Lee, Suk-Yoon Kwon
Summary: By assembling the genomes of two Korean watermelon lines with unique fruit characteristics, researchers identified numerous protein-coding genes and single-nucleotide polymorphisms (SNPs). Through further analysis, they constructed a high-density genetic linkage map and discovered 15 quantitative trait loci (QTLs) associated with watermelon fruit quality traits. Investigation of the mapping intervals revealed 33 candidate genes with coding sequence variants, including a phytoene synthase gene that potentially regulates flesh color changes at the protein level.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Wenyi Chen, Sai Reddy Achakkagari, Martina Stromvik
Summary: This study developed an automated pipeline for the assembly and annotation of plastomes, allowing researchers to load whole genome sequence data with minimal manual input and achieve faster runtime.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Natascha van Lieshout, Martijn van Kaauwen, Linda Kodde, Paul Arens, Marinus J. M. Smulders, Richard G. F. Visser, Richard Finkers
Summary: This study presents the most complete and contiguous chrysanthemum de novo assembly published so far, providing an important step forward in understanding the chrysanthemum genome, evolution, and history.
G3-GENES GENOMES GENETICS
(2022)
Article
Evolutionary Biology
Maria de la Paz Celorio-Mancera, Pasi Rastas, Rachel A. Steward, Soren Nylin, Christopher W. Wheat
Summary: The study assembled and annotated a high-quality genome of the comma butterfly, providing an important resource for investigating coevolutionary dynamics and comparative analyses in Lepidoptera.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Qiuling Zhang, Junzhuo Li, Xiaohui Wen, Chengyan Deng, Xiuzhen Yang, Silan Dai
Summary: In this study, 101 RWP-RKs were identified in Chrysanthemum lavandulifolium, including 38 NIN-like proteins (NLPs) and 31 RWP-RK domain proteins (RKDs), as well as 32 specific expansion members. qRT-PCR results showed that certain ClNLPs were up-regulated at the floral transition stage and negatively regulated by low nitrate conditions. Under optimal nitrate conditions, the flowering time was advanced, and the expression level of certain floral integration genes and ClCRYs was up-regulated.
Article
Biochemical Research Methods
Marina Pupke Marone, Harmeet Chawla Singh, Curtis J. J. Pozniak, Martin Mascher
Summary: This article describes modifications to the TRITEX genome assembly workflow driven by the rise of fast and easy long-read contig assembly in inbred plant genomes and the routine deployment in pangenome projects. New features include the use of dense genetic maps as surrogates or complements, and the introduction of user-editable tables to facilitate the curation of contig placements.
Article
Agronomy
Kenji Fujino, Yoshihiro Kawahara, Kenta Shirasawa
Summary: Gene distributions and population genomics suggest artificial selection of ghd7 osprr37 for extremely early heading date of rice in the Tohoku region of Japan. Mutant alleles of Ghd7 and OsPRR37 appear to have allowed rice cultivation to spread into Hokkaido. Our results show that the mutations of two genes might have occurred in the process of artificial selection during early rice cultivation in the Tohoku region.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Plant Sciences
Kyoka Nagasaka, Soichiro Nishiyama, Mao Fujikawa, Hisayo Yamane, Kenta Shirasawa, Ebrahiem Babiker, Ryutaro Tao
Summary: Genome-wide association study (GWAS) was conducted on a collection of diverse Southern highbush blueberry (SHB) accessions, revealing robust genotype-phenotype association peaks related to blueberry phenological traits. The study also identified the potential introgression of low-chill and late-flowering alleles into the highbush genetic pool.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Kenta Shirasawa, Tomoya Esumi, Akihiro Itai, Sachiko Isobe
Summary: By performing time-course RNA-seq analysis, we gained insights into the genetic mechanisms underlying blooming and petal movement in flowering cherry. Through clustering analysis and Gene Ontology enrichment, we identified genes and biological processes involved in these traits.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Sachiko Kashojiya, Yu Lu, Mariko Takayama, Hiroki Komatsu, Luyen Hieu Thi Minh, Keiji Nishida, Kenta Shirasawa, Kenji Miura, Satoko Nonaka, Jun-ichiro Masuda, Akihiko Kondo, Hiroshi Ezura, Tohru Ariizumi
Summary: Target-AID is a CRISPR/Cas9-based genome-editing tool that confers base-editing capability on the Cas9 system. In this study, we successfully applied the Target-AID system to edit negative regulators of the plant hormone signaling pathway in tomatoes, demonstrating its potential for molecular breeding in tomato crops.
HORTICULTURE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Kenji Fujino, Kenta Shirasawa
Summary: This study elucidated the genetic population structure differences of rice landraces across Japan and identified two phases of differentiation, namely western to eastern and southern to northern phases. These differences may have facilitated the expansion of genetic diversity among local regions.
MOLECULAR GENETICS AND GENOMICS
(2022)
Letter
Plant Sciences
Kosuke Kuwabara, Shin-ichi Arimura, Kenta Shirasawa, Tohru Ariizumi
Article
Plant Sciences
Nozomi Obata, Hiroaki Tabuchi, Miyu Kurihara, Eiji Yamamoto, Kenta Shirasawa, Yuki Monden
Summary: This study used genome-wide association analysis to identify two genetic loci that regulate resistance to SRKN-SP2, which is the major race affecting sweetpotato production in Japan. Selective DNA markers were developed to screen for resistant plants, and the results showed a 70% probability of selecting SRKN-SP2-resistant plants when using these markers.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Kenta Shirasawa, Munetaka Hosokawa, Yasuo Yasui, Atsushi Toyoda, Sachiko Isobe
Summary: We report the genome sequence of Capsicum annuum 'Takanotsume', a popular Japanese chili pepper landrace, obtained through long-read sequencing and optical mapping. The genome assembly consists of 12 pseudomolecules, covering 97.0% of the estimated genome size, and predicts 34,324 high-confidence genes. Comparative genomics analysis reveals nucleotide sequence and genome structure variations between 'Takanotsume' and related Capsicum species. This genome sequence data will accelerate pan-genomics and breeding of Capsicum, and facilitate the study of genetic mechanisms underlying important traits of 'Takanotsume'.
Article
Agronomy
Tomohito Ikegaya, Kenta Shirasawa, Kenji Fujino
Summary: Crop breeding programs can improve traits associated with desirable phenotypic characteristics in response to local environmental conditions. This study investigates the genetic differences underlying the traits of elite rice varieties and proposes the historical evolutionary process of cultivated rice based on genome sequencing and analysis. The fine mapping of a quantitative trait locus (qDTH3) associated with heading date narrows it down to a 158-kb region, and the phenotypic differences in qDTH3 in elite varieties may be derived from a different lineage split from the ancestor.
Article
Agronomy
Akio Ohyama, Hiroshi Matsunaga, Yasushi Kawasaki, Kenta Shirasawa, Satomi Negoro, Koji Miyatake, Hirotaka Yamaguchi, Tsukasa Nunome, Hiroyoshi Iwata, Hiroyuki Fukuoka, Takeshi Hayashi
Summary: Compared to a population derived from bi-parental crosses of pure lines, a customized experimental population derived from multi-parental crosses is advantageous for detecting multiple QTL alleles. A population of recombinant inbred lines (RILs) was established from crossing two commercial elite F-1 hybrid cultivars of tomato. Using two Bayesian mapping methods, significant QTLs for agricultural traits were detected in this population. A practical approach to genomic selection was presented based on the effects of the QTL alleles estimated in this study.
Article
Horticulture
Ken Hoshikawa, Ya-Ping Lin, Roland Schafleitner, Kenta Shirasawa, Sachiko Isobe, Duc Chinh Nguyen, Ryo Ohsawa, Yosuke Yoshioka
Summary: This study analyzed the genetic diversity and population structure of 465 Amaranthus tricolor accessions held by the World Vegetable Center genebank. A total of 10,509 SNPs were found, and 5,638 SNPs without missing data were identified in 440 accessions. These findings contribute to the research and breeding of this species.
SCIENTIA HORTICULTURAE
(2023)
Article
Genetics & Heredity
Kenta Shirasawa, Ryohei Arimoto, Hideki Hirakawa, Motoyuki Ishimori, Andrea Ghelfi, Masami Miyasaka, Makoto Endo, Saneyuki Kawabata, Sachiko N. Isobe
Summary: In this study, a chromosome-scale de novo assembly of E. grandiflorum genome sequences was established using four genetic and genomic approaches. A total of 36,619 high-confidence genes were predicted, and whole-genome duplication was observed after the divergence between Gentianaceae and Rubiaceae. Genetic diversity analysis of commercial E. grandiflorum varieties was performed, and multiple variants were identified. This study provides valuable genomic resources for further genetic and genomic studies in Eustoma and the family Gentianaceae.
G3-GENES GENOMES GENETICS
(2023)
Article
Plant Sciences
Ken-ichi Kurotani, Hideki Hirakawa, Kenta Shirasawa, Yasuhiro Tanizawa, Yasukazu Nakamura, Sachiko Isobe, Michitaka Notaguchi
Summary: Nicotiana benthamiana is a widely used model plant for dicotyledonous angiosperms, but its previous reference genome was fragmented and hindered molecular genetic analysis. However, with improved genome assembly and annotation, N. benthamiana would become more accessible for research purposes.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Plant Sciences
Kenta Shirasawa, Roger Moraga, Andrea Ghelfi, Hideki Hirakawa, Hideki Nagasaki, Kioumars Ghamkhar, Brent A. Barrett, Andrew G. Griffiths, Sachiko N. Isobe
Summary: Subterranean clover (Trifolium subterraneum L., Ts) is an economically important forage legume with a compact genome. A new genome assembly TSUd_3.0 was generated using higher resolution sequence data, which improved prior genome assemblies. Molecular diversity analysis revealed copy number variant (CNV) and single-nucleotide polymorphism (SNP) among 36 cultivars. These findings provide a platform for future gene functional analysis and breeding strategies.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Takashi Akagi, Erika Varkonyi-Gasic, Kenta Shirasawa, Andrew Catanach, Isabelle M. Henry, Daniel Mertten, Paul Datson, Kanae Masuda, Naoko Fujita, Eriko Kuwada, Koichiro Ushijima, Kenji Beppu, Andrew C. Allan, Deborah Charlesworth, Ikuo Kataoka
Summary: Sex chromosome evolution is associated with sexual dimorphisms. We studied kiwifruit genomes and found recurrent sex chromosome turnovers in multiple lineages. The structural evolution of neo-Y chromosomes was driven by rapid transposable element insertions. Surprisingly, sexual dimorphisms were conserved across different species due to the pleiotropic effects of a single Y-chromosome-encoded sex-determining gene, Shy Girl.