Article
Plant Sciences
Yahui Lei, Ling Yang, Shengchang Duan, Siqi Ning, Dawei Li, Zijun Wang, Guisheng Xiang, Ling Yang, Chunping Wang, Shiyu Zhang, Shuangyan Zhang, Shuang Ye, Ling Kui, Pratiksha Singh, Jun Sheng, Yang Dong
Summary: This study conducted population genomic analysis of tea populations in eight main tea-producing areas in Lincang, Yunnan through whole-genome resequencing, revealing the origin centers of Lincang tea and observing low genetic differentiation between geographical tea populations.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Xiaoyu Luo, Jianbo Li, Chentong Xiao, Luyang Sun, Weixuan Xiang, Ningbo Chen, Chuzhao Lei, Hong Lei, Yun Long, Ting Long, Quji Suolang, Kangle Yi
Summary: This study compared the genomic variations of Xiangxi cattle with other breeds and found higher genetic diversity and weaker artificial selection in Xiangxi cattle. The study also identified important genes related to reproduction, growth, meat quality, heat tolerance, and immune response in Xiangxi cattle.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Yongtan Li, Jun Zhang, Shijie Wang, Yiwen Zhang, Minsheng Yang
Summary: Chinese wild pear (Pyrus hopeiensis) is a valuable but endangered wild resource with a small population and limited distribution range. Studies show that natural hybridization and root tiller production are major modes of propagation in the wild population. Whole genome re-sequencing revealed genetic variation and evolutionary relationships within the population, with significant enrichment in certain gene pathways.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Gabriela N. Tenea
Summary: This study utilizes whole-genome resequencing to analyze the genetic variations and annotations of two native probiotic strains. The results show that these strains exhibit differences in their adaptability to stressors and antimicrobial strength. Furthermore, the analysis reveals variations in the antimicrobial gene cluster organization and genomic islands between the strains, indicating high genome variation.
Article
Zoology
Zhi-Qiang Han, Xin-Yu Guo, Qun Liu, Shan-Shan Liu, Zhi-Xin Zhang, Shi-Jun Xiao, Tian-Xiang Gao
Summary: Genetic adaptations of organisms in the northwestern Pacific to heterogeneous environments are not well understood. Population genomics analysis of Japanese whiting specimens revealed genetic divergence between Chinese and Japanese groups due to geographic distance and local adaptation, indicating possible parallel evolution. Candidate genes related to membrane fluidity were identified, potentially underlying adaptation to cold environmental stress. These findings enhance our understanding of rapid genetic adaptations and species responses to climate change.
ZOOLOGICAL RESEARCH
(2021)
Article
Biology
Xiwen Guan, Shuanping Zhao, Weixuan Xiang, Hai Jin, Ningbo Chen, Chuzhao Lei, Yutang Jia, Lei Xu
Summary: This study investigated the genetic structure, diversity, and selective sweep of the Dabieshan cattle population in order to protect the genetic resources of Chinese native cattle breeds. The results revealed that the Dabieshan cattle had ancestral contributions from Chinese indicine and East Asian taurine, with abundant genomic diversity. Candidate genes related to fertility, feed efficiency, immune response, heat resistance, fat deposition, and coat color were identified. The findings provide a foundation for breed improvement and conservation of indigenous cattle breeds.
Article
Genetics & Heredity
Qiuming Chen, Lei Xu, Menghua Zhang, Tao Zhang, Mengjie Yan, Manjun Zhai, Xixia Huang
Summary: We compared the genomes of Xinjiang Brown cattle with eight other breeds and found that Xinjiang Brown cattle have typical genomic characteristics of cross breeds, with the lowest linkage disequilibrium and highest effective population size. Xinjiang Brown cattle inherit 9.88% of their genes from Kazakh cattle and 90.12% from Swiss Brown cattle. The study also identified fixed haplotypes from Swiss Brown cattle that carry genes, pathways, and QTLs related to body measurement and growth traits.
Article
Biochemistry & Molecular Biology
Zhipeng Li, Yiqiong Chen, Yangyan Li, Ying Zeng, Wanying Li, Xiaona Ma, Lili Huang, Yanting Shen
Summary: This study performed whole-genome resequencing on seven representative patchouli accessions, and identified a large number of genetic variants. Patchouli accessions were mainly classified into the Chinese group and the Southeast Asian group, but the Chinese accession SP formed a distinct subgroup within the Southeast Asian group. Unique molecular markers in SP were screened and validated, providing a more accurate identification method for patchouli used in traditional Chinese medicine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Mengting Zhu, Yonglin Yang, Hua Yang, Zongsheng Zhao, Hongmei Zhang, Hugh T. Blair, Wei Zheng, Mingyuan Wang, Chenhui Fang, Qian Yu, Huaqian Zhou, Hangdong Qi
Summary: This study resequenced the genomes of 4 representative sheep breeds in northwest China and found that these breeds had experienced inconsistent selection intensity in the past 10,000 years, resulting in differences in reproductive traits. Genomic regions associated with different reproductive traits were detected, and several candidate genes potentially related to seasonal reproduction were identified through experimental analysis.
Article
Biochemistry & Molecular Biology
Henry L. North, Angela McGaughran, Chris D. Jiggins
Summary: The use of genomic data in invasion biology can provide valuable insights into processes such as invasion routes reconstruction and the importance of balancing selection and hybridization. While currently only a few invasive systems have utilized whole-genome resequencing, these studies have confirmed the significance of leveraging new technologies and approaches for a more comprehensive understanding of invasive species.
Article
Biology
Alexander Igoshin, Nikolay Yudin, Ruslan Aitnazarov, Andrey A. Yurchenko, Denis M. Larkin
Summary: Using whole-genome resequencing of animals showing contrasting phenotypes on temperature maintenance under acute cold stress and existing SNP functional annotations, this study identified chromosomal regions and candidate SNPs controlling body temperature in Siberian cattle populations. The research highlighted multiple candidate genes related to thermal adaptations in cattle and provided insights for cattle breeding strategies in harsh climates, including the Russian Federation.
Article
Plant Sciences
Yueya Zhang, Jin Shi, Chaoqun Shen, Vinh-Trieu To, Qi Shi, Lingzhen Ye, Jianxin Shi, Dabing Zhang, Weiwei Chen
Summary: This study utilized genome resequencing to uncover genome-wide DNA polymorphisms and develop high-density InDel markers in two barley cultivars. The findings provide valuable genetic resources for both basic and applied research in barley.
PLANT CELL REPORTS
(2022)
Article
Agriculture, Dairy & Animal Science
Wondossen Ayalew, Xiaoyun Wu, Getinet Mekuriaw Tarekegn, Tesfaye Sisay Tessema, Rakan Naboulsi, Renaud Van Damme, Erik Bongcam-Rudloff, Zewdu Edea, Solomon Enquahone, Ping Yan
Summary: This study presents the first whole-genome sequencing of Abigar cattle, revealing genes associated with heat tolerance, immune response, and stress resilience in tropical conditions. These findings are of great importance for understanding and improving the adaptive traits of Abigar cattle.
Article
Agriculture, Dairy & Animal Science
Yandong Kang, Shaoke Guo, Xingdong Wang, Mengli Cao, Jie Pei, Ruiwu Li, Pengjia Bao, Jiefeng Wang, Jiebu Lamao, Dangzhi Gongbao, Ji Lamao, Chunnian Liang, Ping Yan, Xian Guo
Summary: Kecai yaks, an important genetic resource in Gansu Province, China, were found to be an independent group within the Chinese yak population. They exhibit excellent production performance and high fecundity, making them valuable for future utilization. The genetic analysis of Kecai yaks also revealed genes associated with adaptation to alpine environments and muscle fat deposition.
Article
Agronomy
Ziqi Sun, Feiyan Qi, Hua Liu, Li Qin, Jing Xu, Lei Shi, Zhongxin Zhang, Lijuan Miao, Bingyan Huang, Wenzhao Dong, Xiao Wang, Mengdi Tian, Jingjing Feng, Ruifang Zhao, Xinyou Zhang, Zheng Zheng
Summary: High-density linkage map was constructed and QTL for oil and protein content, and fatty acid composition in peanut were identified through whole-genome resequencing. The qA05.1 locus showed significant phenotypic effect on oil, protein, and fatty acid contents. Two SNP sites in this region can be potentially utilized as markers for marker-assisted breeding of peanut cultivars with high oil content.
Article
Marine & Freshwater Biology
Yohei Shimura, Takatomo Fujisawa, Yuu Hirose, Naomi Misawa, Yu Kanesaki, Yasukazu Nakamura, Masanobu Kawachi
Summary: This study determined the complete genome sequence of the bloom-forming cyanobacterium Planktothrix agardhii, revealing similarities and differences in genomic structure with other Planktothrix strains, suggesting possible horizontal gene transfer. Additionally, gene clusters for secondary metabolites, inorganic nitrogen and phosphate uptake components, and gas vesicles were identified, contributing to a better understanding of the ecologically important genus Planktothrix.
Article
Biochemistry & Molecular Biology
Nikea J. Ulrich, Hiroko Uchida, Yu Kanesaki, Euichi Hirose, Akio Murakami, Scott R. Miller
Summary: Phenotypic plasticity through horizontal gene transfer can enhance evolutionary adaptation, promote biological diversification, and broaden ecological niches.
Article
Biochemistry & Molecular Biology
Hiroki Akizawa, Shun Saito, Nanami Kohri, Eri Furukawa, Yoshihiro Hayashi, Hanako Bai, Masashi Nagano, Yojiro Yanagawa, Hayato Tsukahara, Masashi Takahashi, Shinjiro Kagawa, Ryouka Kawahara-Miki, Hisato Kobayashi, Tomohiro Kono, Manabu Kawahara
Summary: This study dissected the molecular details of blastocyst stage in cattle using an optimized in vitro culture method, revealing dynamic expressions of key markers in TE cells over time. RNA-seq and qPCR analyses showed that TE cells highly expressed Wnt, FGF, and VEGF signaling pathways-related genes during their functional maturation.
Article
Agriculture, Dairy & Animal Science
Ryo Inaba, Ryouka Kawahara-Miki, Akihisa Shinozawa, Taichi Yasuhara, Takashi Fujii, Keisuke Koyama, Michiko Murata-Okubo, Kousaku Souma, Hiroki Hirayama
Summary: Hormonal induction of parturition in cattle increases the risk of retained fetal membrane. This study revealed the importance of interferon signaling in the immune regulation of placental tissues during parturition.
JOURNAL OF REPRODUCTION AND DEVELOPMENT
(2022)
Article
Multidisciplinary Sciences
Tappei Mishina, Hirohiko Takeshima, Mikumi Takada, Kei'ichiro Iguchi, Chunguang Zhang, Yahui Zhao, Ryouka Kawahara-Miki, Yasuyuki Hashiguchi, Ryoichi Tabata, Takeshi Sasaki, Mutsumi Nishida, Katsutoshi Watanabe
Summary: Research into the genetic diversity of triploid asexual Carassius auratus fish in Japan reveals a mixed genetic composition with alleles from both Japanese and Eurasian lineages. Interestingly, there is a unidirectional gene flow from sexual diploid relatives to sympatric triploids, contributing to the genetic similarity between the two groups. Additionally, the weaker population structure and multiple triploid lineages coexisting in Japanese rivers suggest that interploidy gene flow and increased establishment of immigrants may play a role in the successful distribution of this asexual vertebrate.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Hiroshi Takagi, Ryota Moriuchi, Yu Kanesaki, Satoshi Katsuyama, Masahiro Suzuki, Reo Mochizuki, Ken Yokozawa, Kenji Iwahara, Hideo Dohra
Summary: L. plantarum NMZ-1139, isolated from whisky mash, has a draft genome sequence with 3,117 protein-coding sequences, including genes associated with hop resistance like horA and hitA, making it suitable for sour beer production.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Biology
Yu Kanesaki, Mitsuo Ogura
Summary: The addition of glucose enhanced the expression of extra-cytoplasmic function sigma factors in Bacillus subtilis, and regulatory factors including YqfO, CshA, and YlxR were identified. Further analysis revealed YqfO functions as a global regulator in B. subtilis.
BMC RESEARCH NOTES
(2021)
Article
Multidisciplinary Sciences
Genta Okude, Minoru Moriyama, Ryouka Kawahara-Miki, Shunsuke Yajima, Takema Fukatsu, Ryo Futahashi
Summary: The functional changes and interactions of transcription factors Kr-h1, broad, and E93 are crucial in the metamorphosis of insects. These findings are significant for understanding the evolution of insect metamorphosis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Naoya Kataoka, Minenosuke Matsutani, Nami Matsumoto, Misuzu Oda, Yuki Mizumachi, Kohei Ito, Shuhei Tanaka, Yu Kanesaki, Toshiharu Yakushi, Kazunobu Matsushita
Summary: Acetic acid bacterium Komagataeibacter medellinensis NBRC 3288 was adapted to higher growth temperatures through experimental evolution, resulting in improved growth and fermentation ability. The adapted strains exhibited changes in cell morphology.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Sornsiri Pattanakittivorakul, Tatsuya Tsuzuno, Tomoyuki Kosaka, Masayuki Murata, Yu Kanesaki, Hirofumi Yoshikawa, Savitree Limtong, Mamoru Yamada
Summary: This study aims to develop multi-stress tolerant strains of Kluyveromyces marxianus through a novel evolutionary adaptation procedure called RLCGT, and to increase ethanol production at high temperatures. Four adapted strains showed increased tolerance to ethanol and other stress factors, as well as higher ethanol production at high temperatures. Possible mechanisms of stress tolerance in adapted strains were discussed based on genome and transcriptome analyses.
Article
Plant Sciences
Devi B. Effendi, Toshio Sakamoto, Shuji Ohtani, Koichiro Awai, Yu Kanesaki
Summary: Cyanobacteria strain Nostoc sp. SO-36, isolated from Antarctica, was found to be psychrotolerant and filamentous when grown at 30 degrees Celsius, with the ability to grow diazotrophically. At 10 degrees Celsius, the cells showed reduced growth, smaller size, and increased aggregation with extracellular polymeric substrates (EPSs) to protect from UV damage. The complete genome sequencing revealed the presence of one main chromosome with plasmids and conserved genes for EPS biosynthesis.
JOURNAL OF PLANT RESEARCH
(2022)
Article
Multidisciplinary Sciences
Takafumi Maruyama, Satoru Sumi, Mitsuru Kobayashi, Teppei Ebuchi, Yu Kanesaki, Hirofumi Yoshikawa, Kenji Ueda, Hideaki Takano
Summary: PmlR2 is shown to be an effector protein of PmSB-LOV. The direct association between PmSB-LOV and PmlR2 inhibits the DNA-binding activity of PmlR2, enabling transcription of light-inducible promoters.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Mari Kawaguchi, Wen-Shan Chang, Hazuki Tsuchiya, Nana Kinoshita, Akira Miyaji, Ryouka Kawahara-Miki, Kenji Tomita, Atsushi Sogabe, Makiko Yorifuji, Tomohiro Kono, Toyoji Kaneko, Shigeki Yasumasu
Summary: The seahorse is a unique teleost fish with special morphology, including bony plates and spines, and males possessing a brooding organ called the brood pouch. The flame cone cells, found in the brood pouch and spines, express a gene called pgrich which is not present in related species. This pgrich gene may have originated from the elastin gene with the involvement of transposable elements and obtained its novel function in the flame cone cells during seahorse evolution.
CELL AND TISSUE RESEARCH
(2023)
Article
Ecology
Ryo Matsuzaki, Shigekatsu Suzuki, Haruyo Yamaguchi, Masanobu Kawachi, Yu Kanesaki, Hirofumi Yoshikawa, Toshiyuki Mori, Hisayoshi Nozaki
Summary: The study suggests that the hydrophobicity of RBCS helices is roughly correlated with the presence or absence of pyrenoids within the Reticulata group, and a decrease in hydrophobicity of RBCS helices may have primarily caused pyrenoid loss during the evolution of this group. This provides novel insight into a potential mechanism determining initial evolutionary steps of gain and loss of the pyrenoid.
BMC ECOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Shinya Yoshikawa, Yu Kanesaki, Akira Uemura, Kazumasa Yamada, Maiko Okajima, Tatsuo Kaneko, Kaori Ohki
Summary: In this study, a unicellular cyanobacterium named Chroococcus sp. FPU101 was isolated, which produces a significant amount of exopolysaccharide (EPS). The research determined the growth conditions and chemical composition of EPS produced by Chroococcus sp. FPU101. Results indicated that an increase in NaCl concentration significantly boosted EPS content in the organism.
JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY
(2021)