Article
Biotechnology & Applied Microbiology
Zhiyong Chen, Yancen He, Yasir Iqbal, Yanlan Shi, Hongmei Huang, Zili Yi
Summary: In this study, high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) was used to identify informative single nucleotide polymorphisms (SNPs) in Miscanthus germplasms, and to rapidly characterize the genetic relationships within this genus. The results of this study will support the development of breeding programs focused on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.
Article
Biochemistry & Molecular Biology
Bharat Ravi Iyengar, Andreas Wagner
Summary: Chaperones, proteins that assist in protein folding, have been found to not only buffer the effects of deleterious mutations and increase genetic diversity in evolving proteins, but also aid in purging these mutations and enhancing fluorescence in certain cells, resulting in phenotypic heterogeneity.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Carl-Johan Rubin, Erik D. Enbody, Mariya P. Dobreva, Arhat Abzhanov, Brian W. Davis, Sangeet Lamichhaney, Mats Pettersson, Ashley T. Sendell-Price, C. Grace Sprehn, Carlos A. Valle, Karla Vasco, Ola Wallerman, B. Rosemary Grant, Peter R. Grant, Leif Andersson
Summary: Through studying Darwin's finches, it was found that ancestral haplotype blocks play a crucial role in phenotypic evolution and speciation, serving as key determinants of the unusual phenotypic diversity exhibited by these birds.
Article
Multidisciplinary Sciences
Hailong Ren, Zhenwu Wei, Bo Zhou, Xiang Chen, Qiang Gao, Zhibin Zhang
Summary: This study analyzed the genetic diversity of Medicago polymorpha and developed 52,237 high-quality single nucleotide polymorphism markers. Cluster and PCA analysis divided the M. polymorpha accessions into three distinct groups. Additionally, SSR mining analysis identified polymorphic SSR motifs, which could be valuable markers for further breeding of M. polymorpha.
Article
Environmental Sciences
Xiangyu Wang, Wenjun Wang, Dongmei Zhan, Shanshan Ge, Liuqing Tang
Summary: This study sequenced and analyzed Saccharina cultivars in China, and found that these cultivars could be categorized into two groups. The results provide a scientific basis for Saccharina breeding.
FRONTIERS IN MARINE SCIENCE
(2022)
Review
Biochemical Research Methods
Yangyang Zheng, Kunqiang Hong, Baowei Wang, Dingyu Liu, Tao Chen, Zhiwen Wang
Summary: Adaptive laboratory evolution (ALE) is a widely used tool for improving microbial phenotypes by increasing genetic diversity through mutations. The construction of high-quality mutant libraries is crucial for the success of ALE, and technologies for generating genetic diversity have rapidly developed in recent years.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Genetics & Heredity
Jie Huan, Zhoujian He, Yuting Lei, Wenjun Li, Liqiong Jiang, Xiaomei Luo
Summary: This study analyzed the genetic diversity of 16 Bletilla materials using SLAF-seq and FISH techniques. The results showed that the phylogenetic tree based on SNP data was correlated with the shape and geographical distribution of the materials. The population structure analysis revealed that materials with yellow labellum came from the same ancestor. Principal component analysis helped in determining genetic distance and provided a reference for hybrid parent selection. FISH analysis showed differences in chromosome characteristics and signals among the materials.
Article
Forestry
Yun Zhang, Kun Xin, Baowen Liao, Xihang Ai, Nong Sheng
Summary: The study collected 120 samples of Derris trifoliata from three sites in Guangdong Province, China, and developed single nucleotide polymorphic markers using specific-locus amplified fragment sequencing technology. The analysis revealed medium genetic diversity levels and high clonal diversity in the populations, indicating the importance of sexual propagation in their succession. Additionally, an association analysis showed that nitrogen played a positive role in the formation and maintenance of the populations.
Article
Plant Sciences
Yanwei Li, Yumeng Huo, Yanyan Yang, Zhenbao Wang, Yaling Sun, Bingjiang Liu, Xiong Wu
Summary: In this study, a high-resolution genetic map of onion was constructed using SLAF-seq technology, which contained 10,584 polymorphic SLAFs and 21,250 SNP markers. Four QTLs related to flower stalk height were detected, providing insights into the genetic mechanisms in onion breeding.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Yuan-Yuan Xu, Sheng-Rui Liu, Zhi-Meng Gan, Ren-Fang Zeng, Jin-Zhi Zhang, Chun-Gen Hu
Summary: This study constructed a high-density genetic linkage map for citrus using SSR and SNP markers and identified loci associated with leaf abscission trait, providing valuable information for QTL mapping and genomic studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Chunxiang Li, Minxuan Liu, Fengjie Sun, Xinyu Zhao, Mingyue He, Tianshu Li, Ping Lu, Yue Xu
Summary: Broomcorn millet is one of the earliest domesticated crops in the world, with weedy broomcorn millet thought to be the descendant of the wild ancestor or feral type. Genetic diversity and population structure of weedy and cultivated broomcorn millets were investigated using high-throughput sequencing technology, revealing both wild and feral genotypes in weedy broomcorn millets and the genetic divergence between broomcorn millets from different regions.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Fisheries
Longwu Geng, Minghui Meng, Shuqun Xue, Xiaonan Lv, Ming Zou, Haifeng Jiang, Guangxiang Tong, Yu Yang, Ying Han
Summary: In this study, a linkage map of the Aral barbel was constructed using specific locus amplified fragment sequencing (SLAF-seq) and 72 QTL regions associated with breeding-related traits were predicted.
AQUACULTURE REPORTS
(2022)
Article
Forestry
Yu Wang, Zhongyi Jiao, Jiwei Zheng, Jie Zhou, Baosong Wang, Qiang Zhuge, Xudong He
Summary: The study analyzed the genetic diversity and population structure of Chosenia arbutifolia, finding moderate diversity and significant population differentiation. Molecular variance analysis revealed the genetic background of the species. Landscape genomics analysis identified genetic loci associated with environmental factors, providing insights for conservation and management strategies.
Article
Plant Sciences
Dawei Wang, Lin Yang, Chen Shi, Siguang Li, Hongyan Tang, Chengzhong He, Nianhui Cai, Anan Duan, Hede Gong
Summary: In our study, a high-resolution genetic map of Simao pine using SLAF-seq technology was constructed for the first time. A total of 17 QTLs for four growth-related traits were identified based on this map. This provides valuable information for genomic studies and marker-assisted selection in Simao pine.
Article
Environmental Sciences
Gergely Torda, Kate M. Quigley
Summary: The unprecedented rate of environmental change in the Anthropocene poses evolutionary challenges for wild populations globally. Evolutionary models can be used to evaluate species' adaptation under future climate and the impact of human-mediated interventions on organisms' fitness trajectories.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Fisheries
Tian-Yan Yang, Tian-Xiang Gao, Wei Meng, Yan-Lin Jiang
FISHERIES RESEARCH
(2020)
Article
Fisheries
Tianyan Yang, Yuan Zhang, Wei Meng, Xin Zhong, Yang Shan, Tianxiang Gao
Summary: This study used RNA sequencing to reveal gene expression differences in L. lota lota fish at different temperatures, finding more temperature-responsive genes in the high-temperature groups. HSP70 was identified as an effective biomarker for high-temperature challenges, while the upregulation of FAD could regulate fatty acid composition. Elevated temperature had a significant impact on the immune function of L. lota lota, potentially upregulating immune-related pathways.
AQUACULTURE REPORTS
(2021)
Article
Genetics & Heredity
Shilpi Saha, Na Song, Mohammad Abdul Baki, Tianyan Yang, Tianxiang Gao
Summary: The complete mitochondrial genome of Sillaginopsis panijus was determined for the first time, showing its separation from the genus Sillago in phylogenetic analysis. This supports its taxonomic position based on morphology and will aid in evolutionary analysis.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Tianyan Yang, Zijun Ning, Yuping Liu, Shufei Zhang, Tianxiang Gao
Summary: The study investigated the genomic characteristics and phylogenetic relationships of the snake eel species Ophichthus evermanni through genome survey sequencing analysis. The results revealed the genetic diversity and provided a theoretical basis for further genetic research on snake eels.
BIOSCIENCE REPORTS
(2022)
Article
Environmental Sciences
Tianyan Yang, Xingyu Liu, Zhiqiang Han
Summary: This study used an ensemble model to predict the potential suitable habitat of Japanese Spanish mackerel in different seasons. The results showed a high accuracy of the model. The suitable habitats are expected to significantly decrease in the future, especially under the RCP8.5 scenario. Temperature and depth were identified as the key factors affecting the distribution of this species.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Yuan Zhang, Fangrui Lou, Jianwei Chen, Zhiqiang Han, Tianyan Yang, Tianxiang Gao, Na Song
Summary: This study utilized PacBio isoform sequencing to generate the full-length transcriptome data of S. sinica, revealing a large number of non-redundant transcripts and novel isoforms. This comprehensive transcriptome analysis provides valuable insights for understanding gene function and regulatory mechanisms in S. sinica.
MARINE BIOTECHNOLOGY
(2022)
Article
Oceanography
Yang Tianyan, Huang Xinxin, Jiang Yanlin
Summary: This study used genotyping-by-sequencing technique to reveal the genome-wide genetic characteristics of H. nehereus populations in coastal areas of China. The results showed excess heterozygosity in H. nehereus populations and genetic variation originated within individuals. Water temperature might be the key element affecting the genetic structure of H. nehereus.
JOURNAL OF OCEAN UNIVERSITY OF CHINA
(2022)
Article
Oceanography
Xinxin Huang, Zijun Ning, Tianyan Yang
Summary: In this study, high-throughput sequencing was used to identify microsatellite loci in the H. nehereus transcriptome. A total of 5652 microsatellites were identified, with 26 loci showing high polymorphism and potential for population genetic diversity research of H. nehereus. However, the transferability of these primers was low, likely due to the close relation of the collected species. Future work will focus on excavating simple sequence repeats using genome-based technologies and gathering related species to address the current limitations.
JOURNAL OF OCEAN UNIVERSITY OF CHINA
(2023)
Article
Agriculture, Dairy & Animal Science
Tianyan Yang, Yuping Liu, Zijun Ning
Summary: By studying the mitochondrial genomes of two Ophichthidae species, it was found that Ophichthidae might be a monophyletic group and formed a sister group with Muraenesocidae. Ophichthidae is the largest family in the order Anguilliformes worldwide, with about 359 valid species. Molecular data, such as mitochondrial DNA sequences, are crucial for the correct identification and classification of Ophichthidae fishes.
Article
Biodiversity Conservation
Ziyan Zhu, Yuping Liu, Shufei Zhang, Sige Wang, Tianyan Yang
Summary: Microsatellite loci were screened and analyzed from the genomic data of Dysomma anguillare using bioinformatics for the first time. The study obtained 1160104 microsatellite loci distributed on 770294 scaffolds, with an occurrence frequency of 28.57% and a relative abundance of 743/Mb. This research provides a foundation for the future development of high-quality microsatellite markers for D. anguillare.
BIODIVERSITY DATA JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Tian-yan Yang, Zi-yan Zhu, Yu-ping Liu, Si-ge Wang
Summary: In this study, genomic characteristics and phylogenetic relationships of Dysomma anguillare were analyzed using next-generation sequencing technology. The results revealed the genome size of approximately 1,310 Mb, with a large number of microsatellite sequences that have potential for population structure and genetic diversity research. Additionally, the analysis of the mitochondrial genome confirmed the taxonomic status of D. anguillare.
BIOCHEMICAL GENETICS
(2023)
Article
Ecology
Peiyi Xiao, Yuping Liu, Tianyan Yang
Summary: The complete mitochondrial DNA sequence of Sillago sinica, a new member of Sillaginidae fishes in China, was obtained and analyzed. The gene arrangement and genetic distance among different Sillago fishes were studied. The results provide valuable information for further genetic studies on Sillaginidae.
REGIONAL STUDIES IN MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Tianyan Yang, Xinxin Huang, Zijun Ning, Tianxiang Gao
Summary: In this study, the genome of Harpadon nehereus was analyzed using next-generation sequencing, revealing a genome size of 1315 Mb, a heterozygosity of 0.67%, and a repeat sequence ratio of 52.49%. By studying the mitochondrial genome, the evolutionary relationships within the Harpadon genus were elucidated, aiding in molecular diversity and conservation genetics research.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Chenghao Jia, Tianyan Yang, Takashi Yanagimoto, Tianxiang Gao
Summary: This study conducted whole genome sequencing of Sebastiscus species, estimated genome sizes, and identified genetic relationships, providing important genomic resources for further research.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2021)