Article
Multidisciplinary Sciences
Jisung Jang, Jaehoon Jung, Young Ho Lee, Sanghyun Lee, Myunggi Baik, Heebal Kim
Summary: This study presents the first chromosome-level genome assembly of Hanwoo, an indigenous Korean breed of Bos taurus taurus. A pangenome graph of 14 B. taurus genome assemblies was constructed. The assembly showed high-quality with a genome completeness of 95.8%, contig N50 over 55 Mb, and scaffold N50 over 89 Mb. 27,314 protein-coding genes were identified, including 2,012 unknown proteins, and the pangenome graph revealed non-reference regions and Hanwoo-specific regions.
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
Multidisciplinary Sciences
Chao Xu, Jichao Ji, Xiangzhen Zhu, Ningbo Huangfu, Hui Xue, Li Wang, Kaixin Zhang, Dongyang Li, Lin Niu, Ran Chen, Xueke Gao, Junyu Luo, Jinjie Cui
Summary: A high-quality chromosome-level genome assembly of the oriental armyworm, Mythimna separata, was successfully achieved in this study. This genome assembly provides a significant genetic resource for future studies of this insect and contributes to the development of management strategies.
Article
Biochemistry & Molecular Biology
Seth R. Smith, Eric Normandeau, Haig Djambazian, Pubudu M. Nawarathna, Pierre Berube, Andrew M. Muir, Jiannis Ragoussis, Chantelle M. Penney, Kim T. Scribner, Gordon Luikart, Chris C. Wilson, Louis Bernatchez
Summary: In this study, an annotated, chromosome-anchored genome assembly for Lake Trout was generated using various sequencing techniques, resulting in a highly contiguous assembly. Analysis revealed insights into homeologs resulting from a salmonid-specific autotetraploid event and homologous chromosomes in related taxa, providing valuable resources for future genomic research.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Destaw Worku, Gopal Gowane, Archana Verma
Summary: The aim of this study was to identify genetic variants in the promoter and 5'UTR regions of the LAP3 gene and analyze their associations with milk production traits and clinical mastitis in Sahiwal and Karan Fries cattle. Eleven SNPs were identified within the LAP3 gene region, including seven promoter variants and four 5'UTR variants. The results showed that certain SNPs were significantly associated with milk production traits, and the H1H3 diplotype was linked to higher lactation performance and lower susceptibility to clinical mastitis. These findings suggest that variations in the LAP3 gene promoter could be used as a genetic marker for improving mastitis resistance and milk yield traits in dairy cattle.
Article
Engineering, Marine
Haiyu Gao, Hui Kang, Yaolei Zhang, Jiahao Wang, Wenzhi Lin, Peijun Zhang, Mingli Lin, Mingming Liu, Guangyi Fan, Songhai Li
Summary: This article describes the genome assembly and comparative genomics analysis of the rough-toothed dolphin. The chromosome-level genome assembly and gene sets showed high completeness, and several positively selected genes specific to the species were identified. The research also estimated the demographic dynamics of the dolphin, finding that the population was influenced by climate. This study has important implications for future evolutionary research and the conservation of the species.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Hai-Jian Huang, Yu-Xuan Ye, Zhuang-Xin Ye, Xiao-Tian Yan, Xin Wang, Zhong-Yan Wei, Jian-Ping Chen, Jun-Min Li, Zong-Tao Sun, Chuan-Xi Zhang
Summary: The study reports the genome of the bean bug, Riptortus pedestris, revealing its XO sex chromosome system with the shortest chromosome being the X chromosome. A total of 19,026 protein-coding genes were predicted, with 18,745 genes validated as being expressed. Temporospatial expression analysis showed a large number of genes mainly expressed in gonads and egg periods.
MOLECULAR ECOLOGY RESOURCES
(2021)
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
Horticulture
Tianfa Guo, Qianqian Qiu, Fenfen Yan, Zhongtang Wang, Jingkai Bao, Zhi Yang, Yilei Xia, Jiurui Wang, Cuiyun Wu, Mengjun Liu
Summary: Jujube is an important fruit tree in drought-affected regions, and fruit size is a crucial agronomic trait. This study aimed to construct a high-density genetic map of jujube and identify quantitative trait loci (QTLs) related to fruit size. Through whole-genome resequencing and genetic analysis, 15 QTLs and 113 candidate genes related to fruit size were identified. This research provides valuable information for marker-assisted breeding of jujube and future manipulation of fruit size and shape.
Article
Biochemistry & Molecular Biology
Amanda Souza Camara, Veit Schubert, Martin Mascher, Andreas Houben
Summary: The organization of holocentromeres differs between species, with centromeres aggregating to form line-like structures when chromosomes are condensed into loops, and groove-like structures when a kinetochore complex is simulated along the centromeric line. The interaction between centromeric nucleosomes and structural maintenance of chromosomes (SMC) proteins plays a key role in this process.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Yu-Xuan Ye, Hou-Hong Zhang, Dan-Ting Li, Ji-Chong Zhuo, Yan Shen, Qing-Ling Hu, Chuan-Xi Zhang
Summary: Research has successfully identified and characterized the first Y chromosome in a heterometabolous insect, leading to insights into sex determination, fertility, and chromosome evolution.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Plant Sciences
Fei Li, Zhenyun Han, Weihua Qiao, Junrui Wang, Yue Song, Yongxia Cui, Jiaqi Li, Jinyue Ge, Danjing Lou, Weiya Fan, Danting Li, Baoxuan Nong, Zongqiong Zhang, Yunlian Cheng, Lifang Zhang, Xiaoming Zheng, Qingwen Yang
Summary: The study identified genes associated with important agronomic traits through genome sequencing of weedy rice germplasms, providing insights for overcoming the bottleneck in rice breeding. Additionally, a high-quality genome assembly and genetic map were generated, offering valuable resources for the analysis of genome evolution and identification of key genes for further rice breeding.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biology
Benjamin Istace, Caroline Belser, Cyril Falentin, Karine Labadie, Franz Boideau, Gwenaelle Deniot, Loeiz Maillet, Corinne Cruaud, Laurie Bertrand, Anne-Marie Chevre, Patrick Wincker, Mathieu Rousseau-Gueutin, Jean-Marc Aury
Summary: Reconstructing plant genomes is a challenging task due to their complexities, but advancements in sequencing techniques, including long-read sequencers and long-range technologies, have made chromosome-scale assemblies more feasible at a laboratory scale. This study showcases advanced techniques for reconstructing the genome of Brassica rapa cv. Z1 and emphasizes the importance of selecting the most suitable technology for optimal results.
Article
Plant Sciences
Heling Jiang, Xiaoni Zhang, Luhong Leng, Desheng Gong, Xiaohui Zhang, Junyang Liu, Dan Peng, Zhiqiang Wu, Yingxue Yang
Summary: In this study, the haplotype-resolved genome of D. caryophyllus 'Aili' was assembled for the first time at the chromosome level. The lengths of the two assembled haplotypes were determined, and structural variations between the haplotypes were identified. Phylogenetic analysis revealed the species differentiation time between carnation and gypsophila to be approximately 54.43 million years ago. This assembled and annotated genome will facilitate molecular biology studies and contribute to genome-level evolutionary research.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Xianxin Zhao, Hongxing Xu, Kang He, Zhenmin Shi, Xi Chen, Xinhai Ye, Yang Mei, Yajun Yang, Meizhen Li, Libin Gao, Le Xu, Huamei Xiao, Ying Liu, Zhongxian Lu, Fei Li
Summary: The genome of the rice leaffolder was sequenced and assembled successfully, providing a high-quality resource for further research in insect migration, chromosome evolution, and pest control. The genome assembly revealed insights into repeat sequences, expanded gene families associated with hormone biosynthesis, and high chromosomal synteny with other lepidopteran insects. Specifically, the identification of a near-intact W chromosome with enriched metabolic pathways is a significant finding with potential implications for understanding the species.
MOLECULAR ECOLOGY RESOURCES
(2021)