Chromosome-Level Genome Assembly of the Heptageniid Mayfly Parafronurus youi (Ephemeroptera), and Its Annotation

被引:0
作者
Li, Ran [1 ]
Wang, Ze-Kai [1 ]
Liu, Dong-Kai [1 ]
Zhang, Ying-Xue [1 ]
Li, Xiao-Yu [1 ]
Li, Hai-Xin [1 ]
机构
[1] Qufu Normal Univ, Sch Life Sci, Qufu 273165, Peoples R China
基金
中国国家自然科学基金; 中国博士后科学基金;
关键词
Ephemeroptera; Parafronurus youi; genome assembly; gene annotation; mayfly; ALIGNMENT; PROVIDES; SYSTEM;
D O I
10.1093/gbe/evaf027
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
As a group of winged insects (Pterygota) retaining many primitive characteristics, genomic research on mayflies remains highly limited, posing challenges to the study of their origin and evolution. In this study, we present the first chromosome-level genome assembly of the Chinese endemic mayfly Parafronurus youi utilizing Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. The high-quality genome is 412.90 Mb in size with 99.07% of the sequences anchored to 11 chromosomes (ranging from 24.88 to 45.89 Mb). Genome annotation predicted 15,647 protein-coding genes with an average length of 9,934.7 bp, of which 85.9% were functionally annotated in the UniProtKB database. Repetitive elements accounted for 32.83% of the genome, including 27.33% transposable elements and 4.07% simple repeats. This study not only enriches genomic resources for mayflies but also establishes a foundation for investigating molecular mechanisms underlying ecological adaptation and evolutionary traits, contributing to the conservation of freshwater ecosystems.
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页数:10
相关论文
共 42 条
[1]  
Ares M., 2010, Cold Spring Harbor protocols, V2010, ppdb.prot5439, DOI [DOI 10.1101/PDB.PROT5439, 10.1101/pdb.prot5439]
[2]   Repbase Update, a database of repetitive elements in eukaryotic genomes [J].
Bao, Weidong ;
Kojima, Kenji K. ;
Kohany, Oleksiy .
MOBILE DNA, 2015, 6
[3]  
Bauernfeind E., 2012, The mayflies of Europe (Ephemeroptera)
[4]   GeneMark-EP plus : eukaryotic gene prediction with self-training in the space of genes and proteins [J].
Bruna, Tomas ;
Lomsadze, Alexandre ;
Borodovsky, Mark .
NAR GENOMICS AND BIOINFORMATICS, 2020, 2 (02)
[5]   Fast and sensitive protein alignment using DIAMOND [J].
Buchfink, Benjamin ;
Xie, Chao ;
Huson, Daniel H. .
NATURE METHODS, 2015, 12 (01) :59-60
[6]  
Bushnell B., 2014, BBMap sownload
[7]  
Chan PP, 2019, METHODS MOL BIOL, V1962, P1, DOI 10.1007/978-1-4939-9173-0_1
[8]   Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom [J].
Durand, Neva C. ;
Robinson, James T. ;
Shamim, Muhammad S. ;
Machol, Ido ;
Mesirov, Jill P. ;
Lander, Eric S. ;
Aiden, Erez Lieberman .
CELL SYSTEMS, 2016, 3 (01) :99-101
[9]   Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments [J].
Durand, Neva C. ;
Shamim, Muhammad S. ;
Machol, Ido ;
Rao, Suhas S. P. ;
Huntley, Miriam H. ;
Lander, Eric S. ;
Aiden, Erez Lieberman .
CELL SYSTEMS, 2016, 3 (01) :95-98
[10]   Distribution patterns of Ephemeroptera, Plecoptera, and Trichoptera (EPT) species in the northwestern Rif: environmental and climate change impacts [J].
El Yaagoubi, Sara ;
Errochdi, Sanae ;
Edegbene, Augustine Ovie ;
Kassout, Jalal ;
Harrak, Rihab ;
El Alami, Majida .
HYDROBIOLOGIA, 2025, 852 (06) :1575-1593