Genomic insights into mite phylogeny, fitness, development, and reproduction
Abstract Background Predatory mites (Acari: Phytoseiidae) are the most important beneficial arthropods used in augmentative biological pest control of protected crops around the world. However, the genomes of mites are far less well understood than those of insects and the evolutionary relationships...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-12-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-019-6281-1 |
| _version_ | 1818929222185385984 |
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| author | Yan-Xuan Zhang Xia Chen Jie-Ping Wang Zhi-Qiang Zhang Hui Wei Hai-Yan Yu Hong-Kun Zheng Yong Chen Li-Sheng Zhang Jian-Zhen Lin Li Sun Dong-Yuan Liu Juan Tang Yan Lei Xu-Ming Li Min Liu |
| author_facet | Yan-Xuan Zhang Xia Chen Jie-Ping Wang Zhi-Qiang Zhang Hui Wei Hai-Yan Yu Hong-Kun Zheng Yong Chen Li-Sheng Zhang Jian-Zhen Lin Li Sun Dong-Yuan Liu Juan Tang Yan Lei Xu-Ming Li Min Liu |
| author_sort | Yan-Xuan Zhang |
| collection | DOAJ |
| description | Abstract Background Predatory mites (Acari: Phytoseiidae) are the most important beneficial arthropods used in augmentative biological pest control of protected crops around the world. However, the genomes of mites are far less well understood than those of insects and the evolutionary relationships among mite and other chelicerate orders are contested, with the enigmatic origin of mites at one of the centres in discussion of the evolution of Arachnida. Results We here report the 173 Mb nuclear genome (from 51.75 Gb pairs of Illumina reads) of the predatory mite, Neoseiulus cucumeris, a biocontrol agent against pests such as mites and thrips worldwide. We identified nearly 20.6 Mb (~ 11.93% of this genome) of repetitive sequences and annotated 18,735 protein-coding genes (a typical gene 2888 bp in size); the total length of protein-coding genes was about 50.55 Mb (29.2% of this assembly). About 37% (6981) of the genes are unique to N. cucumeris based on comparison with other arachnid genomes. Our phylogenomic analysis supported the monophyly of Acari, therefore rejecting the biphyletic origin of mites advocated by other studies based on limited gene fragments or few taxa in recent years. Our transcriptomic analyses of different life stages of N. cucumeris provide new insights into genes involved in its development. Putative genes involved in vitellogenesis, regulation of oviposition, sex determination, development of legs, signal perception, detoxification and stress-resistance, and innate immune systems are identified. Conclusions Our genomics and developmental transcriptomics analyses of N. cucumeris provide invaluable resources for further research on the development, reproduction, and fitness of this economically important mite in particular and Arachnida in general. |
| first_indexed | 2024-12-20T03:41:22Z |
| format | Article |
| id | doaj.art-5ef175c6f3ed42c385e5f3c9f37c4074 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-20T03:41:22Z |
| publishDate | 2019-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-5ef175c6f3ed42c385e5f3c9f37c40742022-12-21T19:54:44ZengBMCBMC Genomics1471-21642019-12-0120112210.1186/s12864-019-6281-1Genomic insights into mite phylogeny, fitness, development, and reproductionYan-Xuan Zhang0Xia Chen1Jie-Ping Wang2Zhi-Qiang Zhang3Hui Wei4Hai-Yan Yu5Hong-Kun Zheng6Yong Chen7Li-Sheng Zhang8Jian-Zhen Lin9Li Sun10Dong-Yuan Liu11Juan Tang12Yan Lei13Xu-Ming Li14Min Liu15Research Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural SciencesResearch Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural SciencesAgricultural Bio-Resources Research Institute, Fujian Academy of Agricultural SciencesLandcare Research, Auckland and School of Biological Sciences, The University of AucklandResearch Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural SciencesBiomarker Technologies CorporationBiomarker Technologies CorporationResearch Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural SciencesInstitute of Plant Protection, Chinese Academy of Agricultural SciencesFujian Yanxuan Bio-preventing and Technology Biocontrol CorporationResearch Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural SciencesBiomarker Technologies CorporationBiomarker Technologies CorporationBiomarker Technologies CorporationBiomarker Technologies CorporationBiomarker Technologies CorporationAbstract Background Predatory mites (Acari: Phytoseiidae) are the most important beneficial arthropods used in augmentative biological pest control of protected crops around the world. However, the genomes of mites are far less well understood than those of insects and the evolutionary relationships among mite and other chelicerate orders are contested, with the enigmatic origin of mites at one of the centres in discussion of the evolution of Arachnida. Results We here report the 173 Mb nuclear genome (from 51.75 Gb pairs of Illumina reads) of the predatory mite, Neoseiulus cucumeris, a biocontrol agent against pests such as mites and thrips worldwide. We identified nearly 20.6 Mb (~ 11.93% of this genome) of repetitive sequences and annotated 18,735 protein-coding genes (a typical gene 2888 bp in size); the total length of protein-coding genes was about 50.55 Mb (29.2% of this assembly). About 37% (6981) of the genes are unique to N. cucumeris based on comparison with other arachnid genomes. Our phylogenomic analysis supported the monophyly of Acari, therefore rejecting the biphyletic origin of mites advocated by other studies based on limited gene fragments or few taxa in recent years. Our transcriptomic analyses of different life stages of N. cucumeris provide new insights into genes involved in its development. Putative genes involved in vitellogenesis, regulation of oviposition, sex determination, development of legs, signal perception, detoxification and stress-resistance, and innate immune systems are identified. Conclusions Our genomics and developmental transcriptomics analyses of N. cucumeris provide invaluable resources for further research on the development, reproduction, and fitness of this economically important mite in particular and Arachnida in general.https://doi.org/10.1186/s12864-019-6281-1GenomeAcariEcologyDevelopmentFeedingSex |
| spellingShingle | Yan-Xuan Zhang Xia Chen Jie-Ping Wang Zhi-Qiang Zhang Hui Wei Hai-Yan Yu Hong-Kun Zheng Yong Chen Li-Sheng Zhang Jian-Zhen Lin Li Sun Dong-Yuan Liu Juan Tang Yan Lei Xu-Ming Li Min Liu Genomic insights into mite phylogeny, fitness, development, and reproduction BMC Genomics Genome Acari Ecology Development Feeding Sex |
| title | Genomic insights into mite phylogeny, fitness, development, and reproduction |
| title_full | Genomic insights into mite phylogeny, fitness, development, and reproduction |
| title_fullStr | Genomic insights into mite phylogeny, fitness, development, and reproduction |
| title_full_unstemmed | Genomic insights into mite phylogeny, fitness, development, and reproduction |
| title_short | Genomic insights into mite phylogeny, fitness, development, and reproduction |
| title_sort | genomic insights into mite phylogeny fitness development and reproduction |
| topic | Genome Acari Ecology Development Feeding Sex |
| url | https://doi.org/10.1186/s12864-019-6281-1 |
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