Taxon-specific ultraconserved element probe design for phylogenetic analyses of scale insects (Hemiptera: Sternorrhyncha: Coccoidea)
Scale insects (Coccoidea) are morphologically specialized members of the order Hemiptera, with 56 families recognized to date. However, the phylogenetic relationships within and among families are poorly resolved. In this study, to further characterize the phylogenetic relationships among scale inse...
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| Format: | Article |
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Ecology and Evolution |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fevo.2022.984396/full |
| _version_ | 1811206894207893504 |
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| author | Dajun Liu Dajun Liu Minmin Niu Yunyun Lu Jiufeng Wei Hufang Zhang Hufang Zhang |
| author_facet | Dajun Liu Dajun Liu Minmin Niu Yunyun Lu Jiufeng Wei Hufang Zhang Hufang Zhang |
| author_sort | Dajun Liu |
| collection | DOAJ |
| description | Scale insects (Coccoidea) are morphologically specialized members of the order Hemiptera, with 56 families recognized to date. However, the phylogenetic relationships within and among families are poorly resolved. In this study, to further characterize the phylogenetic relationships among scale insects, an ultraconserved element (UCE) probe set was designed specifically for Coccoidea based on three low-coverage whole genome sequences along with three publicly available genomes. An in silico test including eight additional genomes was performed to evaluate the effectiveness of the probe set. Most scale insect lineages were recovered by the phylogenetic analysis. This study recovered the monophyly of neococcoids. The newly developed UCE probe set has the potential to reshape and improve our understanding of the phylogenetic relationships within and among families of scale insects at the genome level. |
| first_indexed | 2024-04-12T03:54:42Z |
| format | Article |
| id | doaj.art-0d5e5c576c9d4f3a9286acff3461e879 |
| institution | Directory Open Access Journal |
| issn | 2296-701X |
| language | English |
| last_indexed | 2024-04-12T03:54:42Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Ecology and Evolution |
| spelling | doaj.art-0d5e5c576c9d4f3a9286acff3461e8792022-12-22T03:48:51ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2022-09-011010.3389/fevo.2022.984396984396Taxon-specific ultraconserved element probe design for phylogenetic analyses of scale insects (Hemiptera: Sternorrhyncha: Coccoidea)Dajun Liu0Dajun Liu1Minmin Niu2Yunyun Lu3Jiufeng Wei4Hufang Zhang5Hufang Zhang6College of Plant Protection, Shanxi Agricultural University, Jinzhong, ChinaDepartment of Biology, Xinzhou Teachers University, Xinzhou, ChinaCollege of Plant Protection, Shanxi Agricultural University, Jinzhong, ChinaCollege of Plant Protection, Shanxi Agricultural University, Jinzhong, ChinaCollege of Plant Protection, Shanxi Agricultural University, Jinzhong, ChinaCollege of Plant Protection, Shanxi Agricultural University, Jinzhong, ChinaDepartment of Biology, Xinzhou Teachers University, Xinzhou, ChinaScale insects (Coccoidea) are morphologically specialized members of the order Hemiptera, with 56 families recognized to date. However, the phylogenetic relationships within and among families are poorly resolved. In this study, to further characterize the phylogenetic relationships among scale insects, an ultraconserved element (UCE) probe set was designed specifically for Coccoidea based on three low-coverage whole genome sequences along with three publicly available genomes. An in silico test including eight additional genomes was performed to evaluate the effectiveness of the probe set. Most scale insect lineages were recovered by the phylogenetic analysis. This study recovered the monophyly of neococcoids. The newly developed UCE probe set has the potential to reshape and improve our understanding of the phylogenetic relationships within and among families of scale insects at the genome level.https://www.frontiersin.org/articles/10.3389/fevo.2022.984396/fullCoccoideaultraconserved elementsprobe designlow-coverage whole genome sequencingphylogenomics |
| spellingShingle | Dajun Liu Dajun Liu Minmin Niu Yunyun Lu Jiufeng Wei Hufang Zhang Hufang Zhang Taxon-specific ultraconserved element probe design for phylogenetic analyses of scale insects (Hemiptera: Sternorrhyncha: Coccoidea) Frontiers in Ecology and Evolution Coccoidea ultraconserved elements probe design low-coverage whole genome sequencing phylogenomics |
| title | Taxon-specific ultraconserved element probe design for phylogenetic analyses of scale insects (Hemiptera: Sternorrhyncha: Coccoidea) |
| title_full | Taxon-specific ultraconserved element probe design for phylogenetic analyses of scale insects (Hemiptera: Sternorrhyncha: Coccoidea) |
| title_fullStr | Taxon-specific ultraconserved element probe design for phylogenetic analyses of scale insects (Hemiptera: Sternorrhyncha: Coccoidea) |
| title_full_unstemmed | Taxon-specific ultraconserved element probe design for phylogenetic analyses of scale insects (Hemiptera: Sternorrhyncha: Coccoidea) |
| title_short | Taxon-specific ultraconserved element probe design for phylogenetic analyses of scale insects (Hemiptera: Sternorrhyncha: Coccoidea) |
| title_sort | taxon specific ultraconserved element probe design for phylogenetic analyses of scale insects hemiptera sternorrhyncha coccoidea |
| topic | Coccoidea ultraconserved elements probe design low-coverage whole genome sequencing phylogenomics |
| url | https://www.frontiersin.org/articles/10.3389/fevo.2022.984396/full |
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