Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.
Abstract Background The genus Amaranthus L. consists of 70–80 species distributed across temperate and tropical regions of the world. Nine species are dioecious and native to North America; two of which are agronomically important weeds of row crops. The genus has been described as taxonomically cha...
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| Format: | Article |
| Language: | English |
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BMC
2023-05-01
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| Series: | BMC Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12862-023-02121-1 |
| _version_ | 1827952977852235776 |
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| author | Damilola A. Raiyemo Patrick J. Tranel |
| author_facet | Damilola A. Raiyemo Patrick J. Tranel |
| author_sort | Damilola A. Raiyemo |
| collection | DOAJ |
| description | Abstract Background The genus Amaranthus L. consists of 70–80 species distributed across temperate and tropical regions of the world. Nine species are dioecious and native to North America; two of which are agronomically important weeds of row crops. The genus has been described as taxonomically challenging and relationships among species including the dioecious ones are poorly understood. In this study, we investigated the phylogenetic relationships among the dioecious amaranths and sought to gain insights into plastid tree incongruence. A total of 19 Amaranthus species’ complete plastomes were analyzed. Among these, seven dioecious Amaranthus plastomes were newly sequenced and assembled, an additional two were assembled from previously published short reads sequences and 10 other plastomes were obtained from a public repository (GenBank). Results Comparative analysis of the dioecious Amaranthus species’ plastomes revealed sizes ranged from 150,011 to 150,735 bp and consisted of 112 unique genes (78 protein-coding genes, 30 transfer RNAs and 4 ribosomal RNAs). Maximum likelihood trees, Bayesian inference trees and splits graphs support the monophyly of subgenera Acnida (7 dioecious species) and Amaranthus; however, the relationship of A. australis and A. cannabinus to the other dioecious species in Acnida could not be established, as it appears a chloroplast capture occurred from the lineage leading to the Acnida + Amaranthus clades. Our results also revealed intraplastome conflict at some tree branches that were in some cases alleviated with the use of whole chloroplast genome alignment, indicating non-coding regions contribute valuable phylogenetic signals toward shallow relationship resolution. Furthermore, we report a very low evolutionary distance between A. palmeri and A. watsonii, indicating that these two species are more genetically related than previously reported. Conclusions Our study provides valuable plastome resources as well as a framework for further evolutionary analyses of the entire Amaranthus genus as more species are sequenced. |
| first_indexed | 2024-04-09T14:05:48Z |
| format | Article |
| id | doaj.art-bbcd4328a3fd4b46a0b9d06e771e6afc |
| institution | Directory Open Access Journal |
| issn | 2730-7182 |
| language | English |
| last_indexed | 2024-04-09T14:05:48Z |
| publishDate | 2023-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Ecology and Evolution |
| spelling | doaj.art-bbcd4328a3fd4b46a0b9d06e771e6afc2023-05-07T11:03:30ZengBMCBMC Ecology and Evolution2730-71822023-05-0123111810.1186/s12862-023-02121-1Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.Damilola A. Raiyemo0Patrick J. Tranel1Department of Crop Sciences, University of IllinoisDepartment of Crop Sciences, University of IllinoisAbstract Background The genus Amaranthus L. consists of 70–80 species distributed across temperate and tropical regions of the world. Nine species are dioecious and native to North America; two of which are agronomically important weeds of row crops. The genus has been described as taxonomically challenging and relationships among species including the dioecious ones are poorly understood. In this study, we investigated the phylogenetic relationships among the dioecious amaranths and sought to gain insights into plastid tree incongruence. A total of 19 Amaranthus species’ complete plastomes were analyzed. Among these, seven dioecious Amaranthus plastomes were newly sequenced and assembled, an additional two were assembled from previously published short reads sequences and 10 other plastomes were obtained from a public repository (GenBank). Results Comparative analysis of the dioecious Amaranthus species’ plastomes revealed sizes ranged from 150,011 to 150,735 bp and consisted of 112 unique genes (78 protein-coding genes, 30 transfer RNAs and 4 ribosomal RNAs). Maximum likelihood trees, Bayesian inference trees and splits graphs support the monophyly of subgenera Acnida (7 dioecious species) and Amaranthus; however, the relationship of A. australis and A. cannabinus to the other dioecious species in Acnida could not be established, as it appears a chloroplast capture occurred from the lineage leading to the Acnida + Amaranthus clades. Our results also revealed intraplastome conflict at some tree branches that were in some cases alleviated with the use of whole chloroplast genome alignment, indicating non-coding regions contribute valuable phylogenetic signals toward shallow relationship resolution. Furthermore, we report a very low evolutionary distance between A. palmeri and A. watsonii, indicating that these two species are more genetically related than previously reported. Conclusions Our study provides valuable plastome resources as well as a framework for further evolutionary analyses of the entire Amaranthus genus as more species are sequenced.https://doi.org/10.1186/s12862-023-02121-1Amaranthus speciesDioecious amaranthsChloroplast genomePhylogenetic analysesEvolutionary distance |
| spellingShingle | Damilola A. Raiyemo Patrick J. Tranel Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s. BMC Ecology and Evolution Amaranthus species Dioecious amaranths Chloroplast genome Phylogenetic analyses Evolutionary distance |
| title | Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s. |
| title_full | Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s. |
| title_fullStr | Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s. |
| title_full_unstemmed | Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s. |
| title_short | Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s. |
| title_sort | comparative analysis of dioecious amaranthus plastomes and phylogenomic implications within amaranthaceae s s |
| topic | Amaranthus species Dioecious amaranths Chloroplast genome Phylogenetic analyses Evolutionary distance |
| url | https://doi.org/10.1186/s12862-023-02121-1 |
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