Cargando…

Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Raiyemo, Damilola A., Tranel, Patrick J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10164334/
https://www.ncbi.nlm.nih.gov/pubmed/37149567
http://dx.doi.org/10.1186/s12862-023-02121-1
_version_ 1785038047995232256
author Raiyemo, Damilola A.
Tranel, Patrick J.
author_facet Raiyemo, Damilola A.
Tranel, Patrick J.
author_sort Raiyemo, Damilola A.
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-023-02121-1.
format Online
Article
Text
id pubmed-10164334
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-101643342023-05-08 Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s. Raiyemo, Damilola A. Tranel, Patrick J. BMC Ecol Evol Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-023-02121-1. BioMed Central 2023-05-06 /pmc/articles/PMC10164334/ /pubmed/37149567 http://dx.doi.org/10.1186/s12862-023-02121-1 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Raiyemo, Damilola A.
Tranel, Patrick J.
Comparative analysis of dioecious Amaranthus plastomes and phylogenomic implications within Amaranthaceae s.s.
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 Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10164334/
https://www.ncbi.nlm.nih.gov/pubmed/37149567
http://dx.doi.org/10.1186/s12862-023-02121-1
work_keys_str_mv AT raiyemodamilolaa comparativeanalysisofdioeciousamaranthusplastomesandphylogenomicimplicationswithinamaranthaceaess
AT tranelpatrickj comparativeanalysisofdioeciousamaranthusplastomesandphylogenomicimplicationswithinamaranthaceaess