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Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity

The cosmopolitan Thalassionema species are often dominant components of the plankton diatom flora and sediment diatom assemblages in all but the Polar regions, making important ecological contribution to primary productivity. Historical studies concentrated on their indicative function for the marin...

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Autores principales: Zhang, Mengjia, Chen, Nansheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9044688/
https://www.ncbi.nlm.nih.gov/pubmed/35477350
http://dx.doi.org/10.1186/s12864-022-08532-6
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author Zhang, Mengjia
Chen, Nansheng
author_facet Zhang, Mengjia
Chen, Nansheng
author_sort Zhang, Mengjia
collection PubMed
description The cosmopolitan Thalassionema species are often dominant components of the plankton diatom flora and sediment diatom assemblages in all but the Polar regions, making important ecological contribution to primary productivity. Historical studies concentrated on their indicative function for the marine environment based primarily on morphological features and essentially ignored their genomic information, hindering in-depth investigation on Thalassionema biodiversity. In this project, we constructed the complete chloroplast genomes (cpDNAs) of seven Thalassionema strains representing three different species, which were also the first cpDNAs constructed for any species in the order Thalassionematales that includes 35 reported species and varieties. The sizes of these Thalassionema cpDNAs, which showed typical quadripartite structures, varied from 124,127 bp to 140,121 bp. Comparative analysis revealed that Thalassionema cpDNAs possess conserved gene content inter-species and intra-species, along with several gene losses and transfers. Besides, their cpDNAs also have expanded inverted repeat regions (IRs) and preserve large intergenic spacers compared to other diatom cpDNAs. In addition, substantial genome rearrangements were discovered not only among different Thalassionema species but also among strains of a same species T. frauenfeldii, suggesting much higher diversity than previous reports. In addition to confirming the phylogenetic position of Thalassionema species, this study also estimated their emergence time at approximately 38 Mya. The availability of the Thalassionema species cpDNAs not only helps understand the Thalassionema species, but also facilitates phylogenetic analysis of diatoms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08532-6.
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spelling pubmed-90446882022-04-28 Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity Zhang, Mengjia Chen, Nansheng BMC Genomics Research The cosmopolitan Thalassionema species are often dominant components of the plankton diatom flora and sediment diatom assemblages in all but the Polar regions, making important ecological contribution to primary productivity. Historical studies concentrated on their indicative function for the marine environment based primarily on morphological features and essentially ignored their genomic information, hindering in-depth investigation on Thalassionema biodiversity. In this project, we constructed the complete chloroplast genomes (cpDNAs) of seven Thalassionema strains representing three different species, which were also the first cpDNAs constructed for any species in the order Thalassionematales that includes 35 reported species and varieties. The sizes of these Thalassionema cpDNAs, which showed typical quadripartite structures, varied from 124,127 bp to 140,121 bp. Comparative analysis revealed that Thalassionema cpDNAs possess conserved gene content inter-species and intra-species, along with several gene losses and transfers. Besides, their cpDNAs also have expanded inverted repeat regions (IRs) and preserve large intergenic spacers compared to other diatom cpDNAs. In addition, substantial genome rearrangements were discovered not only among different Thalassionema species but also among strains of a same species T. frauenfeldii, suggesting much higher diversity than previous reports. In addition to confirming the phylogenetic position of Thalassionema species, this study also estimated their emergence time at approximately 38 Mya. The availability of the Thalassionema species cpDNAs not only helps understand the Thalassionema species, but also facilitates phylogenetic analysis of diatoms. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08532-6. BioMed Central 2022-04-27 /pmc/articles/PMC9044688/ /pubmed/35477350 http://dx.doi.org/10.1186/s12864-022-08532-6 Text en © The Author(s) 2022 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
Zhang, Mengjia
Chen, Nansheng
Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity
title Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity
title_full Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity
title_fullStr Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity
title_full_unstemmed Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity
title_short Comparative analysis of Thalassionema chloroplast genomes revealed hidden biodiversity
title_sort comparative analysis of thalassionema chloroplast genomes revealed hidden biodiversity
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9044688/
https://www.ncbi.nlm.nih.gov/pubmed/35477350
http://dx.doi.org/10.1186/s12864-022-08532-6
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