Publication: Evolutionary Dynamics of Plastid Genomes in the Genus Tortula (Pottiaceae, Bryophyta)
Authors
Hassannezhaddivkolaei, Hamideh
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Escuela Internacional de Doctorado
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Ros Espín, Rosa María ; Magdy Abdallah Awad, Mahmoud
Publisher
Universidad de Murcia
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DOI
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info:eu-repo/semantics/doctoralThesis
Description
Abstract
Objetivos de la tesis
Los briófitos, que incluyen musgos, hepáticas y antocerotas, desempeñan un papel fundamental en los ecosistemas terrestres al contribuir a la regulación hídrica, el reciclaje de nutrientes y la formación del suelo. Entre ellos, los musgos de la familia Pottiaceae destacan por su amplia distribución y elevada tolerancia a la desecación, especialmente en ambientes áridos y semiáridos. El género Tortula es uno de los más diversos de esta familia, sin embargo, su delimitación taxonómica ha sido objeto de controversias recurrentes, en gran medida debido a la ausencia de enfoques integrativos moleculares que permitan esclarecer con mayor precisión sus relaciones filogenéticas. Los genomas de cloroplasto (plastomas) se han consolidado como recursos de gran valor para los estudios evolutivos, gracias a su organización conservada y a la posibilidad de revelar patrones filogenómicos a distintas escalas. Sin embargo, en Pottiaceae la disponibilidad de plastomas completos es todavía limitada, lo que dificulta el uso de marcadores moleculares robustos y comparables. La presente tesis doctoral constituye el primer estudio integral de plastomas en Tortula, y tiene como objetivo principal evaluar su diversidad como fuente de información sobre la dinámica evolutiva de los briófitos, así como contribuir a la sistemática de la familia Pottiaceae.
Metodología
El estudio incluyó nueve especies del género Tortula y empleó técnicas de secuenciación de alto rendimiento (NGS), ensamblaje y anotación de los plastomas, análisis filogenético basado en plastomas completos y loci individuales hipervariables, junto con análisis bioinformáticos.
Resultados y conclusiones
Los resultados obtenidos mostraron que los plastomas de Tortula conservan una arquitectura estable y homogénea, aunque presentan variaciones entre especies que evidencian procesos de divergencia y revelan huellas evolutivas informativas sobre la historia del grupo. El análisis de microsatélites (SSRs) evidenció la presencia de patrones compartidos entre especies, así como de señales diagnósticas específicas que refuerzan su utilidad como marcadores moleculares. De manera complementaria, el estudio del uso relativo de codones (RSCU) evidenció sesgos asociados a determinados aminoácidos, lo cual sugiere la acción de presiones selectivas específicas. Uno de los aportes más relevantes de este trabajo ha sido la identificación de 11 loci hipervariables con alto potencial filogenético: atpE, cemA, chlN, matK, ndhA, ndhD-trnL, psbB, rbcL, rpoB, rpoC1 y rps7-trnV. Estos superan en resolución a los marcadores tradicionales empleados en musgos y constituyen herramientas de mayor precisión para la identificación de especies. Los análisis filogenéticos realizados confirmaron la separación clara de los dos principales grupos dentro de Tortula, apoyando la monofilia de la sección Cuneifoliae y evidenciando la no monofilia de la sección Tortula. Estos resultados subrayan la necesidad de revisar las circunscripciones históricas, a la luz de la señal molecular aportada por los plastomas. El estudio de las presiones selectivas (dN/dS) mostró que la mayoría de los genes plastidiales se encuentran bajo selección purificadora, preservando así funciones esenciales del cloroplasto. No obstante, algunos genes como cemA, ndhG, ycf1, ycf2 y ycf66 exhibieron señales de selección positiva, mientras que atpE y matK destacaron por su doble valor: capacidad resolutiva en filogenias e indicios de un papel en la evolución molecular adaptativa.
En conclusión, esta investigación proporciona un marco novedoso y necesario para comprender la dinámica evolutiva de los plastomas en Tortula (Pottiaceae). La combinación de estabilidad estructural y divergencias específicas de linaje revela un equilibrio entre conservación funcional y adaptación. Este trabajo genera un conjunto de recursos moleculares aplicables en sistemática, genética de la conservación y biología comparativa. Los loci hipervariables identificados, junto con los perfiles de microsatélites y los análisis de codones, proporcionan herramientas que permitirán no solo mejorar la identificación de especies, sino también monitorear la diversidad genética y reconocer unidades evolutivamente significativas en musgos
Thesis Objectives Bryophytes, which include mosses, liverworts, and hornworts, play a fundamental role in terrestrial ecosystems by contributing to water regulation, nutrient recycling, and soil formation. Among them, mosses of the family Pottiaceae are notable for their wide distribution and high tolerance to desiccation, particularly in arid and semi-arid environments. The genus Tortula is one of the most diverse within this family; however, its taxonomic delimitation has been subject to recurrent controversies, largely due to the lack of integrative molecular approaches that allow a more precise resolution of its phylogenetic relationships. Chloroplast genomes (plastomes) have emerged as valuable resources for evolutionary studies due to their conserved organization and their capacity to reveal phylogenomic patterns at different scales. Nevertheless, in Pottiaceae, the availability of complete plastomes remains limited, hindering the use of robust and comparable molecular markers. This doctoral thesis represents the first comprehensive study of plastomes in Tortula and primarily aims to assess their diversity as a source of information on bryophyte evolutionary dynamics, as well as to contribute to the systematics of the family Pottiaceae. Methodology The study included nine species of the genus Tortula and employed high-throughput sequencing (NGS), plastome assembly and annotation, phylogenetic analyses based on complete plastomes and hypervariable loci, along with bioinformatic analyses. Results and Conclusions The results showed that Tortula plastomes maintain a stable and homogeneous architecture, although they exhibit interspecific variations that reflect divergence processes and reveal informative evolutionary signatures about the group's history. Microsatellites (SSRs) analysis revealed both shared patterns among species and specific diagnostic signals, reinforcing their usefulness as molecular markers. Complementarily, analyses of relative synonymous codon usage (RSCU) indicated biases associated with particular amino acids, suggesting the action of specific selective pressures. One of the most significant contributions of this work was the identification of 11 hypervariable loci with high phylogenetic potential: atpE, cemA, chlN, matK, ndhA, ndhD-trnL, psbB, rbcL, rpoB, rpoC1, and rps7-trnV. These loci surpass the resolution of traditional markers used in mosses and provide more precise tools for species identification. Phylogenetic analyses confirmed the clear separation of the two main groups within Tortula, supporting the monophyly of section Cuneifoliae and demonstrating the non-monophyly of section Tortula. These findings highlight the need to revise historical circumscription in light of the molecular signal provided by plastomes. Selection pressure analyses (dN/dS) showed that most plastid genes are under purifying selection, thereby preserving essential chloroplast functions. However, some genes, including cemA, ndhG, ycf1, ycf2, and ycf66, exhibited signals of positive selection, while atpE and matK stood out for their dual role: phylogenetic resolution and potential involvement in adaptive molecular evolution. In conclusion, this research provides a novel and necessary framework for understanding plastome evolutionary dynamics in Tortula (Pottiaceae). The combination of structural stability and lineage-specific divergences reveals a balance between functional conservation and adaptation. This work generates a set of molecular resources applicable to systematics, conservation genetics, and comparative biology. The identified hypervariable loci, together with microsatellite profiles and codon usage analyses, offer tools that will not only enhance species identification but also enable monitoring of genetic diversity and recognition of evolutionarily significant units in mosses.
Thesis Objectives Bryophytes, which include mosses, liverworts, and hornworts, play a fundamental role in terrestrial ecosystems by contributing to water regulation, nutrient recycling, and soil formation. Among them, mosses of the family Pottiaceae are notable for their wide distribution and high tolerance to desiccation, particularly in arid and semi-arid environments. The genus Tortula is one of the most diverse within this family; however, its taxonomic delimitation has been subject to recurrent controversies, largely due to the lack of integrative molecular approaches that allow a more precise resolution of its phylogenetic relationships. Chloroplast genomes (plastomes) have emerged as valuable resources for evolutionary studies due to their conserved organization and their capacity to reveal phylogenomic patterns at different scales. Nevertheless, in Pottiaceae, the availability of complete plastomes remains limited, hindering the use of robust and comparable molecular markers. This doctoral thesis represents the first comprehensive study of plastomes in Tortula and primarily aims to assess their diversity as a source of information on bryophyte evolutionary dynamics, as well as to contribute to the systematics of the family Pottiaceae. Methodology The study included nine species of the genus Tortula and employed high-throughput sequencing (NGS), plastome assembly and annotation, phylogenetic analyses based on complete plastomes and hypervariable loci, along with bioinformatic analyses. Results and Conclusions The results showed that Tortula plastomes maintain a stable and homogeneous architecture, although they exhibit interspecific variations that reflect divergence processes and reveal informative evolutionary signatures about the group's history. Microsatellites (SSRs) analysis revealed both shared patterns among species and specific diagnostic signals, reinforcing their usefulness as molecular markers. Complementarily, analyses of relative synonymous codon usage (RSCU) indicated biases associated with particular amino acids, suggesting the action of specific selective pressures. One of the most significant contributions of this work was the identification of 11 hypervariable loci with high phylogenetic potential: atpE, cemA, chlN, matK, ndhA, ndhD-trnL, psbB, rbcL, rpoB, rpoC1, and rps7-trnV. These loci surpass the resolution of traditional markers used in mosses and provide more precise tools for species identification. Phylogenetic analyses confirmed the clear separation of the two main groups within Tortula, supporting the monophyly of section Cuneifoliae and demonstrating the non-monophyly of section Tortula. These findings highlight the need to revise historical circumscription in light of the molecular signal provided by plastomes. Selection pressure analyses (dN/dS) showed that most plastid genes are under purifying selection, thereby preserving essential chloroplast functions. However, some genes, including cemA, ndhG, ycf1, ycf2, and ycf66, exhibited signals of positive selection, while atpE and matK stood out for their dual role: phylogenetic resolution and potential involvement in adaptive molecular evolution. In conclusion, this research provides a novel and necessary framework for understanding plastome evolutionary dynamics in Tortula (Pottiaceae). The combination of structural stability and lineage-specific divergences reveals a balance between functional conservation and adaptation. This work generates a set of molecular resources applicable to systematics, conservation genetics, and comparative biology. The identified hypervariable loci, together with microsatellite profiles and codon usage analyses, offer tools that will not only enhance species identification but also enable monitoring of genetic diversity and recognition of evolutionarily significant units in mosses.
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