scholarly journals Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica

2020 ◽  
Author(s):  
Yves Bawin ◽  
Tom Ruttink ◽  
Ariane Staelens ◽  
Annelies Haegeman ◽  
Piet Stoffelen ◽  
...  
Keyword(s):  
Coffea Arabica ◽  
Evolutionary Origin ◽  
Phylogenomic Analysis

scholarly journals Phylogenomic analysis clarifies the evolutionary origin of Coffea arabica L

2020 ◽  
Author(s):  
Yves Bawin ◽  
Tom Ruttink ◽  
Ariane Staelens ◽  
Annelies Haegeman ◽  
Piet Stoffelen ◽  
...  
Keyword(s):  
Coffea Arabica ◽  
Genotyping By Sequencing ◽  
Genetic Distances ◽  
Evolutionary Origin ◽  
Phylogenomic Analysis ◽  
Hybrid Species ◽  
Hybridization Event ◽  
Self Compatibility ◽  
Ancestral States ◽  
Allotetraploid Species

SummaryInterspecific hybridization events have played a major role in plant speciation, yet, the evolutionary origin of hybrid species often remains enigmatic. Here, we inferred the evolutionary origin of the allotetraploid species Coffea arabica, which is widely cultivated for Arabica coffee production.We estimated genetic distances between C. arabica and all species that are known to be closely related to C. arabica using genotyping-by-sequencing (GBS) data. In addition, we reconstructed a time-calibrated multilabeled phylogenetic tree of 24 species to infer the age of the C. arabica hybridization event. Ancestral states of self-compatibility were also reconstructed to infer the evolution of self-compatibility in Coffea.C. canephora and C. eugenioides were confirmed as the putative progenitor species of C. arabica. These species most likely hybridized between 1.08 million and 543 thousand years ago.We inferred the phylogenetic relationships between C. arabica and its closest relatives and shed new light on the evolution of self-compatibility in Coffea. Furthermore, the age of the hybridization event coincides with periods of environmental upheaval, which may have induced range shifts of the progenitor species that facilitated the emergence of C. arabica.

scholarly journals New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

2019 ◽  
Vol 36 (4) ◽  
pp. 757-765 ◽  
Author(s):  
Jürgen F H Strassert ◽  
Mahwash Jamy ◽  
Alexander P Mylnikov ◽  
Denis V Tikhonenkov ◽  
Fabien Burki
Keyword(s):  
Phylogenetic Signal ◽  
Evolutionary Origin ◽  
Phylogenetic Position ◽  
Aquatic Environments ◽  
Phylogenomic Analysis ◽  
Data Sets ◽  
Transcriptome Data ◽  
Phylogenetic Reconstructions ◽  
Phylogenomic Analyses ◽  
Alignment Length

AbstractThe resolution of the broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these “orphan” groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome data sets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker “TSAR” to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

scholarly journals Expanding magnetic organelle biogenesis in the domain Bacteria

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Wei Lin ◽  
Wensi Zhang ◽  
Greig A. Paterson ◽  
Qiyun Zhu ◽  
Xiang Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Biological Significance ◽  
Gene Clusters ◽  
Magnetic Sensors ◽  
Evolutionary Origin ◽  
Phylogenomic Analysis ◽  
Organelle Biogenesis ◽  
Taxonomic Distribution ◽  
Origin And Evolution ◽  
Bacterial Phyla

Abstract Background The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domain Bacteria are considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis. Results Here, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domain Bacteria than previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domain Bacteria. Conclusions These findings expand the taxonomic and phylogenetic diversity of MTB across the domain Bacteria and shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle.

scholarly journals New phylogenomic analysis of the enigmatic phylum Telonemia further resolves the eukaryote tree of life

2018 ◽  
Author(s):  
Jürgen F. H. Strassert ◽  
Mahwash Jamy ◽  
Alexander P. Mylnikov ◽  
Denis V. Tikhonenkov ◽  
Fabien Burki
Keyword(s):  
Phylogenetic Signal ◽  
Evolutionary Origin ◽  
Phylogenetic Position ◽  
Aquatic Environments ◽  
Phylogenomic Analysis ◽  
Heterogeneous Mixture ◽  
Phylogenetic Reconstructions ◽  
Phylogenomic Analyses ◽  
Alignment Length ◽  
Broad Scale

AbstractThe broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these ‘orphan’ groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome datasets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker ‘TSAR’ to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

scholarly journals Genomic insights into the evolutionary origin of Myxozoa within Cnidaria

2015 ◽  
Vol 112 (48) ◽  
pp. 14912-14917 ◽  
Author(s):  
E. Sally Chang ◽  
Moran Neuhof ◽  
Nimrod D. Rubinstein ◽  
Arik Diamant ◽  
Hervé Philippe ◽  
...  
Keyword(s):  
Genome Size ◽  
Cell Communication ◽  
Evolutionary Origin ◽  
Phylogenomic Analysis ◽  
Sea Anemones ◽  
Free Living ◽  
Multicellular Development ◽  
Phylogenetic Studies ◽  
Close Relationship ◽  
Polypodium Hydriforme

The Myxozoa comprise over 2,000 species of microscopic obligate parasites that use both invertebrate and vertebrate hosts as part of their life cycle. Although the evolutionary origin of myxozoans has been elusive, a close relationship with cnidarians, a group that includes corals, sea anemones, jellyfish, and hydroids, is supported by some phylogenetic studies and the observation that the distinctive myxozoan structure, the polar capsule, is remarkably similar to the stinging structures (nematocysts) in cnidarians. To gain insight into the extreme evolutionary transition from a free-living cnidarian to a microscopic endoparasite, we analyzed genomic and transcriptomic assemblies from two distantly related myxozoan species, Kudoa iwatai and Myxobolus cerebralis, and compared these to the transcriptome and genome of the less reduced cnidarian parasite, Polypodium hydriforme. A phylogenomic analysis, using for the first time to our knowledge, a taxonomic sampling that represents the breadth of myxozoan diversity, including four newly generated myxozoan assemblies, confirms that myxozoans are cnidarians and are a sister taxon to P. hydriforme. Estimations of genome size reveal that myxozoans have one of the smallest reported animal genomes. Gene enrichment analyses show depletion of expressed genes in categories related to development, cell differentiation, and cell–cell communication. In addition, a search for candidate genes indicates that myxozoans lack key elements of signaling pathways and transcriptional factors important for multicellular development. Our results suggest that the degeneration of the myxozoan body plan from a free-living cnidarian to a microscopic parasitic cnidarian was accompanied by extreme reduction in genome size and gene content.

Photosynthetic responses of Coffea arabica leaves to a short-term high light exposure in relation to N availability

1997 ◽  
Vol 101 (1) ◽  
pp. 229-239 ◽  
Author(s):  
Jose C. Ramalho ◽  
Thos L. Pons ◽  
Henri W. Groeneveld ◽  
M. Antonieta Nunes
Keyword(s):  
Coffea Arabica ◽  
Light Exposure ◽  
High Light ◽  
N Availability ◽  
Short Term ◽  
Photosynthetic Responses

SISTEMA DE PRODUCCIÓN DE CAFÉ (Coffea arabica L.) EN LA COMUNIDAD DEL CERRO CUATE, ILIATENCO, GUERRERO

2018 ◽  
Vol 11 (10) ◽  
Author(s):  
A. Delgado-Alvarado
Keyword(s):  
Coffea Arabica ◽  
El Sistema ◽  
Coffea Arabica L

Objetivo: Analizar el proceso de producción y comercialización de café en la comunidad del Cerro Cuate, Iliatenco, en la región de la Montaña de Guerrero, México.Diseño/Metodología/aproximación: el trabajo se realizó por; 1) investigación documental), 2) selección del área de estudio, 3) Entrevista estructurada con preguntas abiertas a 22 cafeticultores, soportada con la técnica de encuesta seccional y la herramienta de cédulas de entrevistas, y 4) análisis de la información. El tamaño de muestra se definió por el método de muestreo por conveniencia, y la selección de las unidades de análisis por la técnica bola de nieve. Resultados: El sistema de producción de café que predominó fue el sistema rústico de montaña, intercalado con plátano y frutales. La máxima productividad de las plantaciones se alcanza de 5.5 a 7.5años de edad, la renovación de plantas la hacen a los 12 años. El rendimiento de café fue de 3.7 kg por planta por año. La producción del café la realizan principalmente hombres (77.3%), entre 56 y 70años de edad. La venta se realiza en la presentación de café capulín a granel a intermediarios, a la ARIC, a CAFECO, a la Unión de Ejidos y a la Organización Mixtrui.Limitaciones del estudio/implicaciones: Se da una propuesta de mejora para favorecer el proceso de producción, beneficio y comercialización del café.Hallazgos/conclusiones: Coffea arabica es el principal café que se cultiva, con las variedades Typica, Caturra, Mundo Novo, Garnica y Bourbón. Los factores que limitan su producción y calidad son faltade planeación en manejo del cultivo y no contar con asesoría técnica.

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