scholarly journals Whole plastid genome-based phylogenomics supports an inner placement of the O. insectifera group rather than a basal position in the rapidly diversifying Ophrys genus (Orchidaceae)

2020 ◽  
Author(s):  
Joris A. M. Bertrand ◽  
Anaïs Gibert ◽  
Christel Llauro ◽  
Olivier Panaud
Keyword(s):  
Plastid Genome ◽  
Rapid Evolution ◽  
Genomic Data ◽  
Sister Group ◽  
Hybrid Assembly ◽  
Genome Sequences ◽  
Plastid Genomes ◽  
Molecular Phylogenetic ◽  
Phylogenetic Hypotheses ◽  
Basal Position

Some lineages of the Orchid genus Ophrys exhibit among the highest diversification rates reported so far. As a consequence of a such intense and rapid evolution, the systematics and the taxonomy of this genus remains unclear. A hybrid assembly approach based-on long- and short-read genomic data allowed us to outperform classical methods to successfully assemble whole plastid genomes for two new Ophrys species: O. aymoninii and O. lutea. Along with three other previously Ophrys plastid genome sequences, we then reconstructed the first whole plastome-based molecular phylogeny including representatives of the three mains recognized Ophrys lineages. Our results support the placement of the O. insectifera clade as sister group of ‘non-basal Ophrys’ rather than a basal position. Our findings corroborate recent results obtained from genomic data (RAD-seq and transcriptomes) but contrast with previous ones. These results therefore confirm that molecular phylogenetic hypotheses based on a limited number of loci (e.g. nrITS, matK, rbcL) may have provided a biased picture of phylogenetic relationships within Ophrys and possibly other plant taxa.

scholarly journals Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives

2015 ◽  
Vol 112 (33) ◽  
pp. 10200-10207 ◽  
Author(s):  
Jan Janouškovec ◽  
Denis V. Tikhonenkov ◽  
Fabien Burki ◽  
Alexis T. Howe ◽  
Martin Kolísko ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Sequence Data ◽  
Sister Group ◽  
Molecular Characteristics ◽  
Phylogenomic Analysis ◽  
Free Living ◽  
Plastid Genomes ◽  
Monophyletic Lineage ◽  
Causative Agents ◽  
Close Relatives

Apicomplexans are a major lineage of parasites, including causative agents of malaria and toxoplasmosis. How such highly adapted parasites evolved from free-living ancestors is poorly understood, particularly because they contain nonphotosynthetic plastids with which they have a complex metabolic dependency. Here, we examine the origin of apicomplexan parasitism by resolving the evolutionary distribution of several key characteristics in their closest free-living relatives, photosynthetic chromerids and predatory colpodellids. Using environmental sequence data, we describe the diversity of these apicomplexan-related lineages and select five species that represent this diversity for transcriptome sequencing. Phylogenomic analysis recovered a monophyletic lineage of chromerids and colpodellids as the sister group to apicomplexans, and a complex distribution of retention versus loss for photosynthesis, plastid genomes, and plastid organelles. Reconstructing the evolution of all plastid and cytosolic metabolic pathways related to apicomplexan plastid function revealed an ancient dependency on plastid isoprenoid biosynthesis, predating the divergence of apicomplexan and dinoflagellates. Similarly, plastid genome retention is strongly linked to the retention of two genes in the plastid genome, sufB and clpC, altogether suggesting a relatively simple model for plastid retention and loss. Lastly, we examine the broader distribution of a suite of molecular characteristics previously linked to the origins of apicomplexan parasitism and find that virtually all are present in their free-living relatives. The emergence of parasitism may not be driven by acquisition of novel components, but rather by loss and modification of the existing, conserved traits.

scholarly journals Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastid genomes

2018 ◽  
Vol 123 (5) ◽  
pp. 857-865 ◽  
Author(s):  
Jacqueline Heckenhauer ◽  
Ovidiu Paun ◽  
Mark W Chase ◽  
Peter S Ashton ◽  
A S Kamariah ◽  
...  
Keyword(s):  
Related Species ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Plastid Genome ◽  
Gc Content ◽  
Genome Sequences ◽  
Closely Related Species ◽  
Plastid Genomes ◽  
Snp Data ◽  
Phylogenomic Analyses

Abstract Background and Aims Phylogenetic relationships within tribe Shoreeae, containing the main elements of tropical forests in Southeast Asia, present a long-standing problem in the systematics of Dipterocarpaceae. Sequencing whole plastomes using next-generation sequencing- (NGS) based genome skimming is increasingly employed for investigating phylogenetic relationships of plants. Here, the usefulness of complete plastid genome sequences in resolving phylogenetic relationships within Shoreeae is evaluated. Methods A pipeline to obtain alignments of whole plastid genome sequences across individuals with different amounts of available data is presented. In total, 48 individuals, representing 37 species and four genera of the ecologically and economically important tribe Shoreeae sensu Ashton, were investigated. Phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference. Key Results Here, the first fully sequenced plastid genomes for the tribe Shoreeae are presented. Their size, GC content and gene order are comparable with those of other members of Malvales. Phylogenomic analyses demonstrate that whole plastid genomes are useful for inferring phylogenetic relationships among genera and groups of Shorea (Shoreeae) but fail to provide well-supported phylogenetic relationships among some of the most closely related species. Discordance in placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and those obtained from nuclear single nucleotide polymorphism (SNP) data sets identified in restriction-site associated sequencing (RADseq). Conclusions Phylogenomic analyses of the entire plastid genomes are useful for inferring phylogenetic relationships at lower taxonomic levels, but are not sufficient for detailed phylogenetic reconstructions of closely related species groups in Shoreeae. Discordance in placement of Parashorea was further investigated for evidence of ancient hybridization.

scholarly journals ­Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8392 ◽  
Author(s):  
Janice Valencia-D ◽  
José Murillo-A ◽  
Clara Inés Orozco ◽  
Carlos Parra-O ◽  
Kurt M. Neubig
Keyword(s):  
Plastid Genome ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Bootstrap Support ◽  
Nucleotide Substitutions ◽  
Plastid Genomes ◽  
The Family ◽  
High Bootstrap ◽  
Single Genus

Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.

Setting the Molecular Phylogenetic Framework for the Dermaptera

2003 ◽  
Vol 34 (1) ◽  
pp. 65-79 ◽  
Author(s):  
◽  
◽  
Keyword(s):  
16S Rdna ◽  
18S Rdna ◽  
Sequence Data ◽  
Indirect Evidence ◽  
Sister Group ◽  
Bootstrap Support ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework ◽  
Insect Group ◽  
Basal Position

AbstractThe insect group Dermaptera is traditionally divided into the Forficulina, comprising the majority of the species, the African rodent commensals, Hemimerina, and the Indo-Malayan bat commensals, Arixeniina. Numerous contrasting classifications and phylogenies exist for the Dermaptera, based on morphological, molecular and biogeographic data. We have collected varying number of sequences from fifteen Forficulina and six outgroups to establish a molecular hypothesis of the group's phylogeny. Despite repeated attempts, we were unable to obtain sequence data for Arixeniina and Hemimerina. We obtained partial sequences for four taxa for cytochrome oxidase 1 (with two additional taxa from GenBank), twelve for 16S rDNA, fifteen for 28S rDNA expansion region 1, seven for expansion region 9-10, and nine for 18S rDNA (plus seven sequences from GenBank). In combined analyses, the root of the Dermaptera lies between Anisolabididae and other families. This position is not directly supported by bootstrap analyses. Indirect evidence for the basal position of Anisolabididae, Pygidicranidae and Apachyidae is however found in the association of the four other studied groups (Labiduridae, Spongiphoridae, Chelisochidae and Forficulidae) in a derived clade with significant bootstrap support. The division of Forficulina into Catadermaptera and Eudermaptera is not supported as the former is paraphyletic in the present analyses. Eudermaptera is monophyletic with bootstrap support but is sister group to Labiduridae, a taxon usually assigned to the Catadermaptera.

scholarly journals Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Dong Yan ◽  
Yun Wang ◽  
Tatsuya Murakami ◽  
Yue Shen ◽  
Jianhui Gong ◽  
...  
Keyword(s):  
Green Algae ◽  
Plastid Genome ◽  
Eukaryotic Evolution ◽  
Genome Sequences ◽  
Plastid Genomes ◽  
Prototheca Wickerhamii ◽  
Close Relationship ◽  
Almost All ◽  
Auxenochlorella Protothecoides ◽  
Insight Into

Abstract The forfeiting of photosynthetic capabilities has occurred independently many times throughout eukaryotic evolution. But almost all non-photosynthetic plants and algae still retain a colorless plastid and an associated genome, which performs fundamental processes apart from photosynthesis. Unfortunately, little is known about the forces leading to photosynthetic loss; this is largely because there is a lack of data from transitional species. Here, we compare the plastid genomes of two “transitional” green algae: the photosynthetic, mixotrophic Auxenochlorella protothecoides and the non-photosynthetic, obligate heterotroph Prototheca wickerhamii. Remarkably, the plastid genome of A. protothecoides is only slightly larger than that of P. wickerhamii, making it among the smallest plastid genomes yet observed from photosynthetic green algae. Even more surprising, both algae have almost identical plastid genomic architectures and gene compositions (with the exception of genes involved in photosynthesis), implying that they are closely related. This close relationship was further supported by phylogenetic and substitution rate analyses, which suggest that the lineages giving rise to A. protothecoides and P. wickerhamii diverged from one another around six million years ago.

Inference of phylogenetic relationships among the subfamilies of grasses (Poaceae: Poales) using meso-scale exemplar-based sampling of the plastid genome

Botany ◽  
2010 ◽  
Vol 88 (1) ◽  
pp. 65-84 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Sean W. Graham
Keyword(s):  
Phylogenetic Relationships ◽  
Plastid Genome ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Bayesian Analyses ◽  
Plastid Genomes ◽  
Commelinid Monocots ◽  
Data Partitions ◽  
Intensive Sampling ◽  
Better Than

To clarify phylogenetic relationships among grass (Poaceae) subfamilies and to better resolve the placement of Poaceae in Poales, we surveyed 17 plastid genes and associated noncoding regions (∼15.5 kb per taxon, about 1/10 of the plastid genome) for exemplar representatives from 10 grass subfamilies and a broad sample of related monocots. We found general concordance in relationships and support levels among gene regions and data partitions across analyses, with some exceptions in Bayesian analyses. Different phylogenetic criteria generally agreed on backbone relationships, and the support values we inferred were generally as good as or better than those in other studies that employed more taxa for fewer genes to estimate the same backbone. Within grasses, we found robust support for the monophyly of subfamily Anomochlooideae and for the Bambusoideae–Ehrhartoideae–Pooideae (BEP) clade, and moderate support for a sister-group relationship between Bambusoideae and Pooideae. Most relationships in the strongly supported Panicoideae–Aristidoideae–Chloridoideae–Micrairoideae–Arundinoideae–Danthonioideae (PACMAD) clade were not resolved consistently, probably because the current intensive sampling of genes is still insufficient to resolve short internal branches. Our data infer a well-supported clade that includes the grass family and two small families of grass-like plants, Ecdeiocoleaceae and Joinvilleaceae, but we did not satisfactorily resolve the relationships among these three families. A generally accelerated substitution rate in Poaceae plastid genomes is shared with some, but not all, lineages that are closely related to grasses in the larger clade of commelinid monocots, which may complicate inference of the sister group of the grasses in all current studies.

Improved resolution of recalcitrant nodes in the animal phylogeny through the analysis of genome gene content and morphology

2021 ◽  
Author(s):  
Ksenia Juravel ◽  
Luis Porras ◽  
Sebastian Hoehna ◽  
Davide Pisani ◽  
Gert Wörheide
Keyword(s):  
Common Ancestor ◽  
Sister Group ◽  
The Other ◽  
Gene Content ◽  
Statistical Hypothesis ◽  
Phylogenetic Position ◽  
Last Common Ancestor ◽  
Statistical Hypothesis Testing ◽  
Animal Phylogeny ◽  
Phylogenetic Hypotheses

An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although multi-gene alignments of up to several hundred thousand amino acids are nowadays routinely used to test hypotheses of animal relationships, some nodes towards the root of the animal phylogeny are proving hard to resolve. While the relationships of the non-bilaterian lineages, primarily sponges (Porifera) and comb jellies (Ctenophora), have received much attention since more than a decade, controversies about the phylogenetic position of the worm-like bilaterian lineage Xenacoelomorpha and the monophyly of the "Superphylum" Deuterostomia have more recently emerged. Here we independently analyse novel genome gene content and morphological datasets to assess patterns of phylogenetic congruence with previous amino-acid derived phylogenetic hypotheses. Using statistical hypothesis testing, we show that both our datasets very strongly support sponges as the sister group of all the other animals, Xenoacoelomorpha as the sister group of the other Bilateria, and largely support monophyletic Deuterostomia. Based on these results, we conclude that the last common animal ancestor may have been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.

Taxonomic revision of species of Haematoloechus Looss, 1899 (Digenea: Plagiorchioidea), with molecular phylogenetic analysis and the description of three new species from Mexico

Zootaxa ◽  
2018 ◽  
Vol 4526 (3) ◽  
pp. 251 ◽  
Author(s):  
VIRGINIA LEÓN-RÈGAGNON ◽  
JANET TOPAN
Keyword(s):  
New Species ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Nomen Nudum ◽  
Phylogenetic Hypothesis ◽  
Molecular Phylogenetic ◽  
Phylogenetic Hypotheses ◽  
Three New Species ◽  
Host Parasite ◽  
Species Inquirendae

Lung flukes of the genus Haematoloechus Looss, 1899 are common parasites of anurans worldwide, but the taxonomy of the group has been confusing. In this taxonomic revision, 89 species of Haematoloechus (= Pneumonoeces Looss, 1902, Ostioloides Odening, 1960, Ostiolum Pratt, 1903, Skrjabinoeces Sudarikov, 1950, Neohaematoloechus Odening, 1960, Metahaematoloechus Yamaguti, 1971) are listed. Of these, 70 are considered valid, three are species inquirendae (H. legrandi Mañé–Garzón & Gil, 1959, H. latoricensis Kozák, 1968 & H. vitelloconfluentum (Rai, 1962) Saeed, Al–Barwari & Al-Harmni, 2007), one is a nomen nudum H. sudarikovi Belouss, 1962, 14 are junior synonyms and one belongs to Ostioloides. This publication also describes three new species, H. occidentalis n. sp., H. veracruzanus n. sp. and H. mexicanus n. sp., parasitizing species of Rana Linnaeus in Mexico and redescribes Haematoloechus caballeroi (Skrjabin & Antipin, 1962) Yamaguti, 1971. The phylogenetic hypotheses based on sequences of mitochondrial and ribosomal DNA of Haematoloechus spp. show that genera proposed on the basis of morphological characters are not supported. The host records for species of Haematoloechus, together with the phylogenetic hypothesis of the genus, suggest that this host-parasite association predates the ranid diversification in the Cretaceous. 

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