Reconstructing Phylogenetic Relationships Based on Repeat Sequence Similarities

2019 ◽  
Author(s):  
Daniel Vitales ◽  
Sònia Garcia ◽  
Steven Dodsworth
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Similarity ◽  
Information Source ◽  
Repeat Sequence ◽  
Combined Application ◽  
Novel Approach ◽  
Genome Wide ◽  
History Of ◽  
Sequence Similarities ◽  
Phylogenetic Method

AbstractA recent phylogenetic method based on genome-wide abundance of different repeat types proved to be useful in reconstructing the evolutionary history of several plant and animal groups. Here, we demonstrate that an alternative information source from the repeatome can also be employed to infer phylogenetic relationships among taxa. Specifically, this novel approach makes use of the repeat sequence similarity matrices obtained from the comparative clustering analyses of RepeatExplorer 2, which are subsequently transformed to between-taxa distance matrices. These pairwise matrices are used to construct neighbour-joining trees for each of the top most-abundant clusters and they are finally summarized in a consensus network. This methodology was tested on three groups of angiosperms and one group of insects, resulting in congruent evolutionary hypotheses compared to more standard systematic analyses based on commonly used DNA markers. We propose that the combined application of these phylogenetic approaches based on repeat abundances and repeat sequence similarities could be helpful to understand mechanisms governing genome and repeatome evolution.

scholarly journals Early diversification and permeable species boundaries in the Mediterranean firs

2019 ◽  
Vol 125 (3) ◽  
pp. 495-507 ◽  
Author(s):  
Francisco Balao ◽  
María Teresa Lorenzo ◽  
José Manuel Sánchez-Robles ◽  
Ovidiu Paun ◽  
Juan Luis García-Castaño ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Taxonomic Status ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Early Diversification ◽  
Genome Wide ◽  
History Of ◽  
The Mediterranean ◽  
Independent Species

Abstract Background and Aims Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. Methods We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. Key Results Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene–Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. Conclusions Our phylogenomic results contribute to shed light on conifers’ diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.

scholarly journals A Novel Singleton Giant Phage Yong-XC31 Lytic to the Pyropia Pathogen Vibrio mediterranei

2021 ◽  
Vol 11 (4) ◽  
pp. 1602
Author(s):  
Lihua Xu ◽  
Dengfeng Li ◽  
Yigang Tong ◽  
Jing Fang ◽  
Rui Yang ◽  
...  
Keyword(s):  
Phage Genome ◽  
Sequence Similarity ◽  
Burst Size ◽  
Open Reading Frames ◽  
Related Phage ◽  
Genome Wide ◽  
The Family ◽  
Vibrio Phage ◽  
Sequence Similarities ◽  
Reading Frames

Vibrio mediterranei 117-T6 is extensively pathogenic to several Pyropia species, leading to the death of conchocelis. In this study, the first V. mediterranei phage (named Vibrio phage Yong-XC31, abbreviated as Yong-XC31) was isolated. Yong-XC31 is a giant phage containing an icosahedral head about 113 nm in diameter and a contractible tail about 219 nm in length. The latent period of Yong-XC31 is 30 min, and burst size is 64,227. Adsorption rate of Yong-XC31 to V. mediterranei 117-T6 can reach 93.8% in 2 min. The phage genome consisted of a linear, double-stranded 290,532 bp DNA molecule with a G + C content of 45.87%. Bioinformatic analyses predicted 318 open reading frames (ORFs), 80 of which had no similarity to protein sequences in current (26 January 2021) public databases. Yong-XC31 shared the highest pair-wise average nucleotide identity (ANI) value of 58.65% (below the ≥95% boundary to define a species) and the highest nucleotide sequence similarity of 11.71% (below the >50% boundary to define a genus) with the closest related phage. In the proteomic tree based on genome-wide sequence similarities, Yong-XC31 and three unclassified giant phages clustered in a monophyletic clade independently between the family Drexlerviridae and Herelleviridae. Results demonstrated Yong-XC31 as a new evolutionary lineage of phage. We propose a new phage family in Caudovirales order. This study provides new insights and fundamental data for the study and application of giant phages.

scholarly journals Phylogenetic Relationships, Breeding Implications, and Cultivation History of Hawaiian Taro (Colocasia Esculenta) Through Genome-Wide SNP Genotyping

2017 ◽  
Vol 109 (3) ◽  
pp. 272-282 ◽  
Author(s):  
Martin Helmkampf ◽  
Thomas K Wolfgruber ◽  
M Renee Bellinger ◽  
Roshan Paudel ◽  
Michael B Kantar ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Colocasia Esculenta ◽  
Snp Genotyping ◽  
Genome Wide ◽  
History Of ◽  
Cultivation History

scholarly journals DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II

2004 ◽  
Vol 186 (7) ◽  
pp. 2019-2027 ◽  
Author(s):  
Madhusudan Choudhary ◽  
Yun-Xin Fu ◽  
Chris Mackenzie ◽  
Samuel Kaplan
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequence ◽  
Rhodobacter Sphaeroides ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Sequence Similarity ◽  
Gene Duplications ◽  
Chromosomal Dna ◽  
History Of ◽  
Complex Genome

ABSTRACT The complex genome of Rhodobacter sphaeroides 2.4.1, composed of chromosomes I (CI) and II (CII), has been sequenced and assembled. We present data demonstrating that the R. sphaeroides genome possesses an extensive amount of exact DNA sequence duplication, 111 kb or ∼2.7% of the total chromosomal DNA. The chromosomal DNA sequence duplications were aligned to each other by using MUMmer. Frequency and size distribution analyses of the exact DNA duplications revealed that the interchromosomal duplications occurred prior to the intrachromosomal duplications. Most of the DNA sequence duplications in the R. sphaeroides genome occurred early in species history, whereas more recent sequence duplications are rarely found. To uncover the history of gene duplications in the R. sphaeroides genome, 44 gene duplications were sampled and then analyzed for DNA sequence similarity against orthologous DNA sequences. Phylogenetic analysis revealed that ∼80% of the total gene duplications examined displayed type A phylogenetic relationships; i.e., one copy of each member of a duplicate pair was more similar to its orthologue, found in a species closely related to R. sphaeroides, than to its duplicate, counterpart allele. The data reported here demonstrate that a massive level of gene duplications occurred prior to the origin of the R. sphaeroides 2.4.1 lineage. These findings lead to the conclusion that there is an ancient partnership between CI and CII of R. sphaeroides 2.4.1.

scholarly journals Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation

2018 ◽  
Vol 5 (6) ◽  
pp. 172125 ◽  
Author(s):  
Sean J. Buckley ◽  
Fabricius M. C. B. Domingos ◽  
Catherine R. M. Attard ◽  
Chris J. Brauer ◽  
Jonathan Sandoval-Castillo ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Biogeographic History ◽  
Genome Wide ◽  
Mitochondrial Data ◽  
Australian Continent ◽  
History Of ◽  
Arid Habitat ◽  
East West

Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east–west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east–west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.

scholarly journals Novel phylogeny of angiosperms inferred from whole-genome microsynteny analysis

2020 ◽  
Author(s):  
Tao Zhao ◽  
Jiayu Xue ◽  
Shu-min Kao ◽  
Zhen Li ◽  
Arthur Zwaenepoel ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Genome Structure ◽  
Flowering Plants ◽  
Novel Approach ◽  
Genome Wide ◽  
Core Eudicots ◽  
Alternative Hypotheses ◽  
Angiosperm Species ◽  
Phylogenetic Character ◽  
Relative Gene

AbstractDespite the wealth of genomic and transcriptomic data of pivotal angiosperm species, the phylogenetic relationships of flowering plants are still not fully resolved. Microsynteny, or the conservation of relative gene order, has been recognized as a valuable and alternative phylogenetic character to sequence-based characters (nucleotides or amino acids). Here, we present a novel approach for phylogenetic tree reconstruction based on genome-wide synteny network data. We generated and analyzed synteny networks from 123 species from 52 families across 31 orders of flowering plants, including several lineages for which phylogenetic relationships are ambiguous. We obtained a stable and highly resolved phylogeny that is largely congruent with sequence-based phylogenies. However, our results unveiled several novel relationships for some key clades, such as magnoliids sister to monocots, Vitales as sister to core-eudicots, and Saxifragales sister to Santalales, in turn both sister to Caryophyllales. Our results highlight that phylogenies based on genome structure and organization are complementary to sequence-based phylogenies and provide alternative hypotheses of angiosperm relationships to be further tested.

scholarly journals Variation in VKORC1 Is Associated with Vascular Dementia

2021 ◽  
Vol 80 (3) ◽  
pp. 1329-1337
Author(s):  
Jure Mur ◽  
Daniel L. McCartney ◽  
Daniel I. Chasman ◽  
Peter M. Visscher ◽  
Graciela Muniz-Terrera ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Vascular Dementia ◽  
Genetic Variant ◽  
Warfarin Dose ◽  
Uk Biobank ◽  
Parental History ◽  
Genome Wide ◽  
History Of ◽  
First Time ◽  
The Relationship

Background: The genetic variant rs9923231 (VKORC1) is associated with differences in the coagulation of blood and consequentially with sensitivity to the drug warfarin. Variation in VKORC1 has been linked in a gene-based test to dementia/Alzheimer’s disease in the parents of participants, with suggestive evidence for an association for rs9923231 (p = 1.8×10–7), which was included in the genome-wide significant KAT8 locus. Objective: Our study aimed to investigate whether the relationship between rs9923231 and dementia persists only for certain dementia sub-types, and if those taking warfarin are at greater risk. Methods: We used logistic regression and data from 238,195 participants from UK Biobank to examine the relationship between VKORC1, risk of dementia, and the interplay with warfarin use. Results: Parental history of dementia, APOE variant, atrial fibrillation, diabetes, hypertension, and hypercholesterolemia all had strong associations with vascular dementia (p < 4.6×10–6). The T-allele in rs9923231 was linked to a lower warfarin dose (βperT - allele = –0.29, p < 2×10–16) and risk of vascular dementia (OR = 1.17, p = 0.010), but not other dementia sub-types. However, the risk of vascular dementia was not affected by warfarin use in carriers of the T-allele. Conclusion: Our study reports for the first time an association between rs9923231 and vascular dementia, but further research is warranted to explore potential mechanisms and specify the relationship between rs9923231 and features of vascular dementia.

scholarly journals Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians

2021 ◽  
Vol 7 (13) ◽  
pp. eabe4414
Author(s):  
Guido Alberto Gnecchi-Ruscone ◽  
Elmira Khussainova ◽  
Nurzhibek Kahbatkyzy ◽  
Lyazzat Musralina ◽  
Maria A. Spyrou ◽  
...  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Gene Pools ◽  
Social Rules ◽  
Eurasian Steppe ◽  
Central Asian ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
First Millennium

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

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