Evolution of Buchloë dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 411-416 ◽  
Author(s):  
Hikmet Budak ◽  
Robert C Shearman ◽  
Ismail Dweikat
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Mitochondrial Genomes ◽  
Sequence Information ◽  
Specific Marker ◽  
Buchloe Dactyloides ◽  
A Genome ◽  
Organelle Genomes ◽  
History Of

Buffalograss (Buchloë dactyloides (Nutt.) Englem), a C4 turfgrass species, is native to the Great Plains region of North America. The evolutionary implications of buffalograss are unclear. Sequencing of rbcL and matK genes from plastid and the cob gene from mitochondrial genomes was examined to elucidate buffalograss evolution. This study is the first to report sequencing of these genes from organelle genomes in the genus Buchloë. Comparisons of sequence data from the mitochondrial and plastid genome revealed that all genotypes contained the same cytoplasmic origin. There were some rearrangements detected in mitochondrial genome. The buffalograss genome appears to have evolved through the rearrangements of convergent subgenomic domains. Combined analyses of plastid genes suggest that the evolutionary process in Buchloë accessions studied was monophyletic rather than polyphyletic. However, since plastid and mitochondrial genomes are generally uniparentally inherited, the evolutionary history of these genomes may not reflect the evolutionary history of the organism, especially in a species in which out-crossing is common. The sequence information obtained from this study can be used as a genome-specific marker for investigation of the buffalograss polyploidy complex and testing of the mode of plastid and mitochondrial transmission in genus Buchloë.Key words: buffalograss, evolution, organelle genomes, turfgrass.

scholarly journals A genome-skimmed phylogeny of a widespread bryozoan family, Adeonidae

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Russell J. S. Orr ◽  
Marianne N. Haugen ◽  
Björn Berning ◽  
Philip Bock ◽  
Robyn L. Cumming ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Mitochondrial Genomes ◽  
Sequence Information ◽  
A Genome ◽  
Ribosomal Operon ◽  
History Of ◽  
Genome Skimming ◽  
Phylogenetic Hypotheses ◽  
Cheilostome Bryozoans

Abstract Background Understanding the phylogenetic relationships among species is one of the main goals of systematic biology. Simultaneously, credible phylogenetic hypotheses are often the first requirement for unveiling the evolutionary history of traits and for modelling macroevolutionary processes. However, many non-model taxa have not yet been sequenced to an extent such that statistically well-supported molecular phylogenies can be constructed for these purposes. Here, we use a genome-skimming approach to extract sequence information for 15 mitochondrial and 2 ribosomal operon genes from the cheilostome bryozoan family, Adeonidae, Busk, 1884, whose current systematics is based purely on morphological traits. The members of the Adeonidae are, like all cheilostome bryozoans, benthic, colonial, marine organisms. Adeonids are also geographically widely-distributed, often locally common, and are sometimes important habitat-builders. Results We successfully genome-skimmed 35 adeonid colonies representing 6 genera (Adeona, Adeonellopsis, Bracebridgia, Adeonella, Laminopora and Cucullipora). We also contributed 16 new, circularised mitochondrial genomes to the eight previously published for cheilostome bryozoans. Using the aforementioned mitochondrial and ribosomal genes, we inferred the relationships among these 35 samples. Contrary to some previous suggestions, the Adeonidae is a robustly supported monophyletic clade. However, the genera Adeonella and Laminopora are in need of revision: Adeonella is polyphyletic and Laminopora paraphyletically forms a clade with some Adeonella species. Additionally, we assign a sequence clustering identity using cox1 barcoding region of 99% at the species and 83% at the genus level. Conclusions We provide sequence data, obtained via genome-skimming, that greatly increases the resolution of the phylogenetic relationships within the adeonids. We present a highly-supported topology based on 17 genes and substantially increase availability of circularised cheilostome mitochondrial genomes, and highlight how we can extend our pipeline to other bryozoans.

scholarly journals Deep learning predicts short non-coding RNA functions from only raw sequence data

2020 ◽  
Vol 16 (11) ◽  
pp. e1008415
Author(s):  
Teresa Maria Rosaria Noviello ◽  
Francesco Ceccarelli ◽  
Michele Ceccarelli ◽  
Luigi Cerulo
Keyword(s):  
Secondary Structure ◽  
Sequence Data ◽  
Computational Cost ◽  
Large Data ◽  
Sequence Information ◽  
Structure Information ◽  
Non Coding Rna ◽  
A Genome ◽  
Data Volume ◽  
Biological Functionality

Small non-coding RNAs (ncRNAs) are short non-coding sequences involved in gene regulation in many biological processes and diseases. The lack of a complete comprehension of their biological functionality, especially in a genome-wide scenario, has demanded new computational approaches to annotate their roles. It is widely known that secondary structure is determinant to know RNA function and machine learning based approaches have been successfully proven to predict RNA function from secondary structure information. Here we show that RNA function can be predicted with good accuracy from a lightweight representation of sequence information without the necessity of computing secondary structure features which is computationally expensive. This finding appears to go against the dogma of secondary structure being a key determinant of function in RNA. Compared to recent secondary structure based methods, the proposed solution is more robust to sequence boundary noise and reduces drastically the computational cost allowing for large data volume annotations. Scripts and datasets to reproduce the results of experiments proposed in this study are available at: https://github.com/bioinformatics-sannio/ncrna-deep.

scholarly journals Tumor evolutionary directed graphs and the history of chronic lymphocytic leukemia

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Jiguang Wang ◽  
Hossein Khiabanian ◽  
Davide Rossi ◽  
Giulia Fabbri ◽  
Valter Gattei ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Evolutionary History ◽  
Directed Graphs ◽  
Evolutionary Process ◽  
Genetic Alterations ◽  
Lymphocytic Leukemia ◽  
Cross Sectional ◽  
History Of ◽  
Evolutionary Paths ◽  
Clonal Replacement

Cancer is a clonal evolutionary process, caused by successive accumulation of genetic alterations providing milestones of tumor initiation, progression, dissemination, and/or resistance to certain therapeutic regimes. To unravel these milestones we propose a framework, tumor evolutionary directed graphs (TEDG), which is able to characterize the history of genetic alterations by integrating longitudinal and cross-sectional genomic data. We applied TEDG to a chronic lymphocytic leukemia (CLL) cohort of 70 patients spanning 12 years and show that: (a) the evolution of CLL follows a time-ordered process represented as a global flow in TEDG that proceeds from initiating events to late events; (b) there are two distinct and mutually exclusive evolutionary paths of CLL evolution; (c) higher fitness clones are present in later stages of the disease, indicating a progressive clonal replacement with more aggressive clones. Our results suggest that TEDG may constitute an effective framework to recapitulate the evolutionary history of tumors.

scholarly journals Recurrent hybridization underlies the evolution of novelty in Gentiana (Gentianaceae) in the Qinghai-Tibetan Plateau

AoB Plants ◽  
2020 ◽  
Author(s):  
Peng-Cheng Fu ◽  
Alex D Twyford ◽  
Shan-Shan Sun ◽  
Hong-Yu Wang ◽  
Ming-Ze Xia ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Source Area ◽  
Nuclear Data ◽  
Population History ◽  
Plastid Genomes ◽  
Key Factor ◽  
History Of ◽  
Postglacial Expansion

Abstract The Qinghai-Tibetan Plateau (QTP) and adjacent areas are centers of diversity for several alpine groups. Although the QTP acted as a source area for diversification of the alpine genus Gentiana, the evolutionary process underlying diversity in this genus, especially the formation of narrow endemics, is still poorly understood. Hybridization has been proposed as a driver of plant endemism in the QTP but few cases have been documented with genetic data. Here, we describe a new endemic species in Gentiana section Cruciata as G. hoae sp. nov., and explore its evolutionary history with complete plastid genomes and nuclear ribosomal ITS sequence data. Genetic divergence within G. hoae approximately 3 million years ago was followed by postglacial expansion on the QTP, suggesting Pleistocene glaciations as a key factor shaping the population history of G. hoae. Furthermore, a mismatch between plastid and nuclear data suggest that G. hoae participated in historical hybridization, while population sequencing show this species continues to hybridize with the co-occurring congener G. straminea in three locations. Our results indicate that hybridization may be a common process in the evolution of Gentiana and may be widespread among recently diverged taxa of the QTP.

scholarly journals Evolutionary History of Chimpanzees Inferred from Complete Mitochondrial Genomes

2010 ◽  
Vol 28 (1) ◽  
pp. 615-623 ◽  
Author(s):  
A. Bjork ◽  
W. Liu ◽  
J. O. Wertheim ◽  
B. H. Hahn ◽  
M. Worobey
Keyword(s):  
Evolutionary History ◽  
Mitochondrial Genomes ◽  
History Of ◽  
Complete Mitochondrial Genomes

scholarly journals Genome-scale DNA sequence data and the evolutionary history of placental mammals

Data in Brief ◽  
2018 ◽  
Vol 18 ◽  
pp. 1972-1975 ◽  
Author(s):  
Shaoyuan Wu ◽  
Scott Edwards ◽  
Liang Liu
Keyword(s):  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
History Of ◽  
Genome Scale

scholarly journals Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e16751 ◽  
Author(s):  
Adam C. Silver ◽  
David Williams ◽  
Joshua Faucher ◽  
Amy J. Horneman ◽  
J. Peter Gogarten ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Evolutionary History ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Aeromonas Veronii ◽  
Host Interaction ◽  
History Of ◽  
Complex Evolutionary History

Global distribution of the earliest shelly metazoans

1984 ◽  
Vol 121 (3) ◽  
pp. 185-188 ◽  
Author(s):  
Jiang Zhiwen
Keyword(s):  
Evolutionary History ◽  
Developmental Stages ◽  
Evolutionary Process ◽  
Global Distribution ◽  
Biological Factors ◽  
Animal Kingdom ◽  
Quantum Leap ◽  
History Of ◽  
Logical Extension

abstractThe appearance of the first abundant skeletal organisms in the earliest Cambrian was a quantum leap in the evolutionary history of life. It provided the foundations of the animal kingdom from Cambrian times onwards. This paper demonstrates that this evolutionary process resulted from a combination of environmental and biological factors. The author maintains that the appearance of the oldest shelly fossils is a reasonable criterion for defining the Precambrian–Cambrian boundary. This arises not only from the viewpoint of taking the Cambrian Period as the first period in the Palaeozoic Era, but is also a logical extension of regarding the history of life as being divisible into a series of developmental stages.

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