scholarly journals Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers

Animals ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 148
Author(s):  
Watcharaporn Thapana ◽  
Nattakan Ariyaraphong ◽  
Parinya Wongtienchai ◽  
Nararat Laopichienpong ◽  
Worapong Singchat ◽  
...  
Keyword(s):  
Evolutionary Process ◽  
Mitochondrial Genomes ◽  
Sequence Analyses ◽  
Evolutionary Patterns ◽  
Evolutionary Pattern ◽  
Independent Evolution ◽  
Substitution Saturation ◽  
Varanus Salvator ◽  
Monitor Lizards ◽  
Control Regions

Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.

scholarly journals Maternal Inheritance of U’s Triangle and Evolutionary Process of Brassica Mitochondrial Genomes

2020 ◽  
Vol 11 ◽  
Author(s):  
Jia-Yu Xue ◽  
Yue Wang ◽  
Min Chen ◽  
Shanshan Dong ◽  
Zhu-Qing Shao ◽  
...  
Keyword(s):  
Maternal Inheritance ◽  
Evolutionary Process ◽  
Mitochondrial Genomes

scholarly journals Compositional diversity and evolutionary pattern of coronavirus accessory proteins

2020 ◽  
Author(s):  
Jingzhe Shang ◽  
Na Han ◽  
Ziyi Chen ◽  
Yousong Peng ◽  
Liang Li ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Regulatory Sequence ◽  
Accessory Proteins ◽  
Evolutionary Analysis ◽  
Evolutionary Patterns ◽  
Reading Frame ◽  
Evolutionary Pattern ◽  
Host Interaction ◽  
Sequence Recognition ◽  
Compositional Diversity

Abstract Accessory proteins play important roles in the interaction between coronaviruses and their hosts. Accordingly, a comprehensive study of the compositional diversity and evolutionary patterns of accessory proteins is critical to understanding the host adaptation and epidemic variation of coronaviruses. Here, we developed a standardized genome annotation tool for coronavirus (CoroAnnoter) by combining open reading frame prediction, transcription regulatory sequence recognition and homologous alignment. Using CoroAnnoter, we annotated 39 representative coronavirus strains to form a compositional profile for all of the accessary proteins. Large variations were observed in the number of accessory proteins of 1–10 for different coronaviruses, with SARS-CoV-2 and SARS-CoV having the most (9 and 10, respectively). The variation between SARS-CoV and SARS-CoV-2 accessory proteins could be traced back to related coronaviruses in other hosts. The genomic distribution of accessory proteins had significant intra-genus conservation and inter-genus diversity and could be grouped into 1, 4, 2 and 1 types for alpha-, beta-, gamma-, and delta-coronaviruses, respectively. Evolutionary analysis suggested that accessory proteins are more conservative locating before the N-terminal of proteins E and M (E-M), while they are more diverse after these proteins. Furthermore, comparison of virus-host interaction networks of SARS-CoV-2 and SARS-CoV accessory proteins showed that they share multiple antiviral signaling pathways, those involved in the apoptotic process, viral life cycle and response to oxidative stress. In summary, our study provides a tool for coronavirus genome annotation and builds a comprehensive profile for coronavirus accessory proteins covering their composition, classification, evolutionary pattern and host interaction.

scholarly journals Origins and Evolutionary Patterns of the 1.688 Satellite DNA Family in Drosophila Phylogeny

2020 ◽  
Vol 10 (11) ◽  
pp. 4129-4146
Author(s):  
Leonardo G. de Lima ◽  
Stacey L. Hanlon ◽  
Jennifer L. Gerton
Keyword(s):  
Repetitive Sequences ◽  
Specific Pattern ◽  
Evolutionary Patterns ◽  
Satellite Dnas ◽  
Evolutionary Pattern ◽  
Functional Roles ◽  
Drosophila Phylogeny ◽  
Species Specific ◽  
Future Work ◽  
Eukaryotic Genomes

Satellite DNAs (satDNAs) are a ubiquitous feature of eukaryotic genomes and are usually the major components of constitutive heterochromatin. The 1.688 satDNA, also known as the 359 bp satellite, is one of the most abundant repetitive sequences in Drosophila melanogaster and has been linked to several different biological functions. We investigated the presence and evolution of the 1.688 satDNA in 16 Drosophila genomes. We find that the 1.688 satDNA family is much more ancient than previously appreciated, being shared among part of the melanogaster group that diverged from a common ancestor ∼27 Mya. We found that the 1.688 satDNA family has two major subfamilies spread throughout Drosophila phylogeny (∼360 bp and ∼190 bp). Phylogenetic analysis of ∼10,000 repeats extracted from 14 of the species revealed that the 1.688 satDNA family is present within heterochromatin and euchromatin. A high number of euchromatic repeats are gene proximal, suggesting the potential for local gene regulation. Notably, heterochromatic copies display concerted evolution and a species-specific pattern, whereas euchromatic repeats display a more typical evolutionary pattern, suggesting that chromatin domains may influence the evolution of these sequences. Overall, our data indicate the 1.688 satDNA as the most perduring satDNA family described in Drosophila phylogeny to date. Our study provides a strong foundation for future work on the functional roles of 1.688 satDNA across many Drosophila species.

scholarly journals Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Zelda du Toit ◽  
Morné du Plessis ◽  
Desiré L. Dalton ◽  
Raymond Jansen ◽  
J. Paul Grobler ◽  
...  
Keyword(s):  
Mitochondrial Genomes ◽  
Evolutionary Patterns ◽  
The Family

scholarly journals The Evolutionary Landscape of Pan-Cancer Drives Clinical Aggression

2018 ◽  
Author(s):  
Shichao Pang ◽  
Leilei Wu ◽  
Xin Shen ◽  
Yidi Sun ◽  
Jingfang Wang ◽  
...  
Keyword(s):  
Evolutionary Process ◽  
Protein Interaction Networks ◽  
Cancer Evolution ◽  
Evolutionary Patterns ◽  
Protein Protein Interaction ◽  
Differentially Expressed Protein ◽  
Cancer Types ◽  
Protein Protein Interaction Networks ◽  
The Difference ◽  
Pan Cancer

AbstractAlthough cancer mechanisms differ from occurrence and development, some of them have similar oncogenesis, which leads to similar clinical phenotypes. Most existing genotyping studies look at “omics” data, but intentionally or unintentionally avoided that cancer is a time-dependent evolutionary process, biologically represented by the time evolution of tumor clones. We used the Bayesian mutation landscape approach to reconstruct the evolutionary process of cancer by acquiring somatic mutation data consisting of 21 cancer types. Four representative evolution patterns of pan-cancer have been discovered: trees, chaos, biconvex, and Cambrian, and a strong correlation between these four evolutionary patterns and clinical aggressivity. We further explained the characteristics of the corresponding biological systems in the evolution of pan cancer by analyzing the function of differentially expressed protein-protein interaction networks. Our results explained the difference in clinical aggressivity between cancer evolution patterns from the evolution of tumor clones and exposed the functional mechanism behind.

scholarly journals Anatomy of the Male Reproductive Organ of Water Monitor Lizard, Varanus salvator bivittatus (Reptil: Varanidae)

2019 ◽  
Author(s):  
mahfud
Keyword(s):  
Reproductive Organs ◽  
Reproductive Organ ◽  
Male Reproductive Organ ◽  
Monitor Lizard ◽  
Varanus Salvator ◽  
Biological Aspects ◽  
Male Reproductive Organs ◽  
Monitor Lizards ◽  
Almost All ◽  
Asian Water

One of the majority species of Varanidae is Varanus salvator or which commonly known as water monitor lizards (water monitor) or Asian water monitor lizard. This species is the most widely spread out of the all varanids. In Indonesia, V. salvator are distributed in almost all islands, from Sumatra, Java, Sulawesi, Maluku and Flores. Subspecies V. s. bivittatus was found only in Java, Bali and South East Islands [1]. The information on reproductive biological aspects of the V. s. bivittatus, especially the male reproductive organs is limited. Therefore, the study was aim to explore the male reproductive organs system of V. s. bivittatus that focused on macroscopic evaluation. Two adult male lizards with 45.60 cm SVL from Bogor area were used in this study. The lizard were anesthetized and exanguinated to sacrifice and fixed in 4 % paraformaldehyde through perfusion then followed by visceral observation and morphometric carefully measurement. All the observation finding and collected data were analyzed descriptively and presented in the form of tables and figures. Morphometric data were tabulated in the form of the average (mean) ± standard deviation (SD). Male reproductive organs of the V. s. bivittatus were generally similar to other reptiles such as snakes and lizards, with characteristics a pair of hemipenes. Epididymis was not formed of head, body and radix segment. The deferent duct is a small, straight and short duct which connected the epididymis to cloaca.

scholarly journals Dietary Correlates of Oral and Gut Microbiota in the Water Monitor Lizard, Varanus salvator (Laurenti, 1768)

2022 ◽  
Vol 12 ◽  
Author(s):  
Yu Du ◽  
Jun-Qiong Chen ◽  
Qian Liu ◽  
Jian-Chao Fu ◽  
Chi-Xian Lin ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Water Environment ◽  
Alpha Diversity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Monitor Lizard ◽  
Varanus Salvator ◽  
In The Wild ◽  
Monitor Lizards

Numerous studies have demonstrated that food shapes the structure and composition of the host’s oral and gut microbiota. The disorder of oral and gut microbiota may trigger various host diseases. Here, we collected oral and gut samples from wild water monitor lizards (Varanus salvator) and their captive conspecifics fed with bullfrogs, eggs, and depilated chicken, aiming to examine dietary correlates of oral and gut microbiota. We used the 16S rRNA gene sequencing technology to analyze the composition of the microbiota. Proteobacteria and Bacteroidota were the dominant phyla in the oral microbiota, and so were in the gut microbiota. The alpha diversity of microbiota was significantly higher in the gut than in the oral cavity, and the alpha diversity of oral microbiota was higher in captive lizards than in wild conspecifics. Comparing the relative abundance of oral and gut bacteria and their gene functions, differences among different animal groups presumably resulted from human contact in artificial breeding environments and complex food processing. Differences in gene function might be related to the absolute number and/or the taxonomic abundance of oral and gut microorganisms in the wild and the water environment. This study provides not only basic information about the oral and gut microbiota of captive and wild water monitor lizards, but also an inference that feeding on frogs and aquatic products and reducing human exposure help water monitor lizards maintain a microbiota similar to that in the wild environment.

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 Repeated sequence homogenization between the control and pseudo-control regions in the mitochondrial genomes of the subfamily Aquilinae

2009 ◽  
Vol 312B (3) ◽  
pp. 171-185 ◽  
Author(s):  
Luis Cadahía ◽  
Wilhelm Pinsker ◽  
Juan José Negro ◽  
Mihaela Pavlicev ◽  
Vicente Urios ◽  
...  
Keyword(s):  
Repeated Sequence ◽  
Mitochondrial Genomes ◽  
Control Regions
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