DNA Sequence Matrix Research Articles

Aligned DNA sequence matrix for phylogenetic analyses in the article "A new glassfrog species of the genus Centrolene (Amphibia, Anura, Centrolenidae) from Cordillera del Cóndor, southern Ecuador"

Aligned DNA sequence matrix for phylogenetic analyses in the article "A new glassfrog species of the genus Centrolene (Amphibia, Anura, Centrolenidae) from Cordillera del Cóndor, southern Ecuador"

Reappraisal of Immotthia in Dictyosporiaceae, Pleosporales: Introducing Immotthia bambusae sp. nov. and Pseudocyclothyriella clematidis comb. et gen. nov. Based on Morphology and Phylogeny.

Immotthia is a poorly known genus, and currently, no DNA sequence data are available to ascertain its proper phylogenetic placement and evolutionary relationships with other bitunicate fungi. To date, there are only two species accepted in the genus. During our ongoing research study of bambusicolous fungi in southwest China and Thailand, a fungus associated with stromata of Hypoxylon sp. was found on dead bamboo culms in Loei Province, Thailand. Preliminary morphological identification revealed that the fungal collection belongs to Immotthia. A novel species, Immotthia bambusae, is introduced herein based on a comparison of morphological characteristics with the type specimen of I. hypoxylon (≡ Amphisphaeria hypoxylon Ellis and Everh.), a synonym of I. atrograna (Cooke and Ellis) M. E. Barr. Phylogenetic analyses of a concatenated ITS, LSU, SSU, and TEF1-α DNA sequence matrix showed that Immotthia belongs to Dictyosporiaceae, Pleosporales. Despite I. bambusae strains constituting a supported subclade, they are nested with the genus Pseudocoleophoma. Pseudocoleophoma clematidis is morphologically different from all other Pseudocoleophoma species, while its conidial characteristics are similar to Cyclothyriella. Multigene phylogenetic analyses showed that P. clematidis formed a clade basal to Immotthia, separated from Pseudocoleophoma with strong statistical support. Therefore, we introduce a monotypic genus, Pseudocyclothyriella Phukhams. and Phookamsak, gen. nov. to accommodate the single species, Pseudocyclothyriella clematidis (Phukhams. and K. D. Hyde) Phukhams. and Phookamsak, comb. nov. Detailed descriptions, color micrographs, and phylogenetic trees to show the placement of the new taxa are provided. In addition, an updated taxonomic treatment of the genera Immotthia and Pseudocyclothyriella is also provided based on the study of the type materials and phylogeny generated from DNA sequence data.

Medical Image Protection Algorithm Based on Deoxyribonucleic Acid Chain of Dynamic Length

Current image encryption algorithms have various deficiencies in effectively protecting medical images with large storage capacity and high pixel correlation. This article proposed a new image protection algorithm based on the deoxyribonucleic acid chain of dynamic length, which achieved image encryption by DNA dynamic coding, generation of DNA dynamic chain, and dynamic operation of row chain and column chain. First, the original image is encoded dynamically according to the binary bit from a pixel, and the DNA sequence matrix is scrambled. Second, DNA sequence matrices are dynamically segmented into DNA chains of different lengths. After that, row and column deletion operation and transposition operation of DNA dynamic chain are carried out, respectively, which made DNA chain matrix double shuffle. Finally, the encrypted image is got after recombining DNA chains of different lengths. The proposed algorithm was tested on a list of medical images. Results showed that the proposed algorithm showed excellent security performance, and it is immune to noise attack, occlusion attack, and all common cryptographic attacks.

Rapid diversification rates in Amazonian Chrysobalanaceae inferred from plastid genome phylogenetics

AbstractWe studied the evolutionary history of Chrysobalanaceae with phylogenetic analyses of complete plastid genomes from 156 species to assess the tempo of diversification in the Neotropics and help to unravel the causes of Amazonian plant diversification. These plastid genomes had a mean length of 162 204 base pairs, and the nearly complete DNA sequence matrix, with reliable fossils, was used to estimate a phylogenetic tree. Chrysobalanaceae diversified from 38.9 Mya (95% highest posterior density, 95% HPD: 34.2–43.9 Mya). A single clade containing almost all Neotropical species arose after a single dispersal event from the Palaeotropics into the Amazonian biome c. 29.1 Mya (95% HPD: 25.5–32.6 Mya), with subsequent dispersals into other Neotropical biomes. All Neotropical genera diversified from 10 to 14 Mya, lending clear support to the role of Andean orogeny as a major cause of diversification in Chrysobalanaceae. In particular, the understory genus Hirtella diversified extremely rapidly, producing > 100 species in the last 6 Myr (95% HPD: 4.9–7.4 Myr). Our study suggests that a large fraction of the Amazonian tree flora has been assembled in situ in the last 15 Myr.

Two new species of Amphisphaeria (Amphisphaeriaceae) from northern Thailand

Amphisphaeria flava and A. thailandica sp. nov. collected from dead woody branches in northern Thailand, are described and illustrated in this study. Both taxa share ascomata with a brown outer peridium and 1-septate brown ascospores in uniseriate asci. Amphisphaeria flava is characterized by a pale yellow host surface around the ostiole, a comparatively thin peridium and multi-guttulate mature ascospores. Amphisphaeria thailandica is characterized by subglobose to oval ascospores. Maximum parsimony, maximum likelihood and Bayesian inference analyses of a combined LSU and ITS DNA sequence matrix shows that A. flava and A. thailandica are distinct from other Amphisphaeria species (with molecular data available) in family Amphisphaeriaceae. A key to accepted Amphisphaeria species is provided.

Index-based permutation-diffusion in multiple-image encryption using DNA sequence

To improve the encryption quality and increase the speed of transmission over the internet, this study aims to provide a fast secure multiple-image encryption (MIE) algorithm based on DNA sequence and image matrix indexes. Because multiple images are considered in the proposed MIE algorithm, one big concern refers to the speed of the algorithm. In the first phase of the proposed method, multiple plain- images are attached together to create a single image. Next, this image is converted to one-dimension array. Half of the array indexes are used to permute all the pixels position. During the permutation, the same indexes are associated with DNA sequence to diffuse the pixels gray level. Simulation results demonstrate that using half of indexes for permutation and diffusion make the proposed algorithm very fast and also using DNA sequence encoding gives the algorithm enough power to resist against common attacks in the era of image encryption.

A new color image encryption algorithm based on DNA and spatial chaotic map

In this paper, a color image encryption algorithm based on DNA encoding combined with logistic map and spatial map is proposed. Firstly, the algorithm carries out scrambling by logistic map for R, G, B channels. Then, XOR is operated between channels pixel and sequence matrix controlled by spatial map. After that, realizes the addition of R, G, B by DNA addition after DNA encoding and carries out complement operation by using the DNA sequence matrix controlled by spatial map. What is more, R G B channel images are got after DNA decoding. Finally, gets the encrypted R, G, B images by reconstructing R, G, B components. The results of several experimental, statistical analysis and key sensitivity tests show that the proposed image encryption algorithm provides an efficient and secure way for real-time image encryption and transmission.

An image encryption scheme combining chaos with cycle operation for DNA sequences

An image encryption scheme is proposed using high-dimensional chaotic systems and cycle operation for DNA sequences. In the scheme, the pixels of the original image are encoded randomly with the DNA coding rule controlled by a key stream produced from Chen’s hyper-chaos. In addition to confusion on the DNA sequence matrix with Lorenz system, a cycle operation for DNA sequences is projected to diffuse the pixel values of the image. In order to enhance the diffusion effect, a bitwise exclusive-OR operation is carried out for the decoded matrices with a binary key stream, and then the cipher-image is obtained. Simulation results demonstrate that the proposed image encryption scheme with acceptable robustness is secure against exhaustive attack, statistical attack and differential attack.

CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data

The analysis of next-generation sequence (NGS) data is often a fragmented step-wise process. For example, multiple pieces of software are typically needed to map NGS reads, extract variant sites, and construct a DNA sequence matrix containing only single nucleotide polymorphisms (i.e., a SNP matrix) for a set of individuals. The management and chaining of these software pieces and their outputs can often be a cumbersome and diffi cult task. Here, we present CFSAN SNP Pipeline, which combines into a single package the mapping of NGS reads to a reference genome with Bowtie2, processing of those mapping (BAM) files using SAMtools, identification of variant sites using VarScan, and production of a SNP matrix using custom Python scripts. We also introduce a Python package (CFSAN SNP Mutator) that when given a reference genome will generate variants of known position against which we validate our pipeline. We created 1,000 simulated Salmonella enterica sp. enterica Serovar Agona genomes at 100× and 20× coverage, each containing 500 SNPs, 20 single-base insertions and 20 single-base deletions. For the 100× dataset, the CFSAN SNP Pipeline recovered 98.9% of the introduced SNPs and had a false positive rate of 1.04 × 10 −6 ; for the 20× dataset 98.8% of SNPs were recovered and the false positive rate was 8.34 × 10 −7 . Based on these results, CFSAN SNP Pipeline is a robust and accurate tool that it is among the first to combine into a single executable the myriad steps required to produce a SNP matrix from NGS data. Such a tool is useful to those working in an applied setting (e.g., food safety traceback investigations) as well as for those interested in evolutionary questions.

A novel image fusion encryption algorithm based on DNA sequence operation and hyper-chaotic system

A new image fusion encryption algorithm based on image fusion and DNA sequence operation and hyper-chaotic system is presented. Firstly, two DNA sequences matrices are obtained by encoding the original image and the key image. Secondly, using the chaotic sequences generated by Chen's hyper-chaotic maps to scramble the locations of elements from the DNA sequence matrix which generated form original image. Thirdly, XOR the scrambled DNA matrix and the random DNA matrix by using DNA sequence addition operation. At last, decoding the DNA sequence matrix, we will get the encrypted image. The simulation experimental results and security analysis show that our algorithm not only has good encryption effect, but also has the ability of resisting exhaustive attack and statistical attack.

Design a New Image Encryption using Fuzzy Integral Permutation with Coupled Chaotic Maps

This article introduces a novel image encryption algorithm based on DNA addition combining and coupled two-dimensional piecewise nonlinear chaotic map. This algorithm consists of two parts. In the first part of the algorithm, a DNA sequence matrix is obtained by encoding each color component, and is divided into some equal blocks and then the generated sequence of Sugeno integral fuzzy and the DNA sequence addition operation is used to add these blocks. Next, the DNA sequence matrix from the previous step is decoded and the complement operation to the result of the added matrix is performed by using Sugeno fuzzy integral. In the second part of the algorithm, the three modified color components are encrypted in a coupling fashion in such a way to strengthen the cryptosystem security. It is observed that the histogram, the correlation and avalanche criterion, can satisfy security and performance requirements (Avalanche criterion > 0.49916283). The experimental results obtained for the CVG-UGR image databases reveal the fact that the proposed algorithm is suitable for practical use to protect the security of digital image information over the Internet. .

A Novel Image Encryption Approach using an Index based Chaos and DNA Encoding and its Performance Analysis

Chaotic based image permutation and DNA encoding methods are used extensively in the area of the image encryption. This paper presents a hybrid approach of chaos and DNA encoding methods for image encryption. Chaos sequence is used for permutation and DNA Encoding is used for the diffusion process. Index based chaotic sequence is generated using 1D logistic map for permutation; and DNA sequence matrix is obtained by encoding the permuted image and index based chaotic sequence using DNA encoding rule. The DNA matrices are added using DNA addition operation to generate a new matrix. The generated matrix is decoded using DNA decoding rule and encrypted the image is produced. The proposed approach has two unique characteristics: (i) the way integer sequence is generated from the real valued chaotic logistic sequence; and (ii) the formation of the encoded DNA key matrix. The simulation results indicate that the proposed algorithm is highly secure, is resistant to statistical attacks, and has a larger key space.

A RGB image encryption algorithm based on DNA encoding and chaos map

In this paper, a RGB image encryption algorithm based on DNA encoding combined with chaotic map is proposed aiming at characteristics of RGB image. The algorithm firstly carries out DNA encoding for R, G, B components of RGB image; then realizes the addition of R, G, B by DNA addition and carries out complement operation by using the DNA sequence matrix controlled by Logistic; three gray images are got after decoding; finally gets the encrypted RGB images by reconstructing R, G, B components which use image pixels disturbed by Logistic chaotic sequence. Simulation result shows that the proposed algorithm has a large secret key space and strong secret key sensitivity. Meanwhile, it can resist exhaustive attack, statistical attack, and thus it is suitable for RGB image encryption.

Phylogenomic analyses and improved resolution of Cetartiodactyla

The remarkable antiquity, diversity, and significance in the ecology and evolution of Cetartiodactyla have inspired numerous attempts to resolve their phylogenetic relationships. However, previous analyses based on limited samples of nuclear genes or mitochondrial DNA sequences have generated results that were either inconsistent with one another, weakly supported, or highly sensitive to analytical conditions. Here, we present strongly supported results based upon over 1.4 Mb of an aligned DNA sequence matrix from 110 single-copy nuclear protein-coding genes of 21 Cetartiodactyla species, which represent major Cetartiodactyla lineages, and three species of Perissodactyla and Carnivora as outgroups. Phylogenetic analysis of this newly developed genomic sequence data using a codon-based model and recently developed models of the rate autocorrelation resolved the phylogenetic relationships of the major cetartiodactylan lineages and of those lineages with a high degree of confidence. Cetacea was found to nest within Artiodactyla as the sister group of Hippopotamidae, and Tylopoda was corroborated as the sole base clade of Cetartiodactyla. Within Cetacea, the monophyletic status of Odontoceti relative to Mysticeti, the basal position of Physeteroidea in Odontoceti, the non-monophyly of the river dolphins, and the sister relationship between Delphinidae and Monodontidae + Phocoenidae were strongly supported. In particular, the groups of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins) were validated as unnatural groups. Additionally, a very narrow time frame of ∼3 My (million years) was found for the rapid diversification of delphinids in the late Miocene, which made it difficult to resolve the phylogenetic relationships within the Delphinidae, especially for previous studies with limited data sets. The present study provides a statistically well-supported phylogenetic framework of Cetartiodactyla, which represents an important step toward ending some of the often-heated, century-long debate on their evolution.

Image encryption using DNA addition combining with chaotic maps

A new image encryption scheme based on DNA sequence addition operation and chaos is presented. First, a DNA sequence matrix is obtained by encoding the original image, then, divide the DNA sequence matrix into some equal blocks and use the DNA sequence addition operation to add these blocks. Next, perform the DNA sequence complement operation to the result of the added matrix by using two Logistic maps. Finally, decode the DNA sequence matrix from the third step, and we can get the encrypted image. The simulation experimental results and security analysis show that our scheme not only can achieve good encryption, but can also resist exhaustive attack, statistical attack and differential attack.

Phylogenetic Analysis of DNA C-values provides Evidence for a Small Ancestral Genome Size in Flowering Plants

DNA C-value is a highly variable aspect of plant biodiversity whose origin and significance has often attracted general interest. Evaluation of the phylogenetic component of genome size variation is essential for a full explanation of its evolutionary significance but was previously prevented by insufficient data and lack of phylogenetic consensus. However, the recent development for the angiosperms of a DNA C-values database for 2802 species and a robust phylogenetic tree based on a three-gene DNA sequence matrix and 252 non-molecular characters allows meaningful new investigations of genome size in a phylogenetic context. Superimposing data from the former onto the latter shows that whereas all 15 higher order groups for which data are available contain species with small C-values, very large C-values occur in only two distantly related groups. At the lower taxonomic levels within these two groups similar trends were detected, with very large C-values restricted to species in the more derived families. The most parsimonious explanation for these observations is that ancestral angiosperms almost certainly had small genomes, and the possession of very large genomes represents a derived condition that has arisen independently at least twice. In contrast, gymnosperms (sister group to the angiosperms) are characterized by larger C-values than angiosperms. Thus within extant seed plants the possession of a small genome is a character unique to the angiosperms that was not only present in the ancestral species but has also been retained in most living taxa.