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Author: Bashar Al-Nuaimi
Publisher:
ISBN:
Category :
Languages : en
Pages : 144
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Book Description
The theory of evolution is based on modern biology. All new species emerge of an existing species. As a result, different species share common ancestry,as represented in the phylogenetic classification. Common ancestry may explainthe similarities between all living organisms, such as general chemistry, cell structure,DNA as genetic material and genetic code. Individuals of one species share the same genes but (usually) different allele sequences of these genes. An individual inheritsalleles of their ancestry or their parents. The goal of phylogenetic studies is to analyzethe changes that occur in different organisms during evolution by identifying therelationships between genomic sequences and determining the ancestral sequences and theirdescendants. A phylogeny study can also estimate the time of divergence betweengroups of organisms that share a common ancestor. Phylogenetic trees are usefulin the fields of biology, such as bioinformatics, for systematic phylogeneticsand comparative. The evolutionary tree or the phylogenetic tree is a branched exposure the relationsevolutionary between various biological organisms or other existence depending on the differences andsimilarities in their genetic characteristics. Phylogenetic trees are built infrom molecular data such as DNA sequences and protein sequences. Ina phylogenetic tree, the nodes represent genomic sequences and are calledtaxonomic units. Each branch connects two adjacent nodes. Each similar sequencewill be a neighbor on the outer branches, and a common internal branch will link them to acommon ancestor. Internal branches are called hypothetical taxonomic units. Thus,Taxonomic units gathered in the tree involve being descended from a common ancestor. Ourresearch conducted in this dissertation focuses on improving evolutionary prototypesappropriate and robust algorithms to solve phylogenetic inference problems andancestral information about the order of genes and DNA data in the evolution of the complete genome, as well astheir applications.
Author: Bashar Al-Nuaimi
Publisher:
ISBN:
Category :
Languages : en
Pages : 144
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Book Description
The theory of evolution is based on modern biology. All new species emerge of an existing species. As a result, different species share common ancestry,as represented in the phylogenetic classification. Common ancestry may explainthe similarities between all living organisms, such as general chemistry, cell structure,DNA as genetic material and genetic code. Individuals of one species share the same genes but (usually) different allele sequences of these genes. An individual inheritsalleles of their ancestry or their parents. The goal of phylogenetic studies is to analyzethe changes that occur in different organisms during evolution by identifying therelationships between genomic sequences and determining the ancestral sequences and theirdescendants. A phylogeny study can also estimate the time of divergence betweengroups of organisms that share a common ancestor. Phylogenetic trees are usefulin the fields of biology, such as bioinformatics, for systematic phylogeneticsand comparative. The evolutionary tree or the phylogenetic tree is a branched exposure the relationsevolutionary between various biological organisms or other existence depending on the differences andsimilarities in their genetic characteristics. Phylogenetic trees are built infrom molecular data such as DNA sequences and protein sequences. Ina phylogenetic tree, the nodes represent genomic sequences and are calledtaxonomic units. Each branch connects two adjacent nodes. Each similar sequencewill be a neighbor on the outer branches, and a common internal branch will link them to acommon ancestor. Internal branches are called hypothetical taxonomic units. Thus,Taxonomic units gathered in the tree involve being descended from a common ancestor. Ourresearch conducted in this dissertation focuses on improving evolutionary prototypesappropriate and robust algorithms to solve phylogenetic inference problems andancestral information about the order of genes and DNA data in the evolution of the complete genome, as well astheir applications.
Author: Ralph Bock
Publisher: Springer Science & Business Media
ISBN: 9400729200
Category : Science
Languages : en
Pages : 502
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Book Description
The past decade has witnessed an explosion of our knowledge on the structure, coding capacity and evolution of the genomes of the two DNA-containing cell organelles in plants: chloroplasts (plastids) and mitochondria. Comparative genomics analyses have provided new insights into the origin of organelles by endosymbioses and uncovered an enormous evolutionary dynamics of organellar genomes. In addition, they have greatly helped to clarify phylogenetic relationships, especially in algae and early land plants with limited morphological and anatomical diversity. This book, written by leading experts, summarizes our current knowledge about plastid and mitochondrial genomes in all major groups of algae and land plants. It also includes chapters on endosymbioses, plastid and mitochondrial mutants, gene expression profiling and methods for organelle transformation. The book is designed for students and researchers in plant molecular biology, taxonomy, biotechnology and evolutionary biology.
Author: Bassam Alkindy
Publisher:
ISBN:
Category :
Languages : en
Pages : 142
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Book Description
In Bioinformatics, understanding how DNA molecules have evolved over time remains an open and complex problem.Algorithms have been proposed to solve this problem, but they are limited either to the evolution of a given character (forexample, a specific nucleotide), or conversely focus on large nuclear genomes (several billion base pairs ), the latter havingknown multiple recombination events - the problem is NP complete when you consider the set of all possible operationson these sequences, no solution exists at present. In this thesis, we tackle the problem of reconstruction of ancestral DNAsequences by focusing on the nucleotide chains of intermediate size, and have experienced relatively little recombinationover time: chloroplast genomes. We show that at this level the problem of the reconstruction of ancestors can be resolved,even when you consider the set of all complete chloroplast genomes currently available. We focus specifically on the orderand ancestral gene content, as well as the technical problems this raises reconstruction in the case of chloroplasts. Weshow how to obtain a prediction of the coding sequences of a quality such as to allow said reconstruction and how toobtain a phylogenetic tree in agreement with the largest number of genes, on which we can then support our back in time- the latter being finalized. These methods, combining the use of tools already available (the quality of which has beenassessed) in high performance computing, artificial intelligence and bio-statistics were applied to a collection of more than450 chloroplast genomes.
Author:
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Chloroplast genome structure, gene order and content arehighly conserved in land plants. We sequenced the complete chloroplastgenome sequence of Trachelium caeruleum (Campanulaceae) a member of anangiosperm family known for highly rearranged chloroplast genomes. Thetotal genome size is 162,321 bp with an IR of 27,273 bp, LSC of 100,113bp and SSC of 7,661 bp. The genome encodes 115 unique genes, with 19duplicated in the IR, a tRNA (trnI-CAU) duplicated once in the LSC and aprotein coding gene (psbJ) duplicated twice, for a total of 137 genes. Four genes (ycf15, rpl23, infA and accD) are truncated and likelynonfunctional; three others (clpP, ycf1 and ycf2) are so highly divergedthat they may now be pseudogenes. The most conspicuous feature of theTrachelium genome is the presence of eighteen internally unrearrangedblocks of genes that have been inverted or relocated within the genome, relative to the typical gene order of most angiosperm chloroplastgenomes. Recombination between repeats or tRNAs has been suggested as twomeans of chloroplast genome rearrangements. We compared the relativenumber of repeats in Trachelium to eight other angiosperm chloroplastgenomes, and evaluated the location of repeats and tRNAs in relation torearrangements. Trachelium has the highest number and largest repeats, which are concentrated near inversion endpoints or other rearrangements.tRNAs occur at many but not all inversion endpoints. There is likely nosingle mechanism responsible for the remarkable number of alterations inthis genome, but both repeats and tRNAs are clearly associated with theserearrangements. Land plant chloroplast genomes are highly conserved instructure, gene order and content. The chloroplast genomes of ferns, thegymnosperm Ginkgo, and most angiosperms are nearly collinear, reflectingthe gene order in lineages that diverged from lycopsids and the ancestralchloroplast gene order over 350 million years ago (Raubeson and Jansen,1992). Although earlier mapping studies identified a number of taxa inwhich several rearrangements have occurred (reviewed in Raubeson andJansen, 2005), an extraordinary number of chloroplast genome alterationsare concentrated in several families in the angiosperm order Asterales(sensu APGII, Bremer et al., 2003). Gene mapping studies ofrepresentatives of the Campanulaceae (Cosner, 1993; Cosner et al.,1997,2004) and Lobeliaceae (Knox et al., 1993; Knox and Palmer, 1999)identified large inversions, contraction and expansion of the invertedrepeat regions, and several insertions and deletions in the cpDNAs ofthese closely related taxa. Detailed restriction site and gene mapping ofthe chloroplast genome of Trachelium caeruleum (Campanulaceae) identifiedseven to ten large inversions, families of repeats associated withrearrangements, possible transpositions, and even the disruption ofoperons (Cosner et al., 1997). Seventeen other members of theCampanulaceae were mapped and exhibit many additional rearrangements(Cosner et al., 2004). What happened in this lineage that made itsusceptible to so many chloroplast genome rearrangements? How do normallyvery conserved chloroplast genomes change? The cause of rearrangements inthis group is unclear based on the limited resolution available withmapping techniques. Several mechanisms have been proposed to explain howrearrangements occur: recombination between repeats, transposition, ortemporary instability due to loss of the inverted repeat (Raubeson andJansen, 2005). Sequencing whole chloroplast genomes within theCampanulaceae offers a unique opportunity to examine both the extent andmechanisms of rearrangements within a phylogenetic framework. We reporthere the first complete chloroplast genome sequence of a member of theCampanulaceae, Trachelium caeruleum. This work will serve as a benchmarkfor subsequent, comparative sequencing and analysis of other members ofthis family and close relatives, with the goal of further understandingchloroplast genome evolution. We confirmed features previously identifiedthrough mapping, and discovered many additional structural changes, including several partial to entire gene duplications, deterioration ofat least four normally conserved chloroplast genes into gene fragments, and the nature and position of numerous repeat elements at or nearinversion endpoints. The focus of this paper is on analyses of sequencesat or near these rearrangements in Trachelium caeruleum. Inversions arebelieved to occur due to the presence of repeat elements subject tohomologous recombination (Palmer, 1991; Knox et al., 1993). Repeats mayfacilitate inversions or other genome rearrangements (Achaz et al.,2003), and higher incidences of repeats have been correlated with greaternumbers of rearrangements (Rocha, 2003). Alternatively, repeats mayproliferate within a genome asa result of DNA strand repair mechanismsfollowing a rearrangement event such as an inversion. Gene.
Author: S. H. Mantell
Publisher: Longman
ISBN:
Category : Chloroplast DNA
Languages : en
Pages : 328
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Book Description
Author:
Publisher: Academic Press
ISBN: 0128134585
Category : Science
Languages : en
Pages : 398
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Book Description
Plastid Genome Evolution, Volume 85 provides a summary of recent research on plastid genome variation and evolution across photosynthetic organisms. It covers topics ranging from the causes and consequences of genomic changes, to the phylogenetic utility of plastomes for resolving relationships across the photosynthetic tree of life. This newly released volume presents thorough, up-to-date information on coevolution between the plastid and nuclear genomes, with chapters on plastid autonomy vs. nuclear control over plastid function, establishment and genetic integration of plastids, plastid genomes in alveolate protists, plastid genomes of glaucophytes, the evolution of the plastid genome in chlorophyte and streptophyte green algae, and more. Provides comprehensive coverage of plastid genome variation by leading researchers in the field Presents a broad range of taxonomic groups, ranging from single and multicellular algae, to the major clades of land plants Includes thorough, up-to-date information on coevolution between the plastid and nuclear genomes
Author: Jonathan Wendel
Publisher: Springer Science & Business Media
ISBN: 3709111307
Category : Science
Languages : en
Pages : 282
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Book Description
In this timely new 2-volume treatise, experts from around the world have banded together to produce a first-of-its-kind synopsis of the exciting and fast moving field of plant evolutionary genomics. In Volume I of Plant Genome Diversity, an update is provided on what we have learned from plant genome sequencing projects. This is followed by more focused chapters on the various genomic “residents” of plant genomes, including transposable elements, centromeres, small RNAs, and the evolutionary dynamics of genes and non-coding sequences. Attention is drawn to advances in our understanding of plant mitochondrial and plastid genomes, as well as the significance of duplication in genic evolution and the non-independent evolution among sequences in plant genomes. Finally, Volume I provides an introduction to the vibrant new frontier of plant epigenomics, describing the current state of our knowledge and the evolutionary implications of the epigenomic landscape.
Author: M. Timothy Rabanus-Wallace
Publisher: Springer Nature
ISBN: 3030833836
Category : Science
Languages : en
Pages : 251
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Book Description
This book celebrates the dawn of the rye genomics era with concise, comprehensive, and accessible reviews on the current state of rye genomic research, written by experts in the field for students, researchers and growers. To most, rye is the key ingredient in a flavoursome bread or their favourite American whisky. To a farmer, rye is the remarkable grain that tolerates the harshest winters and the most unforgiving soils, befitting its legacy as the life-giving seed that fed the ancient civilisations of northern Eurasia. Since the mid-1900s, scientists have employed genetic approaches to better understand and utilize rye, but only since the technological advances of the mid-2010s has the possibility of addressing questions using rye genome assemblies become a reality. Alongside the secret of its unique survival abilities, rye genomics has accelerated research on a host of intriguing topics such as the complex history of rye’s domestication by humans, the nature of genes that switch fertility on and off, the function and origin of accessory chromosomes, and the evolution of selfish DNA.
Author: Ignacio Rojas
Publisher: Springer Nature
ISBN: 3031078020
Category : Science
Languages : en
Pages : 485
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Book Description
This volume constitutes the proceedings of the 9th International Work-Conference on IWBBIO 2020, held in Maspalomas, Gran Canaria, Spain, in June 2022. The total of 75 papers presented in the proceedings, was carefully reviewed and selected from 212 submissions. The papers cover the latest ideas and realizations in the foundations, theory, models, and applications for interdisciplinary and multidisciplinary research encompassing disciplines of computer science, mathematics, statistics, biology, bioinformatics, and biomedicine.
Author: Ellsworth Paine Killip
Publisher:
ISBN:
Category : Passifloraceae
Languages : en
Pages : 630
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Book Description
