About Book

Advances in technology have made sequencing the entire genome of an organism essentially routine. A genome is the name for all genetic material that is characteristically present in one organism. So, all the different chromosomes of an organism together make up organism’s genome. A genome therefore contains all the characteristics together that make a frog a frog and that make a banana plant a banana plant. The genome (all the chromosomes together) is present in every individual cell of any living organism. Some organisms consist of only one cell (bacteria), but others are larger, like fungi. Other organisms like plants, dogs or humans are built up of billions of cells. But in one living organism, all cells contain the same genetic material. In recent times, the field of genomics has largely distanced itself from cytogenetics, the field providing insight into chromosome structure, function and evolution. This book is focused on rapid publication of research in the fields of genetics and genomics and from a broad range of biological disciplines. It deals with virtual genomes, artificial chromosomes, gene regulation, viral genomes, meiotic divisions, chromosomes as tools, plant genomes, micrornas sequencing and mitochondrial genomes. The purpose of the book is to provide a glimpse into the dynamic process of genetic analysis by presenting the thoughts of scientists who are engaged in the generation of new idea and techniques employed for the assessment of genetic diversity, often from very different perspectives. The book will appeal to students, researchers, and experts in the area of conservation biology, genetic diversity, and molecular biology.

Preface............................................................................................................v

Chapter 1 Mitochondrial Genomes of Lepidopteran Insects Considered Crop Pests................................................................................................................1

Abstract...................................................................................................1

1. Introduction............................................................................................2

2. Mitochondrial genome in insects.......................................................3

3. Characterization of insect mitogenomes...........................................4

4. Other recent studies with mitogenomes of Lepidopteran

considered crop pests.........................................................................15

5. Novel techniques for pest control using mtDNA........................16

6. Conclusion............................................................................................17

Chapter 2 MicroRNAs Sequencing for Understanding the Genetic Regulation of Plant Genomes.....................................................................................24

1. Introduction..........................................................................................25

2. Plant sRNAs´ classification................................................................25

3. Plant miRNAs´ biogenesis.................................................................27

4. Plant miRNAs´ function and plant development.........................29

5. miRNAs sequencing and prediction...............................................34

6. Conclusions and perspectives...........................................................36

Acknowledgements.............................................................................36

Chapter 3 Strategies for Sequence Assembly of Plant Genomes....................42

Abstract ................................................................................................42

1. Introduction..........................................................................................42

2. The development of Sanger sequencing for de novo assembly of

plant genomes......................................................................................43

3. Next-generation sequencing technologies applied to de novo

assembly of plant genomes...............................................................48

4. Complementary approaches to de novo assembly of plant

genomes................................................................................................54

5. Conclusion............................................................................................59

Acknowledgements.............................................................................60

Chapter 4 Chromosomes as Tools for Discovering Biodiversity – The Case

of Erythrinidae Fish Family...................................................................68

1. Introduction..........................................................................................68

2. Cytogenetics and biological investigation ....................................70

3. Neotropical fish and biodiversity ...................................................75

4. Erythrinidae - A fish family as an example for investigating

biodiversity .........................................................................................78

5. Conclusion ...........................................................................................88

6. Acknowledgements.............................................................................89

Chapter 5 Facing the Correct Pole: The Challenge of Orienting Chromosomes

for Meiotic Divisions .............................................................................95

1. Introduction..........................................................................................95

2. Biorientation of sister chromatids in mitosis................................98

3. Chromosomes are restructured extensively in preparation for

meiosis.................................................................................................101

4. Holding sister together: Monopolin and Rec8 ..........................104

5. Regulating kinetochore-microtubule attachments:

Aurora B function promotes homolog biorientation.................106

6. Regulating chromosome orientation: a role for condensin?.....107

7. Conclusion .........................................................................................109

Chapter 6 Ribosomal Frameshift Signals in Viral Genomes .........................119

1. Introduction........................................................................................119

2. Ribosome frameshift signals are found in diverse viral

genomes .............................................................................................120

3. Programmed ribosomal frameshift signals .................................128

4. Elucidation of frameshifting mechanisms by analysis of viral

frameshift signals .............................................................................133

5. Frameshift signals as antiviral targets .........................................142

6. Conclusion .........................................................................................147

7. Acknowledgment .............................................................................148

Chapter 7 Functionalizing Bacterial Artificial Chromosomes with Transposons

to Explore Gene Regulation.................................................................163

1. Introduction........................................................................................163

2. Exploring gene regulation by distal cis-acting sequences using

BACs ...................................................................................................175

3. List of abbreviations ........................................................................180

4. Acknowledgements .........................................................................180

Chapter 8 Defining the Deletion Size in Williams-Beuren Syndrome

by Fluorescent In Situ Hybridization with Bacterial Artificial

Chromosomes .........................................................................................187

1. Introduction........................................................................................187

2. Patients and methods .....................................................................188

3. Results ................................................................................................192

4. Discussion .........................................................................................195

5. Conclusion .........................................................................................196

Chapter 9 Using Bacterial Artificial Chromosomes to Refine Genome

Assemblies and to Build Virtual Genomes.....................................199

1. Introduction........................................................................................199

2. Materials and methods ...................................................................200

3. Results and discussion.....................................................................205

4. Conclusion .........................................................................................217

5. Acknowledgement ...........................................................................218

Citation......................................................................................................225

Index...........................................................................................................227

About Author

Kelly Kanwal, a Biotechnologist with several years of wet lab research experience, also worked as a Senior Research Fellow at Centre for Genetic Engineering, Tralee. She obtained her Ph.D. in Genetics from Technological University, Lugano. Her field of research include, isolation and molecular characterization of gemini viruses, genome sequencing and gene annotation, and gene silencing using the RNA interference technology. Kanwal has contributed papers in peer-reviewed journals in the field, and has submitted a number of annotated geminiviral genome sequences. She also works as a freelance scientific writer and editor.