Current Genomics (v.13, #2)

It has become a fundamental need to have genome sequence data due to the fact that the basic process of evolution is the change in DNA sequence and genome size. Recent advances in DNA sequencing technology have facilitated the availability of quite a large number of complete genome sequences from simplest prokaryotes to higher eukaryotes. The availability of whole genome sequence data at our fingertips can provide critical insight into how various genomic compositions have contributed to a contemporary understanding of molecular evolution. For this reason, comparative evolutionary genomics has become one of the most rapidly advancing disciplines in the biological sciences. The new generation of comparative genomics offers a powerful aid to studying evolutionary changes among organisms and identifying the genes that are conserved among species, and also the genes that give each organism its own specific characteristics. Informatics related to structural and functional genomics is potentially important in understanding the emergence of new phenotypic characters necessary for the adaptation of organisms. In addition, the evolutionary perspective of genes and genomes is also helpful in understanding disease susceptibility. A large number of scientists from all over the world are involved in determining the genomic underpinnings of morphological, physiological, and behavioral changes. A lot of research has been done to find selection signals on a genomewide scale, and also focusing on specific gene families to learn more about evolutionary mechanisms. Therefore, it is necessary to compile various current aspects of genomic and evolutionary research at some point. This prompts us to devote a special issue we have named “Comparative Genomics and Genome Evolution”. The series of review articles in this issue of Current Genomics present current advances in multiple areas of comparative genomics and molecular evolutionary studies. This special issue is comprised of eight high quality articles which have been selected through a rigorous reviewing process. Several years ago, with the ground-breaking work of Max D. Cooper and colleagues, an adaptive immune system was discovered in a representative jawless vertebrate (lamprey). The first review article describes concordance and divergence in the immunogenetic architecture between two alternative adaptive immune systems of jawed and jawless vertebrates, and discusses in detail the evolution of the jawless vertebrate immune system on the basis of currently available lamprey genomic resources. In the second review paper, Nikolas Nikolaidis and colleagues discuss the current knowledge on the genomics and evolution of the immunoglobulin mulitigene family in vertebrates. To provide further coverage and discussion of the evolutionary dynamics of multigene families, we commissioned Yoshihito Niimura to review the evolutionary genomics of the olfactory receptor multigene family on a genome-wide scale. The fourth review article presents the interesting scenario of the evolution of mammalian sex chromosomes. Yoko Satta and colleagues reviewed evolutionary aspects related to genomic rearrangements and structures of the sex chromosomes. The next review article, by Arnab Gupta and Svetlana Lutsenko, focuses on the origin and evolution of copper transporting ATPases in eukaryotic organisms. In the sixth article, Mariko Kondo and Koji Akasaka highlight the phylogenetic relationships among echinoderms and the current status of echinoderm genome analysis. The seventh article is related to the evolution of microRNAs. In this article, Zhumur Ghosh and Bibekanand Mallick describe advances of genomics, evolution, and biogenesis of microRNAs. Finally, we conclude with an interesting review article by Chitra Dutta and Sandip Paul on microbial genome signature related to different lifestyles. The authors describe how closely related microbial species are diverged on the basis of the genomic signature of ecological kinship throughout microbial evolution. Recognizing the growing interest in evolutionary genomics, we are happy to present this collection of high quality review articles for this special issue. We would like to thank all of the reviewers for their valuable comments meant to improve the quality of articles. In addition, we offer special thanks to the Editor-in-Chief, and the Current Genomics editorial/production staff, who have contributed invaluably to this project. We hope you find the issue timely, scholarly, and interesting.

The study of immune related genes in lampreys and hagfish provides a unique perspective on the evolutionary genetic underpinnings of adaptive immunity and the evolution of vertebrate genomes. Separated from their jawed cousins at the stem of the vertebrate lineage, these jawless vertebrates have many of the gene families and gene regulatory networks associated with the defining morphological and physiological features of vertebrates. These include genes vital for innate immunity, inflammation, wound healing, protein degradation, and the development, signaling and trafficking of lymphocytes. Jawless vertebrates recognize antigen by using leucine-rich repeat (LRR) based variable lymphocyte receptors (VLRs), which are very different from the immunoglobulin (Ig) based T cell receptor (TCR) and B cell receptor (BCR) used for antigen recognition by jawed vertebrates. The somatically constructed VLR genes are expressed in monoallelic fashion by T-like and B-like lymphocytes. Jawless and jawed vertebrates thus share many of the genes that provide the molecular infrastructure and physiological context for adaptive immune responses, yet use entirely different genes and mechanisms of combinatorial assembly to generate diverse repertoires of antigen recognition receptors.

Immunoglobulins (or antibodies) are an essential element of the jawed vertebrate adaptive immune response system. These molecules have evolved over the past 500 million years and generated highly specialized proteins that recognize an extraordinarily large number of diverse substances, collectively known as antigens. During vertebrate evolution the diversification of the immunoglobulin-encoding loci resulted in differences in the genomic organization, gene content, and ratio of functional genes and pseudogenes. The tinkering process in the immunoglobulin-encoding loci often gave rise to lineage-specific characteristics that were formed by selection to increase species adaptation and fitness. Immunoglobulin loci and their encoded antibodies have been shaped repeatedly by contrasting evolutionary forces, either to conserve the prototypic structure and mechanism of action or to generate alternative and diversified structures and modes of function. Moreover, evolution favored the development of multiple mechanisms of primary and secondary antibody diversification, which are used by different species to effectively generate an almost infinite collection of diverse antibody types. This review summarizes our current knowledge on the genomics and evolution of the immunoglobulinencoding loci and their protein products in jawed vertebrates.

Olfaction is essential for the survival of animals. Diverse odor molecules in the environment are detected by the olfactory receptors (ORs) in the olfactory epithelium of the nasal cavity. There are ∼400 and ∼1,000 OR genes in the human and mouse genomes, respectively, forming the largest multigene family in mammals. The relationships between ORs and odorants are multiple-to-multiple, which allows for discriminating almost unlimited number of different odorants by a combination of ORs. However, the OR-ligand relationships are still largely unknown, and predicting the quality of odor from its molecular structure is unsuccessful. Extensive bioinformatic analyses using the whole genomes of various organisms revealed a great variation in number of OR genes among species, reflecting the diversity of their living environments. For example, higher primates equipped with a well-developed vision system and dolphins that are secondarily adapted to the aquatic life have considerably smaller numbers of OR genes than most of other mammals do. OR genes are characterized by extremely frequent gene duplications and losses. The OR gene repertories are also diverse among human individuals, explaining the diversity of odor perception such as the specific anosmia. OR genes are present in all vertebrates. The number of OR genes is smaller in teleost fishes than in mammals, while the diversity is higher in the former than the latter. Because the genome of amphioxus, the most basal chordate species, harbors vertebrate-like OR genes, the origin of OR genes can be traced back to the common ancestor of the phylum Chordata.

Throughout mammalian evolution, recombination between the two sex chromosomes was suppressed in a stepwise manner. It is thought that the suppression of recombination led to an accumulation of deleterious mutations and frequent genomic rearrangements on the Y chromosome. In this article, we review three evolutionary aspects related to genomic rearrangements and structures, such as inverted repeats (IRs) and palindromes (PDs), on the mammalian sex chromosomes. First, we describe the stepwise manner in which recombination between the X and Y chromosomes was suppressed in placental mammals and discuss a genomic rearrangement that might have led to the formation of present pseudoautosomal boundaries (PAB). Second, we describe ectopic gene conversion between the X and Y chromosomes, and propose possible molecular causes. Third, we focus on the evolutionary mode and timing of PD formation on the X and Y chromosomes. The sequence of the chimpanzee Y chromosome was recently published by two groups. Both groups suggest that rapid evolution of genomic structure occurred on the Y chromosome. Our re-analysis of the sequences confirmed the species-specific mode of human and chimpanzee Y chromosomal evolution. Finally, we present a general outlook regarding the rapid evolution of mammalian sex chromosomes.

Copper is an essential nutrient for most life forms, however in excess it can be harmful. The ATP-driven copper pumps (Copper-ATPases) play critical role in living organisms by maintaining appropriate copper levels in cells and tissues. These evolutionary conserved polytopic membrane proteins are present in all phyla from simplest life forms (bacteria) to highly evolved eukaryotes (Homo sapiens). The presumed early function in metal detoxification remains the main function of Copper-ATPases in prokaryotic kingdom. In eukaryotes, in addition to removing excess copper from the cell, Copper-ATPases have another equally important function - to supply copper to copper dependent enzymes within the secretory pathway. This review focuses on the origin and diversification of Copper ATPases in eukaryotic organisms. From a single Copper ATPase in protozoans, a divergence into two functionally distinct ATPases is observed with the evolutionary appearance of chordates. Among the key functional domains of Copper-ATPases, the metal-binding Nterminal domain could be responsible for functional diversification of the copper ATPases during the course of evolution.

Echinoderms have long served as model organisms for a variety of biological research, especially in the field of developmental biology. Although the genome of the purple sea urchin Strongylocentrotus purpuratus has been sequenced, it is the only echinoderm whose whole genome sequence has been reported. Nevertheless, data is rapidly accumulating on the chromosomes and genomic sequences of all five classes of echinoderms, including the mitochondrial genomes and Hox genes. This blossoming new data will be essential for estimating the phylogenetic relationships among echinoderms, and also to examine the underlying mechanisms by which the diverse morphologies of echinoderms have arisen.

Intergenic DNA, often described as “playground of evolution”, harbors a plethora of cis and trans regulatory elements in the form of non-coding RNAs (ncRNAs). The evolution of the silencing mechanism mediated by microRNAs (miRNAs), an important class of ncRNA, involves the proliferation of miRNA biogenesis and effector proteins, continuing innovation of novel families by the diversification of established families and spawning additional paralogous family members. Such evolving miRNA pathways for spatiotemporal regulation of the transcriptome have shaped the evolution of eukaryotic genomes and contributed to the complexity of multicellular organisms. Here, we focus on the emergence of new target specificity of the miRNAs along with the proliferation of core biogenesis and effector modules and show how this has contributed to generate diverse miRNA regulatory pathways.

Microbial Lifestyle and Genome Signatures by Chitra Dutta (153-162).
Microbes are known for their unique ability to adapt to varying lifestyle and environment, even to the extreme or adverse ones. The genomic architecture of a microbe may bear the signatures not only of its phylogenetic position, but also of the kind of lifestyle to which it is adapted. The present review aims to provide an account of the specific genome signatures observed in microbes acclimatized to distinct lifestyles or ecological niches. Niche-specific signatures identified at different levels of microbial genome organization like base composition, GC-skew, purine-pyrimidine ratio, dinucleotide abundance, codon bias, oligonucleotide composition etc. have been discussed. Among the specific cases highlighted in the review are the phenomena of genome shrinkage in obligatory host-restricted microbes, genome expansion in strictly intra-amoebal pathogens, strand-specific codon usage in intracellular species, acquisition of genome islands in pathogenic or symbiotic organisms, discriminatory genomic traits of marine microbes with distinct trophic strategies, and conspicuous sequence features of certain extremophiles like those adapted to high temperature or high salinity.

Models of genetic effects integrate the action of genes, regulatory regions and interactions among alleles across the genome. Such theoretical frameworks are critical for applied studies in at least two ways. First, discovering genetic networks with specific effects underlying traits in populations requires the development of models that implement those effects as parameters–adjusting the implementation of epistasis parameters in genetic models has for instance been a requirement for properly testing for epistasis in gene-mapping studies. Second, studying the properties and implications of models of genetic effects that involve complex genetic networks has proven to be valuable, whether those networks have been revealed for particular organisms or inferred to be of interest from theoretical works and simulations. Here I review the current state of development and recent applications of models of genetic effects. I focus on general models aiming to depict complex genotype-to-phenotype maps and on applications of them to networks of interacting loci.