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Systematic Biology Aug 2023The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA, and tRNA gene complement, but the order of these genes can range from very...
The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA, and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene order variability including, among others, increased substitution rates, base composition differences, structure of noncoding regions, parasitism, living in extreme habitats, short generation times, and biomineralization. However, these analyses were neither done systematically nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits, and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best-predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, variability of the gene order does not predict if a taxon is difficult to place in molecular phylogenetic reconstructions using sequence data or not. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why the canonical views do not always fit to the observed patterns without making some adjustments. [Annelida; compositional biases; ecology; gene order; life history; macroevolution; mitochondrial genomes; substitution rates.].
Topics: Animals; Genome, Mitochondrial; Gene Order; Phylogeny; Annelida; Genes, Mitochondrial; Evolution, Molecular; DNA, Mitochondrial
PubMed: 37083277
DOI: 10.1093/sysbio/syad023 -
PloS One 2019Amblyosyllis is a worldwide distributed group of annelids mainly found in coastal environments. It is well known among the polychaete specialists mostly because of its...
Amblyosyllis is a worldwide distributed group of annelids mainly found in coastal environments. It is well known among the polychaete specialists mostly because of its notable beauty, showing bright colourful patterns and outstanding long and coiled appendices. Amblyosyllis is a monophyletic genus easy to identify due to its distinct diagnostic features; however, the species and their boundaries are, in most cases, not well defined. Herein, we provide an extensive sample of Amblyosyllis material (115 specimens) from several world geographic areas. We have studied the morphological features of each specimen and photographed them alive. Two mitochondrial DNA markers (COI and 16S) and one nuclear gene fragment (28S, D1 region) were sequenced. We performed phylogenetic analyses based on each DNA partition, as well as the combined data sets, obtaining congruent results. Species delimitation methods such as distance analyses, statistical parsimony networks and multi-rate Poisson tree processes were also applied. The combined results obtained from different methodologies and data sets are used to differentiate between, at least, 19 lineages compatible with the separately evolving meta-populations species concept. Four of these lineages are identified as nominal species, including the type species of Amblyosyllis, A. rhombeata. For three other lineages previously synonymized names are recovered, and seven lineages are described as new species. All of these species are described and supported by appropriate iconography. We recognize several morphological characters useful to identify species of Amblyosyllis, which in some cases should also be combined with molecular methods for species delineation. The genetic divergence in the genus is high, contrary to the morphological homogeneity observed. Two species show a wide geographical distribution, while the rest have a more restricted distribution. There are several examples of species with overlapping distribution patterns.
Topics: Animals; Annelida; DNA, Mitochondrial; Phylogeny; Phylogeography; Polychaeta; Species Specificity
PubMed: 30970025
DOI: 10.1371/journal.pone.0214211 -
PLoS Computational Biology 2012A mechanistic understanding of robust self-assembly and repair capabilities of complex systems would have enormous implications for basic evolutionary developmental... (Review)
Review
A mechanistic understanding of robust self-assembly and repair capabilities of complex systems would have enormous implications for basic evolutionary developmental biology as well as for transformative applications in regenerative biomedicine and the engineering of highly fault-tolerant cybernetic systems. Molecular biologists are working to identify the pathways underlying the remarkable regenerative abilities of model species that perfectly regenerate limbs, brains, and other complex body parts. However, a profound disconnect remains between the deluge of high-resolution genetic and protein data on pathways required for regeneration, and the desired spatial, algorithmic models that show how self-monitoring and growth control arise from the synthesis of cellular activities. This barrier to progress in the understanding of morphogenetic controls may be breached by powerful techniques from the computational sciences-using non-traditional modeling approaches to reverse-engineer systems such as planaria: flatworms with a complex bodyplan and nervous system that are able to regenerate any body part after traumatic injury. Currently, the involvement of experts from outside of molecular genetics is hampered by the specialist literature of molecular developmental biology: impactful collaborations across such different fields require that review literature be available that presents the key functional capabilities of important biological model systems while abstracting away from the often irrelevant and confusing details of specific genes and proteins. To facilitate modeling efforts by computer scientists, physicists, engineers, and mathematicians, we present a different kind of review of planarian regeneration. Focusing on the main patterning properties of this system, we review what is known about the signal exchanges that occur during regenerative repair in planaria and the cellular mechanisms that are thought to underlie them. By establishing an engineering-like style for reviews of the molecular developmental biology of biomedically important model systems, significant fresh insights and quantitative computational models will be developed by new collaborations between biology and the information sciences.
Topics: Animals; Annelida; Models, Biological; Regeneration
PubMed: 22570595
DOI: 10.1371/journal.pcbi.1002481 -
Current Biology : CB Mar 2013
Topics: Animal Distribution; Animals; Chemoautotrophic Growth; Gammaproteobacteria; Hydrothermal Vents; Pacific Ocean; Phylogeny; Polychaeta; Symbiosis
PubMed: 23518047
DOI: 10.1016/j.cub.2013.01.039 -
Mechanisms of Development Oct 2017Asymmetries are observed in a great number of taxa in metazoans. More particularly, functional lateralization and neuroanatomical asymmetries within the central nervous... (Review)
Review
Asymmetries are observed in a great number of taxa in metazoans. More particularly, functional lateralization and neuroanatomical asymmetries within the central nervous system have been a matter of intense research for at least two hundred years. While asymmetries of some paired structures/organs (e.g. eyes, ears, kidneys, legs, arms) constitute random deviations from a pure bilateral symmetry, brain asymmetries such as those observed in the cortex and epithalamus are directional. This means that molecular and anatomical features located on one side of a given structure are observed in most individuals. For instance, in humans, the neuronal tract connecting the language areas is enlarged in the left hemisphere. When asymmetries are fixed, their molecular mechanisms can be studied using mutants displaying different phenotypes: left or right isomerism of the structure, reversed asymmetry or random asymmetry. Our understanding of asymmetry in the nervous system has been widely enriched thanks to the characterization of mutants affecting epithalamus asymmetry. Furthermore, two decades ago, pioneering studies revealed that a specific morphogen, Nodal, active only on one side of the embryo during development is an important molecule in asymmetry patterning. In this review, I have gathered important data bringing insight into the origin and evolution of epithalamus asymmetry and the role of Nodal in metazoans. After a short introduction on brain asymmetries (chapter I), I secondly focus on the molecular and anatomical characteristics of the epithalamus in vertebrates and explore some functional aspects such as its photosensitive ability related to the pineal complex (chapter II). Third, I discuss homology relationship of the parapineal organ among vertebrates (chapter III). Fourth, I discuss the possible origin of the epithalamus, presenting cells displaying photosensitive properties and/or asymmetry in the anterior part of the body in non-vertebrates (chapter IV). Finally, I report Nodal signaling expression data and functional experiments performed in different metazoan groups (chapter V).
Topics: Animals; Annelida; Biological Evolution; Body Patterning; Circadian Rhythm; Cnidaria; Fishes; Functional Laterality; Habenula; Humans; Photoreceptor Cells, Invertebrate; Photoreceptor Cells, Vertebrate; Pineal Gland; Vision, Ocular
PubMed: 28986126
DOI: 10.1016/j.mod.2017.09.002 -
Journal of Oleo Science Apr 2022Humoral practice is a fundamental natural biological phenomenon in earthworm defensive system which protects them from infectious bacteria and irritating agents by... (Review)
Review
Humoral practice is a fundamental natural biological phenomenon in earthworm defensive system which protects them from infectious bacteria and irritating agents by different mechanisms. The defensive system of earthworms is highly complicated because they lack antibodies in their blood circulatory system but their body extracts and coelomic fluid comprise of different bioactive agents (i.e. peptides and proteins) that defend these worms. There are various groups of bioactive agents such as proteases (name depends on proteins/peptide function or formal earthworm species name), metabolites (total 59 metabolites found in Eisenia fetida), metal binding proteins (2 proteins such as Ca binding calmodulin and metallothionein), active proteins (include lysozyme, lysenin and eiseniapore etc.), antimicrobial peptides (antibacterial vermi-peptides family (AVPF), antimicrobial peptide I (PP-I), coelomic cytolytic factor (CCF, CCF-I and CCF like protein), fetidin, lysenin, lumbricin (lumbricin I, lumbricin PG, and lumbricusin), organic acids (fatty acids, succinic acids, and lauric acid) and other organic compounds (such as purine and vitamin D). The presence of above mentioned molecules confer therapeutic potential that affect energy intake and involve in decreasing oxidative stress, metabolic disturbances and pro-inflammatory conditions. The future perspectives of earthworm bioactive compounds are concerned with the development of provisional standards, purification and classification for utilizations in pharma industry.
Topics: Animals; Anti-Bacterial Agents; Anti-Infective Agents; Bacteria; Oligochaeta
PubMed: 35283417
DOI: 10.5650/jos.ess21379 -
EMBO Reports Dec 2002Neuroglobin and cytoglobin are two recently discovered members of the vertebrate globin family. Both are intracellular proteins endowed with hexacoordinated heme-Fe... (Review)
Review
Neuroglobin and cytoglobin are two recently discovered members of the vertebrate globin family. Both are intracellular proteins endowed with hexacoordinated heme-Fe atoms, in their ferrous and ferric forms, and display O2 affinities comparable with that of myoglobin. Neuroglobin, which is predominantly expressed in nerve cells, is thought to protect neurons from hypoxic-ischemic injury. It is of ancient evolutionary origin, and is homologous to nerve globins of invertebrates. Cytoglobin is expressed in many different tissues, although at varying levels. It shares common ancestry with myoglobin, and can be traced to early vertebrate evolution. The physiological roles of neuroglobin and cytoglobin are not completely understood. Although supplying cells with O2 is the likely function, it is also possible that both globins act as O2-consuming enzymes or as O2 sensors. Here, we review what is currently known about neuroglobin and cytoglobin in terms of their function, tissue distribution and relatedness to the well-known hemoglobin and myoglobin. Strikingly, the data reveal that O2 metabolism in cells is more complicated than was thought before, requiring unexpected O2-binding proteins with potentially novel functional features.
Topics: Amino Acid Sequence; Animals; Annelida; Brain; Brain Chemistry; Conserved Sequence; Cytoglobin; Globins; Heme; Humans; Mice; Molecular Sequence Data; Nerve Tissue Proteins; Neuroglobin; Oxygen; Sequence Alignment; Zebrafish
PubMed: 12475928
DOI: 10.1093/embo-reports/kvf248 -
Parasite (Paris, France) Sep 2008Annelids have had a long history in comparative embryology and morphology, which has helped to establish them in zoology textbooks as an ideal system to understand the... (Review)
Review
Annelids have had a long history in comparative embryology and morphology, which has helped to establish them in zoology textbooks as an ideal system to understand the evolution of the typical triploblastic, coelomate, protostome condition. In recent years there has been a relative upsurge in embryological data, particularly with regard to the expression and function of developmental control genes. Polychaetes, as well as other annelids such as the parasitic leech, are now also entering the age of comparative genomics. All of this comparative data has had an important impact on our views of the ancestral conditions at various levels of the animal phylogeny, including the bilaterian ancestor and the nature of the annelid ancestor. Here we review some of the recent advances made in annelid comparative development and genomics, revealing a hitherto unsuspected level of complexity in these ancestors. It is also apparent that the transition to a parasitic lifestyle leads to, or requires, extensive modifications and derivations at both the genomic and embryological levels.
Topics: Animals; Annelida; Biological Evolution; Developmental Biology; Genomics
PubMed: 18814702
DOI: 10.1051/parasite/2008153321 -
Philosophical Transactions of the Royal... Feb 2010It is proposed here that a biphasic life cycle with partial dedifferentiation of intermediate juvenile or larval stages represents the mainstream developmental mode of... (Review)
Review
It is proposed here that a biphasic life cycle with partial dedifferentiation of intermediate juvenile or larval stages represents the mainstream developmental mode of metazoans. Developmental plasticity of differentiated cells is considered the essential characteristic of indirect development, rather than the exclusive development of the adult from 'set-aside' cells. Many differentiated larval cells of indirect developers resume proliferation, partially dedifferentiate and contribute to adult tissues. Transcriptional pluripotency of differentiated states has premetazoan origins and seems to be facilitated by histone variant H2A.Z. Developmental plasticity of differentiated states also facilitates the evolution of polyphenism. Uncertainty remains about whether the most recent common ancestor of protostomes and deuterostomes was a direct or an indirect developer, and how the feeding larvae of bilaterians are related to non-feeding larvae of sponges and cnidarians. Feeding ciliated larvae of bilaterians form their primary gut opening by invagination, which seems related to invagination in cnidarians. Formation of the secondary gut opening proceeds by protostomy or deuterostomy, and gene usage suggests serial homology of the mouth and anus. Indirect developers do not use the Hox vector to build their ciliated larvae, but the Hox vector is associated with the construction of the reproductive portion of the animal during feeding-dependent posterior growth. It is further proposed that the original function of the Hox cluster was in gonad formation rather than in anteroposterior diversification.
Topics: Animals; Annelida; Biological Evolution; Cell Differentiation; Cell Transdifferentiation; Gastrulation; Gene Expression Regulation, Developmental; Gene Regulatory Networks; Genes, Homeobox; Genitalia; Growth and Development; Larva; Life Cycle Stages; Models, Biological; Phylogeny; Stem Cells
PubMed: 20083640
DOI: 10.1098/rstb.2009.0253 -
Journal of Experimental Zoology. Part... May 2024Germ cells (reproductive cells and their progenitors) give rise to the next generation in sexually reproducing organisms. The loss or removal of germ cells often leads... (Review)
Review
Germ cells (reproductive cells and their progenitors) give rise to the next generation in sexually reproducing organisms. The loss or removal of germ cells often leads to sterility in established research organisms such as the fruit fly, nematodes, frog, and mouse. The failure to regenerate germ cells in these organisms reinforced the dogma of germline-soma barrier in which germ cells are set-aside during embryogenesis and cannot be replaced by somatic cells. However, in stark contrast, many animals including segmented worms (annelids), hydrozoans, planaria, sea stars, sea urchins, and tunicates can regenerate germ cells. Here I review germ cell and gonad regeneration in annelids, a rich history of research that dates back to the early 20th century in this highly regenerative group. Examples include annelids from across the annelid phylogeny, across developmental stages, and reproductive strategies. Adult annelids regenerate germ cells as a part of regeneration, grafting, and asexual reproduction. Annelids can also recover germ cells after ablation of germ cell progenitors in the embryos. I present a framework to investigate cellular sources of germ cell regeneration in annelids, and discuss the literature that supports different possibilities within this framework, where germ-soma separation may or may not be preserved. With contemporary genetic-lineage tracing and bioinformatics tools, and several genetically enabled annelid models, we are at the brink of answering the big questions that puzzled many for over more than a century.
Topics: Animals; Annelida; Germ Cells; Gonads; Regeneration; Models, Animal
PubMed: 38078561
DOI: 10.1002/jez.b.23233