Alexander Ochoa, Alyssa T. B. Hassinger, Matthew L. Holding, H. Lisle Gibbs
{"title":"Genetic characterization of potential venom resistance proteins in California ground squirrels (Otospermophilus beecheyi) using transcriptome analyses","authors":"Alexander Ochoa, Alyssa T. B. Hassinger, Matthew L. Holding, H. Lisle Gibbs","doi":"10.1002/jez.b.23145","DOIUrl":"10.1002/jez.b.23145","url":null,"abstract":"<p>Understanding the molecular basis of adaptations in coevolving species requires identifying the genes that underlie reciprocally selected phenotypes, such as those involved in venom in snakes and resistance to the venom in their prey. In this regard, California ground squirrels (CGS; <i>Otospermophilus beecheyi</i>) are eaten by northern Pacific rattlesnakes (<i>Crotalus oreganus oreganus</i>), but individual squirrels may still show substantial resistance to venom and survive bites. A recent study using proteomics identified venom interactive proteins (VIPs) in the blood serum of CGS. These VIPs represent possible resistance proteins, but the sequences of genes encoding them are unknown despite the value of such data to molecular studies of coevolution. To address this issue, we analyzed a de novo assembled transcriptome from CGS liver tissue—where many plasma proteins are synthesized—and other tissues from this species. We then examined VIP sequences in terms of three characteristics that identify them as possible resistance proteins: evidence for positive selection, high liver expression, and nonsynonymous variation across CGS populations. Based on these characteristics, we identified five VIPs (i.e., α-2-macroglobulin, α-1-antitrypsin-like protein GS55-LT, apolipoprotein A-II, hibernation-associated plasma protein HP-20, and hibernation-associated plasma protein HP-27) as the most likely candidates for resistance proteins among VIPs identified to date. Four of these proteins have been previously implicated in conferring resistance to the venom in mammals, validating our approach. When combined with the detailed information available for rattlesnake venom proteins, these results set the stage for future work focused on understanding coevolutionary interactions at the molecular level between these species.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23145","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9625662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Irene del Olmo, Aida Verdes, Patricia Álvarez-Campos
{"title":"Distinct patterns of gene expression during regeneration and asexual reproduction in the annelid Pristina leidyi","authors":"Irene del Olmo, Aida Verdes, Patricia Álvarez-Campos","doi":"10.1002/jez.b.23143","DOIUrl":"10.1002/jez.b.23143","url":null,"abstract":"<p>Regeneration, the ability to replace lost body parts, is a widespread phenomenon in the animal kingdom often connected to asexual reproduction or fission, since the only difference between the two appears to be the stimulus that triggers them. Both developmental processes have largely been characterized; however, the molecular toolkit and genetic mechanisms underlying these events remain poorly unexplored. Annelids, in particular the oligochaete <i>Pristina leidyi</i>, provide a good model system to investigate these processes as they show diverse ways to regenerate, and can reproduce asexually through fission under laboratory conditions. Here, we used a comparative transcriptomics approach based on RNA-sequencing and differential gene expression analyses to understand the molecular mechanisms involved in anterior regeneration and asexual reproduction. We found 291 genes upregulated during anterior regeneration, including several regeneration-related genes previously reported in other annelids such as <i>frizzled</i>, <i>paics</i>, and <i>vdra</i>. On the other hand, during asexual reproduction, 130 genes were found upregulated, and unexpectedly, many of them were related to germline development during sexual reproduction. We also found important differences between anterior regeneration and asexual reproduction, with the latter showing a gene expression profile more similar to that of control individuals. Nevertheless, we identified 35 genes that were upregulated in both conditions, many of them related to cell pluripotency, stem cells, and cell proliferation. Overall, our results shed light on the molecular mechanisms that control anterior regeneration and asexual reproduction in annelids and reveal similarities with other animals, suggesting that the genetic machinery controlling these processes is conserved across metazoans.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c6/14/JEZ-338-405.PMC9790225.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10450660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Domestication and the comparative embryology of birds","authors":"Gerardo A. Cordero, Ingmar Werneburg","doi":"10.1002/jez.b.23144","DOIUrl":"10.1002/jez.b.23144","url":null,"abstract":"<p>Studies of domesticated animals have greatly contributed to our understanding of avian embryology. Foundational questions in developmental biology were motivated by Aristotle's observations of chicken embryos. By the 19th century, the chicken embryo was at the center stage of developmental biology, but how closely does this model species mirror the ample taxonomic diversity that characterizes the avian tree of life? Here, we provide a brief overview of the taxonomic breadth of comparative embryological studies in birds. We particularly focused on staging tables and papers that attempted to document the timing of developmental transformations. We show that most of the current knowledge of avian embryology is based on Galliformes (chicken and quail) and Anseriformes (duck and goose). Nonetheless, data are available for some ecologically diverse avian subclades, including Struthioniformes (e.g., ostrich, emu) and Sphenisciformes (penguins). Thus far, there has only been a handful of descriptive embryological studies in the most speciose subclade of Aves, that is, the songbirds (Passeriniformes). Furthermore, we found that temporal variances for developmental events are generally uniform across a consensus chronological sequence for birds. Based on the available data, developmental trajectories for chicken and other model species appear to be highly similar. We discuss future avenues of research in comparative avian embryology in light of the currently available wealth of data on domesticated species and beyond.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23144","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10743188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Francisca M. Real, Miguel Lao-Pérez, Miguel Burgos, Stefan Mundlos, Darío G. Lupiáñez, Rafael Jiménez, Francisco J. Barrionuevo
{"title":"Cell adhesion and immune response, two main functions altered in the transcriptome of seasonally regressed testes of two mammalian species","authors":"Francisca M. Real, Miguel Lao-Pérez, Miguel Burgos, Stefan Mundlos, Darío G. Lupiáñez, Rafael Jiménez, Francisco J. Barrionuevo","doi":"10.1002/jez.b.23142","DOIUrl":"10.1002/jez.b.23142","url":null,"abstract":"<p>In species with seasonal breeding, male specimens undergo substantial testicular regression during the nonbreeding period of the year. However, the molecular mechanisms that control this biological process are largely unknown. Here, we report a transcriptomic analysis on the Iberian mole, <i>Talpa occidentalis</i>, in which the desquamation of live, nonapoptotic germ cells is the major cellular event responsible for testis regression. By comparing testes at different reproductive states (active, regressing, and inactive), we demonstrate that the molecular pathways controlling the cell adhesion function in the seminiferous epithelium, such as the MAPK, ERK, and TGF-β signaling, are altered during the regression process. In addition, inactive testes display a global upregulation of genes associated with immune response, indicating a selective loss of the “immune privilege” that normally operates in sexually active testes. Interspecies comparative analyses using analogous data from the Mediterranean pine vole, a rodent species where testis regression is controlled by halting meiosis entry, revealed a common gene expression signature in the regressed testes of these two evolutionary distant species. Our study advances in the knowledge of the molecular mechanisms associated to gonadal seasonal breeding, highlighting the existence of a conserved transcriptional program of testis involution across mammalian clades.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23142","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9628822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Observing Evolution: Peppered Moths and the Discovery of Parallel Melanism. By Bruce S. Grant. Johns Hopkins University Press (2021).","authors":"Richard Gawne","doi":"10.1002/jez.b.23136","DOIUrl":"10.1002/jez.b.23136","url":null,"abstract":"","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41350324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Evolution and functionalization of vitellogenin genes in the termite Reticulitermes speratus","authors":"Hajime Yaguchi, Shogo Suzuki, Naoto Kanasaki, Yudai Masuoka, Ryutaro Suzuki, Ryouhei H. Suzuki, Yoshinobu Hayashi, Shuji Shigenobu, Kiyoto Maekawa","doi":"10.1002/jez.b.23141","DOIUrl":"10.1002/jez.b.23141","url":null,"abstract":"<p>Eusociality has been commonly observed in distinct animal lineages. The reproductive division of labor is a particular feature, achieved by the coordination between fertile and sterile castes within the same nest. The sociogenomic approach in social hymenopteran insects indicates that <i>vitellogenin</i> (<i>Vg</i>) has undergone neo-functionalization in sterile castes. Here, to know whether <i>Vgs</i> have distinct roles in nonreproductive castes in termites, we investigated the unique characteristics of <i>Vgs</i> in the rhinotermitid termite <i>Reticulitermes speratus</i>. The four <i>Vg</i>s were identified from <i>R. speratus</i> (<i>RsVg1−4</i>), and <i>RsVg3</i> sequences were newly identified using the RACE method. Molecular phylogenetic analysis supported the monophyly of the four termite <i>Vg</i>s. Moreover, the termites <i>Vg1−3</i> and <i>Vg4</i> were positioned in two different clades. The <i>dN</i>/<i>dS </i>ratios indicated that the branch leading to the common ancestor of termite <i>Vg4</i> was under weak purifying selection. Expression analyses among castes (reproductives, workers, and soldiers) and females (nymphs, winged alates, and queens) showed that <i>RsVg1−3</i> was highly expressed in fertile queens. In contrast, <i>RsVg4</i> was highly expressed in workers and female nonreproductives (nymphs and winged adults). Localization of <i>RsVg4</i> messenger RNA was confirmed in the fat body of worker heads and abdomens. These results suggest that <i>Vg</i> genes are functionalized after gene duplication during termite eusocial transition and that <i>Vg4</i> is involved in nonreproductive roles in termites.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9236044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"How body patterning might have worked in the evolution of arthropods—A case study of the mystacocarid Derocheilocaris remanei (Crustacea, Oligostraca)","authors":"Martin Fritsch, Stefan Richter","doi":"10.1002/jez.b.23140","DOIUrl":"10.1002/jez.b.23140","url":null,"abstract":"<p>Body organization within arthropods is enormously diverse, but a fusion of segments into “functional groups” (tagmatization) is found in all species. Within Tetraconata/Pancrustacea, an anterior head, a locomotory thorax region, and a posterior, mostly limbless tagma known as the abdomen is present. The posterior-most tagma in crustaceans is frequently confused with the malacostracan, for example, decapod pleon often misleadingly termed abdomen, however, its evolutionary and developmental origin continues to pose a riddle, especially the completely limbless abdomen of the “entomostracan morphotype” (e.g., fairy shrimps). Since the discovery of Hox genes and their involvement in specifying the morphology or identity of segments, tagmata, or regions along the anteroposterior axis of an organism, only a few studies have focused on model organisms representing the “entomostracan morphotype” and used a variety of dedicated Hox genes and their transcription products to shine light on abdomen formation. The homeotic genes or the molecular processes that determine the identity of the entomostracan abdomen remain unknown to date. This study focuses on the “entomostracan morphotype” representative <i>Derocheilocaris remanei</i> (Mystacocarida). We present a complete overview of development throughout larval stages and investigate homeotic gene expression data using the antibody FP6.87 that binds specifically to epitopes of <i>Ultrabithorax</i>/<i>Abdominal-A</i> proteins. Our results suggest that the abdomen in Mystacocarida is bipartite (<i><b>abdomen I</b></i> + <i><b>abdomen II</b></i>). We suggest that the limbless abdomen is an evolutionary novelty that evolved several times independently within crustaceans and which might be the result of a progressive reduction of former thoracic segments into abdominal segments.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23140","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84689154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jumpei Ikenaga, Satoe Aratake, Kaoru Yoshida, Manabu Yoshida
{"title":"A novel role for ATP2B in ascidians: Ascidian-specific mutations in ATP2B contribute to sperm chemotaxis","authors":"Jumpei Ikenaga, Satoe Aratake, Kaoru Yoshida, Manabu Yoshida","doi":"10.1002/jez.b.23133","DOIUrl":"10.1002/jez.b.23133","url":null,"abstract":"<p>Sperm chemotaxis, in which sperms are attracted to conspecific eggs via species-specific attractants, plays an important role in fertilization. This phenomenon has been observed in various animals and species-specific sperm attractants have been reported in some species. However, the mechanisms involved in the reception and recognition of the species-specific attractant by the sperms is poorly studied. Previously, we found that the plasma membrane-type Ca<sup>2+</sup>/ATPase (PMCA) is the receptor for the sperm-activating and -attracting factor (SAAF) in the ascidian <i>Ciona intestinalis</i>. To determine the role of PMCA in species-specific sperm chemotaxis, we identified the amino acid sequences of PMCAs derived from six Phlebobranchia species. The testis-specific splice variant of PMCA was found to be present in all the species investigated and the ascidian-specific sequence was detected near the 3′-terminus. Moreover, dN/dS analysis revealed that the extracellular loops 1, 2, and 4 in ascidian PMCA underwent a positive selection. These findings suggest that PMCA recognizes the species-specific structure of SAAF at the extracellular loops 1, 2, and 4, and its testis-specific C-terminal region is involved in the activation and chemotaxis of ascidian sperms.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73085772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nikolai P. Melnikov, Fyodor V. Bolshakov, Veronika S. Frolova, Kseniia V. Skorentseva, Alexander V. Ereskovsky, Alina A. Saidova, Andrey I. Lavrov
{"title":"Tissue homeostasis in sponges: Quantitative analysis of cell proliferation and apoptosis","authors":"Nikolai P. Melnikov, Fyodor V. Bolshakov, Veronika S. Frolova, Kseniia V. Skorentseva, Alexander V. Ereskovsky, Alina A. Saidova, Andrey I. Lavrov","doi":"10.1002/jez.b.23138","DOIUrl":"https://doi.org/10.1002/jez.b.23138","url":null,"abstract":"<p>Tissues of multicellular animals are maintained due to a tight balance between cell proliferation and programmed cell death. Sponges are early branching metazoans essential to understanding the key mechanisms of tissue homeostasis. This article is dedicated to the comparative analysis of proliferation and apoptosis in intact tissues of two sponges, <i>Halisarca dujardinii</i> (class Demospongiae) and <i>Leucosolenia variabilis</i> (class Calcarea). Labeled nucleotides EdU and anti-phosphorylated histone 3 antibodies reveal a considerable number of cycling cells in intact tissues of both species. Quantitative DNA staining reveals the classic cell cycle distribution curve. The main type of cycling cells are choanocytes - flagellated cells of the aquiferous system. The rate of proliferation remains constant throughout various areas of sponge bodies that contain choanocytes. The EdU tracking experiments conducted in <i>H. dujardinii</i> indicate that choanocytes may give rise to mesohyl cells through migration. The number of apoptotic cells in tissues of both species is insignificant, although being comparable to the renewing tissues of other animals. <i>In vivo</i> studies with tetramethylrhodamine ethyl ester and CellEvent Caspase-3/7 indicate that apoptosis might be independent of mitochondrial outer membrane permeabilization. Altogether, a combination of confocal laser scanning microscopy and flow cytometry provides a quantitative description of cell proliferation and apoptosis in sponges displaying either rapid growth or cell turnover.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138083505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Juan Sebastian Chahda, Priscilla Ambrosi, Claudia M. Mizutani
{"title":"The nested embryonic dorsal domains of BMP-target genes are not scaled to size during the evolution of Drosophila species","authors":"Juan Sebastian Chahda, Priscilla Ambrosi, Claudia M. Mizutani","doi":"10.1002/jez.b.23137","DOIUrl":"10.1002/jez.b.23137","url":null,"abstract":"<p>Egg size is a fast-evolving trait among Drosophilids expected to change the spatial distribution of morphogens that pattern the embryonic axes. Here we asked whether the patterning of the dorsal region of the embryo by the Decapentaplegic/Bone Morphogenetic Protein-4 (DPP/BMP-4) gradient is scaled among <i>Drosophila</i> species with different egg sizes. This region specifies the extra-embryonic tissue amnioserosa and the ectoderm. We find that the entire dorsal region scales with embryo size, but the gene expression patterns regulated by DPP are not proportional, suggesting that the DPP gradient is differentially scaled during evolution. To further test whether the DPP gradient can scale or not in <i>Drosophila melanogaster</i>, we created embryos with expanded dorsal regions that mimic changes in scale seen in other species and measured the resulting domains of DPP-target genes. We find that the proportions of these domains are not maintained, suggesting that the DPP gradient is unable to scale in the embryo. These and previous findings suggest that the embryonic dorso-ventral patterning lack scaling in the ventral and dorsal sides but is robust in the lateral region where the neuroectoderm is specified and two opposing gradients, Dorsal/NFkappa-B and DPP, intersect. We propose that the lack of scaling of the DPP gradient may contribute to changes in the size of the amnioserosa and the numbers of ectodermal cells with specific cortical tensions, which are expected to generate distinct mechanical forces for gastrulating embryos of different sizes.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2022-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b4/9a/JEZ-340-131.PMC9587137.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9276535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}