Journal of experimental zoology. Part B, Molecular and developmental evolution最新文献

{"title":"Cave beetle lineages gained genes before going down under: An example of repeated genomic exaptation?","authors":"Markus Friedrich","doi":"10.1002/jez.b.23245","DOIUrl":"10.1002/jez.b.23245","url":null,"abstract":"<p>The adaptation of animals to subterranean habitats like caves and aquifers stereotypically leads to dramatic trait-loss consequences like the lack of eyes and body pigmentation. These body plan regression trends are expected to be tied to gene loss as well. Indeed, previous studies documented the degeneration of vision genes in obligate cave dwellers. Contradicting this picture, the first broad-scale comparative transcriptome-wide study of gene content evolution in separate subterranean Australian and Mediterranean beetle clades unearthed evidence of global gene gain and retention. This suggests that the transition to cave life may be more contingent on gene repertoire expansion than contraction. Future studies, however, will need to examine how much the observed patterns of gene content evolution reflect subfunctionalization and fitness-securing genetic redundancy outcomes following gene duplication as opposed to adaptive trajectories.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 4","pages":"380-384"},"PeriodicalIF":2.2,"publicationDate":"2024-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139899989","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":"Cis-regulatory control of mammalian Trps1 gene expression","authors":"Muhammad Abrar,&nbsp;Shahid Ali,&nbsp;Irfan Hussain,&nbsp;Hizran Khatoon,&nbsp;Fatima Batool,&nbsp;Shakira Ghazanfar,&nbsp;Dylan Corcoran,&nbsp;Yasuhiko Kawakami,&nbsp;Amir Ali Abbasi","doi":"10.1002/jez.b.23246","DOIUrl":"10.1002/jez.b.23246","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 <p><i>TRPS1</i> serves as the causative gene for tricho-rhino phalangeal syndrome, known for its craniofacial and skeletal abnormalities. The <i>Trps1</i> gene encodes a protein that represses Wnt signaling through strong interactions with Wnt signaling inhibitors. The identification of genomic cis-acting regulatory sequences governing <i>Trps1</i> expression is crucial for understanding its role in embryogenesis. Nevertheless, to date, no investigations have been conducted concerning these aspects of <i>Trps1</i>. To identify deeply conserved noncoding elements (CNEs) within the <i>Trps1</i> locus, we employed a comparative genomics approach, utilizing slowly evolving fish such as coelacanth and spotted gar. These analyses resulted in the identification of eight CNEs in the intronic region of the <i>Trps1</i> gene. Functional characterization of these CNEs in zebrafish revealed their regulatory potential in various tissues, including pectoral fins, heart, and pharyngeal arches. RNA in-situ hybridization experiments revealed concordance between the reporter expression pattern induced by the identified set of CNEs and the spatial expression pattern of the <i>trps1</i> gene in zebrafish. Comparative in vivo data from zebrafish and mice for CNE7/hs919 revealed conserved functions of these enhancers. Each of these eight CNEs was further investigated in cell line-based reporter assays, revealing their repressive potential. Taken together, in vivo and in vitro assays suggest a context-dependent dual functionality for the identified set of <i>Trps1</i>-associated CNE enhancers. This functionally characterized set of CNE-enhancers will contribute to a more comprehensive understanding of the developmental roles of <i>Trps1</i> and can aid in the identification of noncoding DNA variants associated with human diseases.</p>\u0000 </section>\u0000 </div>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 2","pages":"85-100"},"PeriodicalIF":2.2,"publicationDate":"2024-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139899990","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":"A review of the reproductive biology of mormyroid fishes: An emerging model for biomedical research","authors":"Alyssa N. Saunders,&nbsp;Jason R. Gallant","doi":"10.1002/jez.b.23242","DOIUrl":"10.1002/jez.b.23242","url":null,"abstract":"<p>Mormyroidea is a superfamily of weakly electric African fishes with great potential as a model in a variety of biomedical research areas including systems neuroscience, muscle cell and craniofacial development, ion channel biophysics, and flagellar/ciliary biology. However, they are currently difficult to breed in the laboratory setting, which is essential for any tractable model organism. As such, there is a need to better understand the reproductive biology of mormyroids to breed them more reliably in the laboratory to effectively use them as a biomedical research model. This review seeks to (1) briefly highlight the biomedically relevant phenotypes of mormyroids and (2) compile information about mormyroid reproduction including sex differences, breeding season, sexual maturity, gonads, gametes, and courtship/spawning behaviors. We also highlight areas of mormyroid reproductive biology that are currently unexplored and/or have the potential for further investigation that may provide insights into more successful mormyroid laboratory breeding methods.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"144-163"},"PeriodicalIF":2.2,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23242","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139741159","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":"Anciently duplicated genes continuously recruited to heart expression in vertebrate evolution are associated with heart chamber increase","authors":"Yangyun Zou,&nbsp;Jingwen Yang,&nbsp;Jingqi Zhou,&nbsp;Gangbiao Liu,&nbsp;Libing Shen,&nbsp;Zhan Zhou,&nbsp;Zhixi Su,&nbsp;Xun Gu","doi":"10.1002/jez.b.23248","DOIUrl":"10.1002/jez.b.23248","url":null,"abstract":"<p>Although gene/genome duplications in the early stage of vertebrates have been thought to provide major resources of raw genetic materials for evolutionary innovations, it is unclear whether they continuously contribute to the evolution of morphological complexity during the course of vertebrate evolution, such as the evolution from two heart chambers (fishes) to four heart chambers (mammals and birds). We addressed this issue by our heart RNA-Seq experiments combined with published data, using 13 vertebrates and one invertebrate (sea squirt, as an outgroup). Our evolutionary transcriptome analysis showed that number of ancient paralogous genes expressed in heart tends to increase with the increase of heart chamber number along the vertebrate phylogeny, in spite that most of them were duplicated at the time near to the origin of vertebrates or even more ancient. Moreover, those paralogs expressed in heart exert considerably different functions from heart-expressed singletons: the former are functionally enriched in cardiac muscle and muscle contraction-related categories, whereas the latter play more basic functions of energy generation like aerobic respiration. These findings together support the notion that recruiting anciently paralogous genes that are expressed in heart is associated with the increase of chamber number in vertebrate evolution.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 2","pages":"106-114"},"PeriodicalIF":2.2,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139741160","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":"Both-strand gene coding in a plastome-like mitogenome of an enoplid nematode","authors":"Olga V. Nikolaeva,&nbsp;Leonid Yu Rusin,&nbsp;Kirill V. Mikhailov,&nbsp;Vladimir V. Aleoshin,&nbsp;Paul De Ley","doi":"10.1002/jez.b.23241","DOIUrl":"10.1002/jez.b.23241","url":null,"abstract":"<p>The phylum Nematoda remains very poorly sampled for mtDNA, with a strong bias toward parasitic, economically important or model species of the Chromadoria lineage. Most chromadorian mitogenomes share a specific order of genes encoded on one mtDNA strand. However, the few sequenced representatives of the Dorylaimia lineage exhibit a variable order of mtDNA genes encoded on both strands. While the ancestral arrangement of nematode mitogenome remains undefined, no evidence has been reported for Enoplia, the phylum's third early divergent major lineage. We describe the first mitogenome of an enoplian nematode, <i>Campydora demonstrans</i>, and contend that the complete 37-gene repertoire and both-strand gene encoding are ancestral states preserved in Enoplia and Dorylaimia versus the derived mitogenome arrangement in some Chromadoria. The <i>C. demonstrans</i> mitogenome is 17,018 bp in size and contains a noncoding perfect inverted repeat with 2013 bp-long arms, subdividing the mitogenome into two coding regions. This mtDNA arrangement is very rare among animals and instead resembles that of chloroplast genomes in land plants. Our report broadens mtDNA taxonomic sampling of the phylum Nematoda and adds support to the applicability of <i>cox1</i> gene as a phylogenetic marker for establishing nematode relationships within higher taxa.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 6","pages":"419-424"},"PeriodicalIF":1.8,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691996","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":"Substantial gene expression shifts during larval transitions in the pearl oyster Pinctada margaritifera","authors":"T. Destanque,&nbsp;J. Le Luyer,&nbsp;V. Quillien,&nbsp;M. Sham Koua,&nbsp;P. Auffrey,&nbsp;C.-L. Ky","doi":"10.1002/jez.b.23243","DOIUrl":"10.1002/jez.b.23243","url":null,"abstract":"<p>Early development stages in marine bivalve are critical periods where larvae transition from pelagic free-life to sessile mature individuals. The successive metamorphosis requires the expression of key genes, the functions of which might be under high selective pressure, hence understanding larval development represents key knowledge for both fundamental and applied research. Phenotypic larvae development is well known, but the underlying molecular mechanisms such as associated gene expression dynamic and molecular cross-talks remains poorly described for several nonmodel species, such as <i>P. margaritifera</i>. We designed a whole transcriptome RNA-sequencing analysis to describe such gene expression dynamics following four larval developmental stages: \u0000<span>d</span>-shape, Veliger, Umbo and Eye-spot. Larval gene expression and annotated functions drastically diverge. Metabolic function (gene expression related to lipid, amino acid and carbohydrate use) is highly upregulated in the first development stages, with increasing demand from \u0000<span>d</span>-shape to umbo. Morphogenesis and larval transition are partly ordered by Thyroid hormones and Wnt signaling. While larvae shells show some similar characteristic to adult shells, the cause of initialization of biomineralization differ from the one found in adults. The present study provides a global overview of <i>Pinctada margaritifera</i> larval stages <i>transitioning</i> through gene expression dynamics, molecular mechanisms and ontogeny of biomineralization, immune system, and sensory perception processes.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 2","pages":"76-84"},"PeriodicalIF":2.2,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23243","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691997","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":"Acclimation of intertidally reproducing sea-snails protects embryos from lethal effects of transient hyperthermia","authors":"Morgan Q. Goulding","doi":"10.1002/jez.b.23240","DOIUrl":"10.1002/jez.b.23240","url":null,"abstract":"<p>Embryos of <i>Ilyanassa obsoleta</i> (from Massachusetts and Florida) and <i>Phrontis vibex</i> (from Florida) were exposed to temperatures from 33 to 37°C. In both species, very young embryos are especially sensitive to thermal stress. Brief early heat shock did not disturb spiral cleavage geometry but led to variable, typically severe defects in larval morphogenesis and tissue differentiation. In <i>Ilyanassa</i> but not <i>P. vibex</i>, early heat shock resulted in immediate slowing or arrest of interphase progression during early cleavage. This reversible arrest was correlated with improved prognosis for larval development and (in Massachusetts snails, at least) depended on parental acclimation to warm temperature (~25.5°C). Embryos from Massachusetts snails housed at lower temperature (16°C) exhibited cytokinesis failure when briefly incubated at 33°C during early cleavage, and tissue differentiation failure during incubation at 33°C begun at later stages. This preliminary study reveals a case in which stress-conditioned parents may endow embryos with protection against potentially lethal thermal stress during the most vulnerable stages of life.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 2","pages":"101-105"},"PeriodicalIF":2.2,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139642275","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":"Unraveling stress resilience: Insights from adaptations to extreme environments by Astyanax mexicanus cavefish","authors":"Ansa E. Cobham,&nbsp;Nicolas Rohner","doi":"10.1002/jez.b.23238","DOIUrl":"10.1002/jez.b.23238","url":null,"abstract":"<p>Extreme environmental conditions have profound impacts on shaping the evolutionary trajectory of organisms. Exposure to these conditions elicits stress responses, that can trigger phenotypic changes in novel directions. The Mexican Tetra, <i>Astyanax mexicanus</i>, is an excellent model for understanding evolutionary mechanisms in response to extreme or new environments. This fish species consists of two morphs; the classical surface-dwelling fish and the blind cave-dwellers that inhabit dark and biodiversity-reduced ecosystems. In this review, we explore the specific stressors present in cave environments and examine the diverse adaptive strategies employed by cave populations to not only survive but thrive as successful colonizers. By analyzing the evolutionary responses of <i>A. mexicanus</i>, we gain valuable insights into the genetic, physiological, and behavioral adaptations that enable organisms to flourish under challenging environmental conditions.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"178-188"},"PeriodicalIF":2.2,"publicationDate":"2024-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23238","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512550","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":"In the Spotlight—Early Career Researcher","authors":"B. Duygu Özpolat","doi":"10.1002/jez.b.23239","DOIUrl":"10.1002/jez.b.23239","url":null,"abstract":"","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 2","pages":"63-64"},"PeriodicalIF":2.2,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139491563","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":"3D spheroid culturing of Astyanax mexicanus liver-derived cell lines recapitulates distinct transcriptomic and metabolic states of in vivo tissue environment","authors":"Tathagata Biswas,&nbsp;Naresh Rajendran,&nbsp;Huzaifa Hassan,&nbsp;Hua Li,&nbsp;Chongbei Zhao,&nbsp;Nicolas Rohner","doi":"10.1002/jez.b.23236","DOIUrl":"10.1002/jez.b.23236","url":null,"abstract":"<p>In vitro assays are crucial tools for gaining detailed insights into various biological processes, including metabolism. Cave morphs of the river-dwelling fish species, <i>Astyanax mexicanus</i>, have adapted their metabolism allowing them to thrive in the biodiversity-deprived and nutrient-limited environment of caves. Liver-derived cells from the cave and river morphs of <i>A. mexicanus</i> have proven to be excellent in vitro resources to better understand the unique metabolism of these fish. However, the current 2D cultures have not fully captured the complex metabolic profile of the <i>Astyanax</i> liver. It is known that 3D culturing can modulate the transcriptomic state of cells when compared to its 2D monolayer culture. Therefore, to broaden the possibilities of the in vitro system by modeling a wider gamut of metabolic pathways, we cultured the liver-derived <i>Astyanax</i> cells of both surface and cavefish into 3D spheroids. We successfully established 3D cultures at various cell seeding densities for several weeks and characterized the resultant transcriptomic and metabolic variations. We found that the 3D cultured <i>Astyanax</i> cells exhibit an altered transcriptomic profile and consequently represent a wider range of metabolic pathways, including cell cycle changes and antioxidant activities, associated with liver functioning as compared to its monolayer culture. Enzymatic assay measuring antioxidants in 2D culture and 3D spheroids also revealed enhanced antioxidative capacity of 3D cultured spheroids, in line with the differential gene expression data. Additionally, the spheroids also exhibited surface and cave-specific metabolic signatures, making it a suitable system for evolutionary studies associated with cave adaptation. Notably, cavefish derived spheroids enriched for genes responding to xenobiotic stimulus, while the ones from surface enriched for immune response, both of which resonated with known physiologically adaptations associated with each morph. Taken together, the liver-derived spheroids prove to be a promising in vitro model for widening our understanding of metabolism in <i>A. mexicanus</i> and of vertebrates in general.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"342 3","pages":"301-312"},"PeriodicalIF":2.2,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23236","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139403055","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}