Due to the unique microstructure and diverse opsin genes of the trinocular compound eye,stomatopoda possess an extraordinary ability to perceive multiple properties of light.They not only can detect natural light(NL)a...Due to the unique microstructure and diverse opsin genes of the trinocular compound eye,stomatopoda possess an extraordinary ability to perceive multiple properties of light.They not only can detect natural light(NL)and linearly polarized light(LPL),but also are the only animals capable of recognizing circularly polarized light(CPL).Here,we integrated single-cell RNA sequencing,previously published Illumina data,and in-situ hybridization(ISH)to quantify and localize functional opsin genes in Oratosquilla oratoria,a common stomatopoda species in the China Sea.A total of high-quality 31777 cells were captured for the first time in the O.oratoria compound eye,which were classified into 25 cell subpopulations,and hypothesized that cluster 22 is a critical cell subpopulation responsible for light(whether NL,LPL,or CPL)response in O.oratoria.Furthermore,we propose that the long-wavelengthsensitive opsin gene(lws)gene family,retinol dehydrogenase(rdh),voltage-gated ion channel(vgic),arrestin(arr),and myosin(myo)collectively mediate the light response in O.oratoria.Considering that very few vision-related opsin genes show differential expression in right-handed CPL(RCPL)-vs.-dark(DL),which provides additional evidence that stomatopoda cannot recognize RCPL.Meanwhile,we believe that UV-stimulated scaffold protein A(uvssa)and red pigment concentrating hormone(rpch)play special contributions in the left-handed CPL(LCPL)environment response.ISH revealing that 16 lws,6 middle-wavelength-sensitive(mws),and 2 ultraviolet(uv)opsin genes were expressed in the photoreceptors of the O.oratoria compound eye.Although the inability to determine the functional types of cell subpopulations limits the resolution of opsin genes,these findings systematically elucidate the specific expression patterns of opsin genes in O.oratoria and represent a significant step toward refining the visual ecological theory of O.oratoria and other stomatopod species.展开更多
Eye degeneration is a common troglomorphic character of cave-dwelling organisms. Comparing the morphology and molecular biology of cave species and their close surface relatives is a powerful tool for studying regress...Eye degeneration is a common troglomorphic character of cave-dwelling organisms. Comparing the morphology and molecular biology of cave species and their close surface relatives is a powerful tool for studying regressive eye evolution and other adaptive phenotypes. We compared two co-occurring and closely-related species of the fish genus Sinocyclocheilus, which is endemic to China and includes both surface- and cave-dwelling species. Sinocyclocheilus tileihornes, a cave species, had smaller eyes than Sinocyclocheilus angustiporus, a surface species. Histological and immunohistochemical analyses revealed that the cave- fish had shorter cones and more disorderly rods than did the surface-dwelling species. Using quantitative PCR and in situ hybri- dization, we found that rhodopsin and a long-wavelength sensitive opsin had significantly lower expression levels in the cavefish. Furthermore, one of two short-wavelength-sensitive opsins was expressed at significantly higher levels in the cavefish. Changes in the expression ofopsin genes may have played a role in the degeneration of cavefish eyes [Current Zoology 59 （2）： 170-174, 2013].展开更多
Reptiles are the most morphologically and physiologically diverse tetrapods,with the squamates having the most diverse habitats.Lizard is an important model system for understanding the role of visual ecology,phylogen...Reptiles are the most morphologically and physiologically diverse tetrapods,with the squamates having the most diverse habitats.Lizard is an important model system for understanding the role of visual ecology,phylogeny and behavior on the structure of visual systems.In this study,we compared three opsin genes(RH2,LWS and SWS1)among 49 reptile species to detect positively selected genes as well as amino acid sites.Our results indicated that visual opsin genes have undergone divergent selection pressures in all lizards and RH2 and LWS suffered stronger positive selection than SWS1.Twelve positively selected sites were picked out for RH2 and LWS.Moreover,many diagnostic sites were found between geckos and non-gecko lizards,most of which were located near the positively selected sites and some of them have already been reported to be responsible for significant shifts of the wavelength of maximum absorption(λ_(max)).The results indicated that the gecko lineage accelerated the evolution of these genes to adapt to the dim-light environment or nocturnality as well as the switch between nocturnality and diurnality.展开更多
With the appearance of eutherian mammals,3 visual pigments were retained in their retina,mediating light sensitivity.Of them,rhodopsin is expressed in rod photoreceptor celis to conduct dim-light vision,while the othe...With the appearance of eutherian mammals,3 visual pigments were retained in their retina,mediating light sensitivity.Of them,rhodopsin is expressed in rod photoreceptor celis to conduct dim-light vision,while the other 2 visual pigments,middle/long wavelength-sensitive(M/LWS)and short wavelength-sensitive type 1(SWS1)visual pigments,expressed in cones are for color vision(Chi et al.2020).Murid rodents(order Rodentia:family Muridae),originated 17-22 million years ago(Mya)and represent more than 10%of living mammal species(Aghova et al.2018).Within these murid species,their SWS1 pigment retained the ancestral ultraviolet(UV)sensitivity,which is generally associated with a nocturnal lifestyle(Emerling et al.2015).In contrast,the spectral sensitivities of murid M/LWS are more diversifed,with wavelengths of maximum absorption(amax)ranging from 490 to 509 nm(Yokoyama et al.2008;Chi et al.2020).展开更多
The large yellow croaker(Larimichthys crocea)is a flagship marine fish in China given its extreme commercial value and golden-yellow coloration.However,the genetic mechanisms underlying golden-yellow coloration remain...The large yellow croaker(Larimichthys crocea)is a flagship marine fish in China given its extreme commercial value and golden-yellow coloration.However,the genetic mechanisms underlying golden-yellow coloration remain unclear.Here,we construct a telomere-to-telomere gap-free genome assembly(T2TLarcro_1.0)spanning 716.87 Mb,with a contig N50 of 31.75 Mb.Compared to the current reference genome(L_crocea_2.0),T2T-Larcro_1.0 incorporates 112.70 Mb of previously unassembled regions and 2368 newly anchored genes.This assembly facilitates comparative genomics analyses in sciaenids by identifying several candidate genes(e.g.,OPNVA,nNOS,RDH13)potentially involved in evolution of golden-yellow coloration.Transcriptomic analyses further confirm expression of OPNVA-encoded vertebrate ancient opsin(VA opsin)in skin tissues of the large yellow croaker,suggesting its role as an extraretinal photoreceptor regulating localized golden-yellow coloration.Integrating genomics and transcriptomics results,we uncover the triggering effect of VA opsin linking skin and neural photoreception to physiological regulation of body color change(golden-yellow to silvery-white)in L.crocea.Collectively,our findings provide molecular evidence that elucidate the underlying evolutionary mechanism of goldenyellow coloration in L.crocea.This high-quality genome assembly also serves as an improved resource for biological evolution,genetic improvement,and selective breeding of L.crocea.展开更多
基金Supported by the Natural Science Foundation of Shandong Province(No.ZR2021QD110)the National Natural Science Foundation of China(No.42106128)。
文摘Due to the unique microstructure and diverse opsin genes of the trinocular compound eye,stomatopoda possess an extraordinary ability to perceive multiple properties of light.They not only can detect natural light(NL)and linearly polarized light(LPL),but also are the only animals capable of recognizing circularly polarized light(CPL).Here,we integrated single-cell RNA sequencing,previously published Illumina data,and in-situ hybridization(ISH)to quantify and localize functional opsin genes in Oratosquilla oratoria,a common stomatopoda species in the China Sea.A total of high-quality 31777 cells were captured for the first time in the O.oratoria compound eye,which were classified into 25 cell subpopulations,and hypothesized that cluster 22 is a critical cell subpopulation responsible for light(whether NL,LPL,or CPL)response in O.oratoria.Furthermore,we propose that the long-wavelengthsensitive opsin gene(lws)gene family,retinol dehydrogenase(rdh),voltage-gated ion channel(vgic),arrestin(arr),and myosin(myo)collectively mediate the light response in O.oratoria.Considering that very few vision-related opsin genes show differential expression in right-handed CPL(RCPL)-vs.-dark(DL),which provides additional evidence that stomatopoda cannot recognize RCPL.Meanwhile,we believe that UV-stimulated scaffold protein A(uvssa)and red pigment concentrating hormone(rpch)play special contributions in the left-handed CPL(LCPL)environment response.ISH revealing that 16 lws,6 middle-wavelength-sensitive(mws),and 2 ultraviolet(uv)opsin genes were expressed in the photoreceptors of the O.oratoria compound eye.Although the inability to determine the functional types of cell subpopulations limits the resolution of opsin genes,these findings systematically elucidate the specific expression patterns of opsin genes in O.oratoria and represent a significant step toward refining the visual ecological theory of O.oratoria and other stomatopod species.
文摘Eye degeneration is a common troglomorphic character of cave-dwelling organisms. Comparing the morphology and molecular biology of cave species and their close surface relatives is a powerful tool for studying regressive eye evolution and other adaptive phenotypes. We compared two co-occurring and closely-related species of the fish genus Sinocyclocheilus, which is endemic to China and includes both surface- and cave-dwelling species. Sinocyclocheilus tileihornes, a cave species, had smaller eyes than Sinocyclocheilus angustiporus, a surface species. Histological and immunohistochemical analyses revealed that the cave- fish had shorter cones and more disorderly rods than did the surface-dwelling species. Using quantitative PCR and in situ hybri- dization, we found that rhodopsin and a long-wavelength sensitive opsin had significantly lower expression levels in the cavefish. Furthermore, one of two short-wavelength-sensitive opsins was expressed at significantly higher levels in the cavefish. Changes in the expression ofopsin genes may have played a role in the degeneration of cavefish eyes [Current Zoology 59 （2）： 170-174, 2013].
基金Financial support was provided by the National Natural Science Foundation of China(NSFC)(Grant No.31672269,31000949 to J.YAN)the Natural Science Foundation of the Jiangsu Higher Education Institutions of China(19KJA330001 to P.LI)+1 种基金the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)Top-Notch Academic Programs Project of Jiangsu Higher Education Institutions(TAPP,PPZY2015B117)。
文摘Reptiles are the most morphologically and physiologically diverse tetrapods,with the squamates having the most diverse habitats.Lizard is an important model system for understanding the role of visual ecology,phylogeny and behavior on the structure of visual systems.In this study,we compared three opsin genes(RH2,LWS and SWS1)among 49 reptile species to detect positively selected genes as well as amino acid sites.Our results indicated that visual opsin genes have undergone divergent selection pressures in all lizards and RH2 and LWS suffered stronger positive selection than SWS1.Twelve positively selected sites were picked out for RH2 and LWS.Moreover,many diagnostic sites were found between geckos and non-gecko lizards,most of which were located near the positively selected sites and some of them have already been reported to be responsible for significant shifts of the wavelength of maximum absorption(λ_(max)).The results indicated that the gecko lineage accelerated the evolution of these genes to adapt to the dim-light environment or nocturnality as well as the switch between nocturnality and diurnality.
基金supported by the Natural Science Basic Research Program of Shaanxi(2022JQ-169)the China Postdoctoral Science Foundation(2021M702063)to S.S.,the National Natural Science Foundation of China(32270462)the Fundamental Research Funds for the Central Universities(GK202401001)to Y.L.
文摘With the appearance of eutherian mammals,3 visual pigments were retained in their retina,mediating light sensitivity.Of them,rhodopsin is expressed in rod photoreceptor celis to conduct dim-light vision,while the other 2 visual pigments,middle/long wavelength-sensitive(M/LWS)and short wavelength-sensitive type 1(SWS1)visual pigments,expressed in cones are for color vision(Chi et al.2020).Murid rodents(order Rodentia:family Muridae),originated 17-22 million years ago(Mya)and represent more than 10%of living mammal species(Aghova et al.2018).Within these murid species,their SWS1 pigment retained the ancestral ultraviolet(UV)sensitivity,which is generally associated with a nocturnal lifestyle(Emerling et al.2015).In contrast,the spectral sensitivities of murid M/LWS are more diversifed,with wavelengths of maximum absorption(amax)ranging from 490 to 509 nm(Yokoyama et al.2008;Chi et al.2020).
基金supported by the National Key Research and Development Program of China(2023YFD2401901)the Fundamental Research Funds for Zhejiang Provincial Universities and Research Institutes(2024J004)。
文摘The large yellow croaker(Larimichthys crocea)is a flagship marine fish in China given its extreme commercial value and golden-yellow coloration.However,the genetic mechanisms underlying golden-yellow coloration remain unclear.Here,we construct a telomere-to-telomere gap-free genome assembly(T2TLarcro_1.0)spanning 716.87 Mb,with a contig N50 of 31.75 Mb.Compared to the current reference genome(L_crocea_2.0),T2T-Larcro_1.0 incorporates 112.70 Mb of previously unassembled regions and 2368 newly anchored genes.This assembly facilitates comparative genomics analyses in sciaenids by identifying several candidate genes(e.g.,OPNVA,nNOS,RDH13)potentially involved in evolution of golden-yellow coloration.Transcriptomic analyses further confirm expression of OPNVA-encoded vertebrate ancient opsin(VA opsin)in skin tissues of the large yellow croaker,suggesting its role as an extraretinal photoreceptor regulating localized golden-yellow coloration.Integrating genomics and transcriptomics results,we uncover the triggering effect of VA opsin linking skin and neural photoreception to physiological regulation of body color change(golden-yellow to silvery-white)in L.crocea.Collectively,our findings provide molecular evidence that elucidate the underlying evolutionary mechanism of goldenyellow coloration in L.crocea.This high-quality genome assembly also serves as an improved resource for biological evolution,genetic improvement,and selective breeding of L.crocea.
