The inverted retina is a basic characteristic of the vertebrate eye.This implies that vertebrates must have a common ancestor with an inverted retina.Of the two groups of chordates,cephalochordates have an inverted re...The inverted retina is a basic characteristic of the vertebrate eye.This implies that vertebrates must have a common ancestor with an inverted retina.Of the two groups of chordates,cephalochordates have an inverted retina and urochordates a direct retina.Surprisingly,recent genetics studies favor urochordates as the closest ancestor to vertebrates.The evolution of increasingly complex organs such as the eye implies not only tissular but also structural modifications at the organ level.How these configurational modifications give rise to a functional eye at any step is still subject to debate and speculation.Here we propose an orderly sequence of phylogenetic events that closely follows the sequence of developmental eye formation in extant vertebrates.The progressive structural complexity has been clearly recorded during vertebrate development at the period of organogenesis.Matching the chain of increasing eye complexity in Mollusca that leads to the bicameral eye of the octopus and the developmental sequence in vertebrates,we delineate the parallel evolution of the two-chambered eye of vertebrates starting with an early ectodermal eye.This sequence allows for some interesting predictions regarding the eyes of not preserved intermediary species.The clue to understanding the inverted retina of vertebrates and the similarity between the sequence followed by Mollusca and chordates is the notion that the eye in both cases is an ectodermal structure,in contrast to an exclusively(de novo)neuroectodermal origin in the eye of vertebrates.This analysis places cephalochordates as the closest branch to vertebrates contrary to urochordates,claimed as a closer branch by some researchers that base their proposals in a genetic analysis.展开更多
Aim was to gather relevant knowledge in evolution and development to find a rational explanation for the intricate and elaborate anatomy of the nose. According to classic embryology, the philtrum of the upper lip, nas...Aim was to gather relevant knowledge in evolution and development to find a rational explanation for the intricate and elaborate anatomy of the nose. According to classic embryology, the philtrum of the upper lip, nasal dorsum, septum and primary palate develop from the intermaxillary process, and the lateral walls of the nasal pyramid from the lateral nasal processes. The palatal shelves, which are outgrowths of the maxillary processes, form the secondary palate. The median nasal septum develops inferiorly from the roof of the nasal cavity. These valuable embryologic data do not explain the complex intricacy of the many anatomical structures comprising the nose. The evo-devo theory offers a rational explanation to this complex anatomy. Phylogenically, the nose develops as an olfactory organ in fish before becoming respiratory in tetrapods. During development, infolding of the olfactory placodes occurs, bringing the medial olfactory processes to form the septolateral cartilage while the lateral olfactory processes form the alar cartilages. The olfactory fascia units these cartilages to the olfactory mucosa, that stays separated from brain by the cartilaginous olfactory capsule(the ethmoid bone forerunner). Phylogenically, the respiratory nose develops between mouth and olfactory nose by rearrangement of the dermal bones of the secondary palate, which appears in early tetrapods. During development, the palatal shelves develop into the palatine processes of the maxillary bones, and with the vomer, palatine, pterygoid and inferior turbinate bones form the walls of the nasal cavity after regression of the transverse lamina. Applying the evolutionary developmental biology(evo-devo) discipline on our present knowledge of development, anatomy and physiology of the nose, significantly expands and places this knowledge in proper perspective. The clinicopathologies of nasal polyposis, for example, occurs specifically in the ethmoid labyrinth or, woodworker's adenocarcinomas, occurring only in the olfactory cleft can now be explained by employing the evo-devo approach. A full understanding of the evo-devo discipline, as it pertains to head and neck anatomy, has profound implications to the otolaryngologist empowering his skills and abilities, and ultimately translating in improving surgical outcomes and maximizing patient care.展开更多
The flower is an evolutionary innovation in angiosperms that drives the evolution of biodiversity.The carpel is integral to a flower and develops into fruits after fertilization,while the perianth,consisting of the ca...The flower is an evolutionary innovation in angiosperms that drives the evolution of biodiversity.The carpel is integral to a flower and develops into fruits after fertilization,while the perianth,consisting of the calyx and corolla,is decorative to facilitate pollination and protect the internal organs,including the carpels and stamens.Therefore,the nature of flower origin is carpel and stamen origin,which represents one of the greatest and fundamental unresolved issues in plant evolutionary biology.Here,we briefly summarize the main progress and key genes identified for understanding floral development,focusing on the origin and development of the carpels.Floral ABC models have played pioneering roles in elucidating flower development,but remain insufficient for resolving flower and carpel origin.The genetic basis for carpel origin and subsequent diversification leading to fruit diversity also remains elusive.Based on current research progress and technological advances,simplified floral models and integrative evolutionary-developmental(evodevo)strategies are proposed for elucidating the genetics of carpel origin and fruit evolution.Stepwise birth of a few master regulatory genes and subsequent functional diversification might play a pivotal role in these evolutionary processes.Among the identified transcription factors,AGAMOUS(AG)and CRABS CLAW(CRC)may be the two core regulatory genes for carpel origin as they determine carpel organ identity,determinacy,and functionality.Therefore,a comparative identification of their protein-protein interactions and downstream target genes between flowering and non-flowering plants from an evo-devo perspective may be primary projects for elucidating carpel origin and development.展开更多
The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers.We analyzed 897 transcriptomes from three Cetartiodactyla lineages:rumi...The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers.We analyzed 897 transcriptomes from three Cetartiodactyla lineages:ruminants,camels and cetaceans,as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations.We identified genes with relatively high expression in the rumen,of which many appeared to be recruited from other tissues.These genes show functional enrichment in ketone body metabolism,regulation of microbial community,and epithelium absorption,which are the most prominent biological processes involved in rumen innovations.Several modes of genetic change underlying rumen functional innovations were uncovered,including coding mutations,genes newly evolved,and changes of regulatory elements.We validated that the key ketogenesis rate-limiting gene(HMGCS2)with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals.Two newly evolved genes(LYZ1 and DEFB1)are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium.Furthermore,we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment.These results greatly improve our understanding of rumen evolution and organ evo-devo in general.展开更多
The N6-methylation of RNA adenosines(N6-methyladenosine,m^(6)A)is an important regulator of gene expression with critical implications in vertebrate and insect development.However,the developmental significance of epi...The N6-methylation of RNA adenosines(N6-methyladenosine,m^(6)A)is an important regulator of gene expression with critical implications in vertebrate and insect development.However,the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown.Using methylated RNA immunoprecipitation sequencing(MeRIP-seq),we generated transcriptome-wide m^(6)A-RNA methylomes covering the entire development of the oyster from oocytes to juveniles.Oyster RNA classes display specific m^(6)A signatures,with messenger RNAs(mRNAs)and long non-coding RNAs(lncRNAs)exhibiting distinct profiles and being highly methylated compared to transposable element(TE)transcripts.Epitranscriptomes are dynamic and correspond to the chronological steps of development(cleavage,gastrulation,organogenesis,and metamorphosis),with minimal mRNA and lncRNA methylation at the morula stage followed by a global increase.mRNA m^(6)A levels are correlated with transcript levels,and shifts in methylation profiles correspond to expression kinetics.Differentially methylated transcripts cluster according to embryo-larval stages and bear the corresponding developmental functions(cell division,signal transduction,morphogenesis,and cell differentiation).The m^(6)A level of TE transcripts is also regulated and peaks during the gastrulation.We demonstrate that m^(6)A-RNA methylomes are dynamic and associated with gene expression regulation during oyster development.The putative epitranscriptome implication in the cleavage,maternal-to-zygotic transition,and cell differentiation in a lophotrochozoan model brings new insights into the control and evolution of developmental processes.展开更多
After more than one hundred fifty years of the publication of On the Origin of Species by Darwin, scientists are still arguing on the relative importance of mutation and natural selection, on the driving force of orga...After more than one hundred fifty years of the publication of On the Origin of Species by Darwin, scientists are still arguing on the relative importance of mutation and natural selection, on the driving force of organismal evolution, on microevo- lution and macroevolution, etc. Such periodically repeated debates appeared to have introduced more chaos than musings. What happened and why？ Have we really considered our views, opinions and arguments under the big picture of evolution before pos- ing the questions？ Or are we talking past each other？ We do need some reflections. While we believe that the current evolutionary theory is doing fine, perhaps a refinement or re-encapsulation of its knowledge framework can help promote a better understanding of the evolutionary science as a whole and blow offthe mist over the big picture [Current Zoology 61 （1）： 217-220, 2015 ].展开更多
Rewiring and reprogramming of transcriptional regulation took place during bacterial speciation. The mechanistic alterations among tran- scription factors, cis-regulatory elements and target genes confer bacteria nove...Rewiring and reprogramming of transcriptional regulation took place during bacterial speciation. The mechanistic alterations among tran- scription factors, cis-regulatory elements and target genes confer bacteria novel ability to adapt to stochastic environmental changes. This process is critical to their survival, especially for bacterial pathogens subjected to accelerated evolution. In the past two decades, the investigators not only completed the sequences of numerous bacterial genomes, but also made great progress in understanding the molecular basis of evolution. Here we briefly reviewed the current knowledge on the mechanistic changes among orthologous, paralogous and xenogenic regulatory circuits, which were caused by genetic recombinations such as gene duplication, horizontal gene transfer, transposable elements and different genetic contexts. We also discussed the potential impact of this area on theoretical and applied studies of microbes.展开更多
The paper introduces the classical ABC model of floral development and thereafter ABCD, ABCDE and quartet models, and presents achievements in the studies on floral evolution such as the improved understanding on the ...The paper introduces the classical ABC model of floral development and thereafter ABCD, ABCDE and quartet models, and presents achievements in the studies on floral evolution such as the improved understanding on the relationship of reproductive organs between gnetophytes and angiosperms, new results in perianth evolution and identified homology of floral organs between dicots and monocots. The evo-devo studies on plant taxa at different evolutionary levels are useful to better understanding the homology of floral organs, and to clarifying the mysteries of the origin and sub-sequent diversification of flowers.展开更多
文摘The inverted retina is a basic characteristic of the vertebrate eye.This implies that vertebrates must have a common ancestor with an inverted retina.Of the two groups of chordates,cephalochordates have an inverted retina and urochordates a direct retina.Surprisingly,recent genetics studies favor urochordates as the closest ancestor to vertebrates.The evolution of increasingly complex organs such as the eye implies not only tissular but also structural modifications at the organ level.How these configurational modifications give rise to a functional eye at any step is still subject to debate and speculation.Here we propose an orderly sequence of phylogenetic events that closely follows the sequence of developmental eye formation in extant vertebrates.The progressive structural complexity has been clearly recorded during vertebrate development at the period of organogenesis.Matching the chain of increasing eye complexity in Mollusca that leads to the bicameral eye of the octopus and the developmental sequence in vertebrates,we delineate the parallel evolution of the two-chambered eye of vertebrates starting with an early ectodermal eye.This sequence allows for some interesting predictions regarding the eyes of not preserved intermediary species.The clue to understanding the inverted retina of vertebrates and the similarity between the sequence followed by Mollusca and chordates is the notion that the eye in both cases is an ectodermal structure,in contrast to an exclusively(de novo)neuroectodermal origin in the eye of vertebrates.This analysis places cephalochordates as the closest branch to vertebrates contrary to urochordates,claimed as a closer branch by some researchers that base their proposals in a genetic analysis.
文摘Aim was to gather relevant knowledge in evolution and development to find a rational explanation for the intricate and elaborate anatomy of the nose. According to classic embryology, the philtrum of the upper lip, nasal dorsum, septum and primary palate develop from the intermaxillary process, and the lateral walls of the nasal pyramid from the lateral nasal processes. The palatal shelves, which are outgrowths of the maxillary processes, form the secondary palate. The median nasal septum develops inferiorly from the roof of the nasal cavity. These valuable embryologic data do not explain the complex intricacy of the many anatomical structures comprising the nose. The evo-devo theory offers a rational explanation to this complex anatomy. Phylogenically, the nose develops as an olfactory organ in fish before becoming respiratory in tetrapods. During development, infolding of the olfactory placodes occurs, bringing the medial olfactory processes to form the septolateral cartilage while the lateral olfactory processes form the alar cartilages. The olfactory fascia units these cartilages to the olfactory mucosa, that stays separated from brain by the cartilaginous olfactory capsule(the ethmoid bone forerunner). Phylogenically, the respiratory nose develops between mouth and olfactory nose by rearrangement of the dermal bones of the secondary palate, which appears in early tetrapods. During development, the palatal shelves develop into the palatine processes of the maxillary bones, and with the vomer, palatine, pterygoid and inferior turbinate bones form the walls of the nasal cavity after regression of the transverse lamina. Applying the evolutionary developmental biology(evo-devo) discipline on our present knowledge of development, anatomy and physiology of the nose, significantly expands and places this knowledge in proper perspective. The clinicopathologies of nasal polyposis, for example, occurs specifically in the ethmoid labyrinth or, woodworker's adenocarcinomas, occurring only in the olfactory cleft can now be explained by employing the evo-devo approach. A full understanding of the evo-devo discipline, as it pertains to head and neck anatomy, has profound implications to the otolaryngologist empowering his skills and abilities, and ultimately translating in improving surgical outcomes and maximizing patient care.
基金supported by grants from the National Natural Science Foundation of China(31930007)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB27010106)the K.C.Wong Education Foundation(GJTD-2020-05)。
文摘The flower is an evolutionary innovation in angiosperms that drives the evolution of biodiversity.The carpel is integral to a flower and develops into fruits after fertilization,while the perianth,consisting of the calyx and corolla,is decorative to facilitate pollination and protect the internal organs,including the carpels and stamens.Therefore,the nature of flower origin is carpel and stamen origin,which represents one of the greatest and fundamental unresolved issues in plant evolutionary biology.Here,we briefly summarize the main progress and key genes identified for understanding floral development,focusing on the origin and development of the carpels.Floral ABC models have played pioneering roles in elucidating flower development,but remain insufficient for resolving flower and carpel origin.The genetic basis for carpel origin and subsequent diversification leading to fruit diversity also remains elusive.Based on current research progress and technological advances,simplified floral models and integrative evolutionary-developmental(evodevo)strategies are proposed for elucidating the genetics of carpel origin and fruit evolution.Stepwise birth of a few master regulatory genes and subsequent functional diversification might play a pivotal role in these evolutionary processes.Among the identified transcription factors,AGAMOUS(AG)and CRABS CLAW(CRC)may be the two core regulatory genes for carpel origin as they determine carpel organ identity,determinacy,and functionality.Therefore,a comparative identification of their protein-protein interactions and downstream target genes between flowering and non-flowering plants from an evo-devo perspective may be primary projects for elucidating carpel origin and development.
基金supported by the National Natural Science Foundation of China(31822052,31572381)the National Thousand Youth Talents Plan to Y.J.+3 种基金National Natural Science Foundation of China(31660644)to S.H.National Natural Science Foundation of China(41422604)to S.L.The Villum Foundation(VKR 023447)the Independent Research Fund Denmark(8049-00098B)。
文摘The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers.We analyzed 897 transcriptomes from three Cetartiodactyla lineages:ruminants,camels and cetaceans,as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations.We identified genes with relatively high expression in the rumen,of which many appeared to be recruited from other tissues.These genes show functional enrichment in ketone body metabolism,regulation of microbial community,and epithelium absorption,which are the most prominent biological processes involved in rumen innovations.Several modes of genetic change underlying rumen functional innovations were uncovered,including coding mutations,genes newly evolved,and changes of regulatory elements.We validated that the key ketogenesis rate-limiting gene(HMGCS2)with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals.Two newly evolved genes(LYZ1 and DEFB1)are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium.Furthermore,we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment.These results greatly improve our understanding of rumen evolution and organ evo-devo in general.
基金supported by the French national program CNRS EC2CO ECODYN(Ecosphère Continentale et Cótière’HERITAGe’Grant No.2019-200919362L)awarded to Guillaume Rivière and the Council of the Normandy Region(RIN ECUMEGrant No.18E01643-18P02383)awarded to Pascal Favrel.
文摘The N6-methylation of RNA adenosines(N6-methyladenosine,m^(6)A)is an important regulator of gene expression with critical implications in vertebrate and insect development.However,the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown.Using methylated RNA immunoprecipitation sequencing(MeRIP-seq),we generated transcriptome-wide m^(6)A-RNA methylomes covering the entire development of the oyster from oocytes to juveniles.Oyster RNA classes display specific m^(6)A signatures,with messenger RNAs(mRNAs)and long non-coding RNAs(lncRNAs)exhibiting distinct profiles and being highly methylated compared to transposable element(TE)transcripts.Epitranscriptomes are dynamic and correspond to the chronological steps of development(cleavage,gastrulation,organogenesis,and metamorphosis),with minimal mRNA and lncRNA methylation at the morula stage followed by a global increase.mRNA m^(6)A levels are correlated with transcript levels,and shifts in methylation profiles correspond to expression kinetics.Differentially methylated transcripts cluster according to embryo-larval stages and bear the corresponding developmental functions(cell division,signal transduction,morphogenesis,and cell differentiation).The m^(6)A level of TE transcripts is also regulated and peaks during the gastrulation.We demonstrate that m^(6)A-RNA methylomes are dynamic and associated with gene expression regulation during oyster development.The putative epitranscriptome implication in the cleavage,maternal-to-zygotic transition,and cell differentiation in a lophotrochozoan model brings new insights into the control and evolution of developmental processes.
文摘After more than one hundred fifty years of the publication of On the Origin of Species by Darwin, scientists are still arguing on the relative importance of mutation and natural selection, on the driving force of organismal evolution, on microevo- lution and macroevolution, etc. Such periodically repeated debates appeared to have introduced more chaos than musings. What happened and why？ Have we really considered our views, opinions and arguments under the big picture of evolution before pos- ing the questions？ Or are we talking past each other？ We do need some reflections. While we believe that the current evolutionary theory is doing fine, perhaps a refinement or re-encapsulation of its knowledge framework can help promote a better understanding of the evolutionary science as a whole and blow offthe mist over the big picture [Current Zoology 61 （1）： 217-220, 2015 ].
基金supported by the National Basic Research Program(No.2011CB 100700)of the Ministry of Science and Technology of Chinathe National Natural Science Foundation of China(Nos.30771401 and 31070081)the Startup Fund from the Institute of Microbiology,Chinese Academy of Sciences
文摘Rewiring and reprogramming of transcriptional regulation took place during bacterial speciation. The mechanistic alterations among tran- scription factors, cis-regulatory elements and target genes confer bacteria novel ability to adapt to stochastic environmental changes. This process is critical to their survival, especially for bacterial pathogens subjected to accelerated evolution. In the past two decades, the investigators not only completed the sequences of numerous bacterial genomes, but also made great progress in understanding the molecular basis of evolution. Here we briefly reviewed the current knowledge on the mechanistic changes among orthologous, paralogous and xenogenic regulatory circuits, which were caused by genetic recombinations such as gene duplication, horizontal gene transfer, transposable elements and different genetic contexts. We also discussed the potential impact of this area on theoretical and applied studies of microbes.
基金supported by the National Natural Science Foundation of China(Grant Nos.30130030 and 30121003).
文摘The paper introduces the classical ABC model of floral development and thereafter ABCD, ABCDE and quartet models, and presents achievements in the studies on floral evolution such as the improved understanding on the relationship of reproductive organs between gnetophytes and angiosperms, new results in perianth evolution and identified homology of floral organs between dicots and monocots. The evo-devo studies on plant taxa at different evolutionary levels are useful to better understanding the homology of floral organs, and to clarifying the mysteries of the origin and sub-sequent diversification of flowers.
