Limb loss shows recurrent phenotypic evolution across squamate lineages.Here,based on three de novo-assembled genomes of limbless lizards from different lineages,we showed that divergence of conserved non-coding eleme...Limb loss shows recurrent phenotypic evolution across squamate lineages.Here,based on three de novo-assembled genomes of limbless lizards from different lineages,we showed that divergence of conserved non-coding elements(CNEs)played an important role in limb development.These CNEs were associated with genes required for limb initiation and outgrowth,and with regulatory signals in the early stage of limb development.Importantly,we identified the extensive existence of insertions and deletions(In Dels)in the CNEs,with the numbers ranging from 111 to 756.Most of these CNEs with In Dels were lineagespecific in the limbless squamates.Nearby genes of these In Del CNEs were important to early limb formation,such as Tbx4,Fgf10,and Gli3.Based on functional experiments,we found that nucleotide mutations and In Dels both affected the regulatory function of the CNEs.Our study provides molecular evidence underlying limb loss in squamate reptiles from a developmental perspective and sheds light on the importance of regulatory element In Dels in phenotypic evolution.展开更多
基金the Strategic Priority Research Program of Chinese Academy of Sciences(XDB31000000)the National Natural Science Foundation of China(32220103004,32000296)+2 种基金the Second Tibetan Plateau Scientific Expedition and Research Program(2019QZKK0501)the International Partnership Program of Chinese Academy of Sciences(151751KYSB20190024)the Sichuan Science and Technology Program(2021JDJQ0002)。
文摘Limb loss shows recurrent phenotypic evolution across squamate lineages.Here,based on three de novo-assembled genomes of limbless lizards from different lineages,we showed that divergence of conserved non-coding elements(CNEs)played an important role in limb development.These CNEs were associated with genes required for limb initiation and outgrowth,and with regulatory signals in the early stage of limb development.Importantly,we identified the extensive existence of insertions and deletions(In Dels)in the CNEs,with the numbers ranging from 111 to 756.Most of these CNEs with In Dels were lineagespecific in the limbless squamates.Nearby genes of these In Del CNEs were important to early limb formation,such as Tbx4,Fgf10,and Gli3.Based on functional experiments,we found that nucleotide mutations and In Dels both affected the regulatory function of the CNEs.Our study provides molecular evidence underlying limb loss in squamate reptiles from a developmental perspective and sheds light on the importance of regulatory element In Dels in phenotypic evolution.
