Right before the excystment of an Euplotes encysti-cus sawtooth-like folds appeared among the pellicle plas- malemma, the inner and outer alveolar membranes were still sticking together, and were not distinguishable. ...Right before the excystment of an Euplotes encysti-cus sawtooth-like folds appeared among the pellicle plas- malemma, the inner and outer alveolar membranes were still sticking together, and were not distinguishable. Mi- crotubular layers already formed at the sites beneath the dorsal cortical pellicle corresponding to vegetative cells,but they still proceed to be organized on the ventral struc-tures. Cristae, highly-tangled with tubular-type struc-tures, appeared on the mitochondria, and were morpho-logically similar to that of vegetative cells. In the cor-tical ciliatures, such as ciliary shafts, kinetosomes, sur-rounding fibrillar cirral baskets, and attached structures of ciliatures, etc., they are different from those in rest- ing cysts which are degenerated or lost. All the cilia- ture microtubules of ciliary shafts are of the 9+2 pattern,but the microtubule-like structure aggregates at triplet - microtubule centers of many kinetosmes, are still under various stages of differentiation. Microtubules beneath the kinetosomal rows are of a developmentally elongated stage; crowded chromatins of various shapes and sizes are found in macronucleus, but there are no nuclear pores (formed by nuclear membrane as in resting cysts) on the nuclear membrane where these chromatins attached.展开更多
Paramecium,a group of ciliates with a long evolutionary history,plays essential roles in freshwater ecosystems and has been model for genetic,cellular,and evolutionary studies for over a century.Despite the valuable c...Paramecium,a group of ciliates with a long evolutionary history,plays essential roles in freshwater ecosystems and has been model for genetic,cellular,and evolutionary studies for over a century.Despite the valuable contributions of genomic resources such as ParameciumDB,genomic data are still mostly limited to species in and near the P.aurelia group.This study addresses this gap by HiFi sequencing,assembling,and annotating the macronuclear genomes of five rare Paramecium species:P.calkinsi,P.duboscqui,P.nephridiatum,P.putrinum,and P.woodruffi.These genomes enable a comprehensive exploration of genomic diversity,genome evolution,and phylogenomic relationships within the genus Paramecium.The genome sizes range from 47.78 to 113.16 Mb,reflecting unexpected variation in genomic content,and genic features differ from those of other reported Paramecium genomes,such as larger intron sizes and higher GC content.Nonetheless,the de novo assemblies indicate that macronuclear genomes of all Paramecium are highly streamlined,with~77%being protein-coding gene regions.Based on gene-duplication depths,synonymous mutations in paralogs,and phylogenomic relationships,we discovered that the five species experienced at least three whole-genome duplication(WGD)events,independent of those previously found in the P.aurelia complex.Using all available WGD data for Paramecium,we further explore the paralog dynamics after WGD events by modeling.This study contributed to a more comprehensive and deeper understanding of genome architecture and evolution in Paramecium.展开更多
Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcrib...Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the macronucleus and peristomial lip might be the important phylogenetic characteristics within the genus Epistylis.展开更多
文摘Right before the excystment of an Euplotes encysti-cus sawtooth-like folds appeared among the pellicle plas- malemma, the inner and outer alveolar membranes were still sticking together, and were not distinguishable. Mi- crotubular layers already formed at the sites beneath the dorsal cortical pellicle corresponding to vegetative cells,but they still proceed to be organized on the ventral struc-tures. Cristae, highly-tangled with tubular-type struc-tures, appeared on the mitochondria, and were morpho-logically similar to that of vegetative cells. In the cor-tical ciliatures, such as ciliary shafts, kinetosomes, sur-rounding fibrillar cirral baskets, and attached structures of ciliatures, etc., they are different from those in rest- ing cysts which are degenerated or lost. All the cilia- ture microtubules of ciliary shafts are of the 9+2 pattern,but the microtubule-like structure aggregates at triplet - microtubule centers of many kinetosmes, are still under various stages of differentiation. Microtubules beneath the kinetosomal rows are of a developmentally elongated stage; crowded chromatins of various shapes and sizes are found in macronucleus, but there are no nuclear pores (formed by nuclear membrane as in resting cysts) on the nuclear membrane where these chromatins attached.
基金supported by the Laoshan Laboratory(LSKJ202203203)the National Natural Science Foundation of China(31961123002,32270435 and 32471688)+1 种基金the National Institutes of Health(R35-GM122566-01)the National Science Foundation(DBI-2119963,DEB-1927159 and 1911449).
文摘Paramecium,a group of ciliates with a long evolutionary history,plays essential roles in freshwater ecosystems and has been model for genetic,cellular,and evolutionary studies for over a century.Despite the valuable contributions of genomic resources such as ParameciumDB,genomic data are still mostly limited to species in and near the P.aurelia group.This study addresses this gap by HiFi sequencing,assembling,and annotating the macronuclear genomes of five rare Paramecium species:P.calkinsi,P.duboscqui,P.nephridiatum,P.putrinum,and P.woodruffi.These genomes enable a comprehensive exploration of genomic diversity,genome evolution,and phylogenomic relationships within the genus Paramecium.The genome sizes range from 47.78 to 113.16 Mb,reflecting unexpected variation in genomic content,and genic features differ from those of other reported Paramecium genomes,such as larger intron sizes and higher GC content.Nonetheless,the de novo assemblies indicate that macronuclear genomes of all Paramecium are highly streamlined,with~77%being protein-coding gene regions.Based on gene-duplication depths,synonymous mutations in paralogs,and phylogenomic relationships,we discovered that the five species experienced at least three whole-genome duplication(WGD)events,independent of those previously found in the P.aurelia complex.Using all available WGD data for Paramecium,we further explore the paralog dynamics after WGD events by modeling.This study contributed to a more comprehensive and deeper understanding of genome architecture and evolution in Paramecium.
基金The work was supported by the National Natural Science Foundation of China (Grant No. 39730070).
文摘Phylogenetic relationships among six species of Epistylis (i. e. E. plicatilis, E. urceolata, E. chrysemydis, E. hentscheli, E. wenrichi, and E. galea) were investigated using sequences of the first internal transcribed spacer region (ITS-1) of ribosomal DNA (rDNA). Amplified rDNA fragment sequences consisted of 215 or 217 bases of the flanking 18S and 5.8S regions, and the entire ITS-1 region (from 145 to 155 bases). There were more than 33 variable bases between E. galea and the other five species in both the 18S region and the ITS-1 region. The affiliation of them was assessed using Neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML) analyses. In all the NJ, MP and ML analyses E. galea, whose macronucleic position and shape are distinctly different from those of the other five species, was probably diverged from the ancestor of Epistylis earlier than the other five species. The topology in which E. plicatilis and E. hentscheli formed a strongly supported sister clade to E. urceolata, E. chrysemydis, and E. wenrichi was consistent with variations in the thickness of the peristomial lip. We concluded that the macronucleus and peristomial lip might be the important phylogenetic characteristics within the genus Epistylis.
