Phylogenomic Analysis Of Major Groups Of Ciliated Protozoa

Ciliates belong to phylum Ciliophora of Protozoa.They are a kind of single-celled microbial eukaryotes with a high diversity and more than 8,000 species have been reported,which widely distributed in sea,fresh water,soil and even in extreme environments.Spirotrichea is the most complex and diverse group of ciliates,accounting for about a quarter of the total reported ciliates.Due to the limitation of phylogenetic studies of single gene and multi-gene molecular analyses and the lack of omics data,the phylogenetic relationship within the Ciliophora remains controversial.Therefore,we used the single-cell sequencing technology to conduct high-throughput sequencing of 11 species of ciliates from 7 classes,10 orders,11 families and 11 genus.By means of phylogenomic analysis,and in combination with other published ciliate omics data,to explore the phylogenetic relationship between the main groups of Ciliophora and the groups within the class Spirotrichea,which has long been controversial.The main finds are:(1)Phylogenomic analysis based on 111 genes(35 067 amino acid residues)from 30 species cover 26 species,26 genus,25 families,21 orders and 10 classes of Ciliophora.In order to cover more class-order data of ciliates,data of 9 newly sequenced ciliates were used in this analysis,respectively: Chilodonella sp.,Coleps sp.,Cyrtolophosis sp.,Dileptus sp.,Evaginogenida sp.,Nyctotherus sp.,Spirostomum sp.,Notohymena australis and Uroleptus sp.The results support that the phylum Ciliophora is monophyletic;the subclass Postciliodesmatophora and Intramacronucleata are monophyletic;SAL supergroup and CONthreeP supergroup are monophyletic in Intramacronucleata subclass.In SAL supergroup,Spirotrichea is closely related to Armophorea,and Litostomatea is clustered at the base of SAL supergroup.In CONthreeP supergroup,Oligohymenophorea is closely related to Prostomatea,the Colpodea is closely related to Nassophorea.(2)To cover more data of class Spirotrichea,the phylogenomic analysis of 51 596 amino acid residues of 151 genes,based on 37 species,included 19 species,14 genus,11 families,7 orders and 4 subclasses of Spirotrichea,four of which are new sequenced species: Notohymena australis,Uroleptus sp.,Aspidisca sp.and Halteria sp..The results support the four subclass(Hypotrichia,Choreotrichia,Oligotrichia,Euplotia)of Spirotrichea are monophyletic.In the subclass Hypotrichia,the order Urostylida is polyphyletic: Uroleptus cluster with the Oxytrichidae in the order Sporadotrichida,supporting Uroleptus belong to the order Sporadotrichida.