One of the most diverse clades of ciliated protozoa,the class Spirotrichea,displays a series of unique characters in terms of eukaryotic macronuclear(MAC)genome,including high fragmentation that produces nanochromosom...One of the most diverse clades of ciliated protozoa,the class Spirotrichea,displays a series of unique characters in terms of eukaryotic macronuclear(MAC)genome,including high fragmentation that produces nanochromosomes.However,the genomic diversity and evolution of nanochromosomes and gene families for spirotrich MAC genomes are poorly understood.In this study,we assemble the MAC genome of a representative euplotid(a new model organism in Spirotrichea)species,Euplotes aediculatus.Our results indicate that:(a)the MAC genome includes 35,465 contigs with a total length of 97.3 Mb and a contig N50 of 3.4 kb,and contains 13,145 complete nanochromosomes and 43,194 predicted genes,with the majority of these nanochromosomes containing tiny introns and harboring only one gene;(b)genomic comparisons between E.aediculatus and other reported spirotrichs indicate that average GC content and genome fragmentation levels exhibit interspecifc variation,and chromosome breaking sites(CBSs)might be lost during evolution,resulting in the increase of multi-gene nanochromosome;(c)gene families associated with chitin metabolism and FoxO signaling pathway are expanded in E.aediculatus,suggesting their potential roles in environment adaptation and survival strategies of E.aediculatus;and(d)a programmed ribosomal frameshift(PRF)with a conservative motif 5′-AAATAR-3′tends to occur in longer genes with more exons,and PRF genes play an important role in many cellular regulation processes.展开更多
基金This work was financially supported by the National Natural Science Foundation of China(Project Nos.2030015,32270512)the Natural Science Foundation of Jiangsu Province(BK20220268)+1 种基金the Fundamental Research Funds for the Central Universities(GK202207014)a National Institutes of Health grant No.P40OD010964 subaward to NAS.The content is solely the responsibility of the authors and does not necessarily represent the ofcial views of the National Institutes of Health.Many thanks are given to Prof.Weibo Song(Ocean University of China[OUC])for his help during drafting the manuscript.We thank Ruitao Gong(OUC)for helping with species identifcation,DNA,and RNA extraction.We acknowledge the computing resources provided on the IEMB-1,a high-performance computing cluster operated by the Institute of Evolution and Marine Biodiversity,OUC.
文摘One of the most diverse clades of ciliated protozoa,the class Spirotrichea,displays a series of unique characters in terms of eukaryotic macronuclear(MAC)genome,including high fragmentation that produces nanochromosomes.However,the genomic diversity and evolution of nanochromosomes and gene families for spirotrich MAC genomes are poorly understood.In this study,we assemble the MAC genome of a representative euplotid(a new model organism in Spirotrichea)species,Euplotes aediculatus.Our results indicate that:(a)the MAC genome includes 35,465 contigs with a total length of 97.3 Mb and a contig N50 of 3.4 kb,and contains 13,145 complete nanochromosomes and 43,194 predicted genes,with the majority of these nanochromosomes containing tiny introns and harboring only one gene;(b)genomic comparisons between E.aediculatus and other reported spirotrichs indicate that average GC content and genome fragmentation levels exhibit interspecifc variation,and chromosome breaking sites(CBSs)might be lost during evolution,resulting in the increase of multi-gene nanochromosome;(c)gene families associated with chitin metabolism and FoxO signaling pathway are expanded in E.aediculatus,suggesting their potential roles in environment adaptation and survival strategies of E.aediculatus;and(d)a programmed ribosomal frameshift(PRF)with a conservative motif 5′-AAATAR-3′tends to occur in longer genes with more exons,and PRF genes play an important role in many cellular regulation processes.
