From germline genome to highly fragmented somatic genome:genome-wide DNA rearrangement during the sexual process in ciliated protists  

作　　者：Liping Lyu Xue Zhang Yunyi Gao Tengteng Zhang Jinyu Fu Naomi A.Stover Feng Gao 

机构地区：[1]Key Laboratory of Evolution&Marine Biodiversity(Ministry of Education),and Institute of Evolution&Marine Biodiversity,Ocean University of China,Qingdao 266003,China [2]Department of Biology,Bradley University,Peoria,IL 61625,USA [3]Laoshan Laboratory,Qingdao 266237,China

出　　处：《Marine Life Science & Technology》2024年第1期31-49,共19页海洋生命科学与技术（英文）

基　　金：funded by the Laoshan Laboratory(No.LSKJ202203202);the National Natural Science Foundation of China(32270539,31922013,31961123002);the Natural Science Foundation of Shandong Province(ZR2020JQ13);Royal Society/NSFC International Exchanges Cost Share Project(IEC\NSFC\201024);National Institutes of Health(P40OD010964);the Fundamental Research Funds for the Central Universities(202141004).

摘　　要：Genomes are incredibly dynamic within diverse eukaryotes and programmed genome rearrangements(PGR)play important roles in generating genomic diversity.However,genomes and chromosomes in metazoans are usually large in size which prevents our understanding of the origin and evolution of PGR.To expand our knowledge of genomic diversity and the evolutionary origin of complex genome rearrangements,we focus on ciliated protists(ciliates).Ciliates are single-celled eukaryotes with highly fragmented somatic chromosomes and massively scrambled germline genomes.PGR in ciliates occurs extensively by removing massive amounts of repetitive and selfish DNA elements found in the silent germline genome dur-ing development of the somatic genome.We report the partial germline genomes of two spirotrich ciliate species,namely Strombidium cf.sulcatum and Halteria grandinella,along with the most compact and highly fragmented somatic genome for S.cf.sulcatum.We provide the first insights into the genome rearrangements of these two species and compare these features with those of other ciliates.Our analyses reveal:(1)DNA sequence loss through evolution and during PGR in S.cf.sulcatum has combined to produce the most compact and efficient nanochromosomes observed to date;(2)the compact,transcriptome-like somatic genome in both species results from extensive removal of a relatively large number of shorter germline-specific DNA sequences;(3)long chromosome breakage site motifs are duplicated and retained in the somatic genome,revealing a complex model of chromosome fragmentation in spirotrichs;(4)gene scrambling and alternative pro-cessing are found throughout the core spirotrichs,offering unique opportunities to increase genetic diversity and regulation in this group.

关 键 词：Alternative processing CILIATES Gene scrambling Genome rearrangement Germline genome Somatic genome 

分 类 号：Q78[生物学—分子生物学]