Chromosome organization and gene expansion in the highly fragmented genome of the ciliate <i>Strombidium stylifer</i>

Chao Li; Xiao Chen; Weibo Zheng; Thomas G. Doak; Guangyi Fan; Weibo Song; Ying Yan

doi:10.1016/j.jgg.2021.05.014

Volume 48 Issue 10

Oct. 2021

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Article Navigation > Journal of Genetics and Genomics > 2021 > 48(10): 908-916

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Chromosome organization and gene expansion in the highly fragmented genome of the ciliate Strombidium stylifer

doi: 10.1016/j.jgg.2021.05.014

a. Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China;
b. Marine College, Shandong University, Weihai 264209, China;
c. School of Life Sciences, Ludong University, Yantai 264025, China;
d. Department of Biology, Indiana University, Bloomington, IN 47405, USA;
e. National Center for Genome Analysis Support, Indiana University, Bloomington, IN 47405, USA;
f. BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China;
g. State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China;
h. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China

Funds:

This work was supported by the project of the National Natural Science Foundation of China (32030015) and the Fundamental Research Funds for the Central Universities (862101013143, 202141007). Many thanks are given to Dr. Hongan Long (Ocean University of China), Dr. Miao Miao (University of Chinese Academy of Sciences), and Dr. Fangqing Zhao (Chinese Academy of Sciences) for their technical and institutional support. We acknowledge the computing resources provided on IEMB-1, a high-performance computing cluster operated by the Institute of Evolution and Marine Biodiversity. We also appreciate Dr. Ruanlin Wang (Shanxi University, China) and Dr. Jie Xiong (Institute of Hydrobiology, CAS) for providing the genomic data of Euplotes octocarinatus.

Received Date: 2021-01-22
Accepted Date: 2021-05-13
Rev Recd Date: 2021-04-29
Publish Date: 2021-07-03

Abstract

Abstract

Chromosomes are well-organized carriers of genetic information in eukaryotes and are usually quite long, carrying hundreds and thousands of genes. Intriguingly, a clade of single-celled ciliates, Spirotrichea, feature nanochromosomes—also called “gene-sized chromosomes”. These chromosomes predominantly carry only one gene, flanked by short telomere sequences. However, the organization and copy number variation of the chromosomes in these highly fragmented genomes remain unexplored in many groups of Spirotrichea, including the marine Strombidium. Using deep genome sequencing, we assembled the macronuclear genome of Strombidium stylifer into more than 18,000 nanochromosomes (~2.4 Kb long on average). Our results show that S. stylifer occupies an intermediate position during the evolutionary history of Strombidium lineage and experienced significant expansions in several gene families related to guanyl ribonucleotide binding. Based on the nucleotide distribution bias analysis and conserved motifs search in non-genic regions, we found that the subtelomeric regions have a conserved adenine-thymine (AT)-rich sequence motif. We also found that the copy number of nanochromosomes lacks precise regulation. This work sheds light on the unique features of chromosome structure in eukaryotes with highly fragmented genomes and reveals that a rather specialized evolutionary strategy at the genomic level has resulted in great diversity within the ciliated lineages.
- Ciliate,
- Copy number,
- Nanochromosome,
- Nucleotide distribution bias,
- Strombidium stylifer

These authors contributed equally to this work.

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References(60)

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