Comparative Genome Analysis Reveals Cis-Regulatory Elements on Gene-Sized Chromosomes of Ciliated Protists

Abstract

Gene-sized chromosomes are a distinct feature of the macronuclear genome in ciliated protists known as spirotrichs. These nanochromosomes are often only several kilobase pairs long and contain a coding region for a single gene. However, the ways in which transcription is regulated on nanochromosomes is still largely unknown. Here, we generated macronuclear genome assemblies for two species of Pseudokeronopsis ciliates to better understand transcription regulation on gene-sized chromosomes. We searched within the short subtelomeric regions for potential cis-regulatory elements and identified distinct AT-rich sequences conserved in both species, at both the 5’ and 3’ end of each gene. We further acquired transcriptomic data for these species, which showed the 5’ cis-regulatory element is associated with active gene expression. Gene family evolution analysis suggests nanochromosomes in spirotrichs may originated approximately 900 million years ago. Together our comparative genomic analyses reveal novel insights into the biological roles of cis-regulatory elements on gene-sized chromosomes.

Decryption of the survival “black box”: gene family expansion promotes the encystment in ciliated protists

“…This study reports the MAC genome of the urostylid ciliate Pseudourostyla cristata , which is highly fragmented into nanochromosomes. This is consistent with previous reports on the MAC genomes of other hypotrich ciliates [ 18 – 22 , 25 ]. In addition, based on correlation analyses, we find that the length and GC content of the nanochromosomes are mainly determined by the coding region of the genes they carry (Fig.…”

“…Generally, MAC genomes of hypotrichous ciliates are fragmented into gene-sized nanochromosomes [ 21 , 22 , 25 ]. To further dissect the genomic features of hypotrichs, we identified and compared complete chromosomes containing telomeres at both ends in six hypotrichous ciliate genomes ( Oxytricha trifallax , Stylonychia lemnae , Halteria grandinella , Pseudourostyla cristata, Pseudokeronopsis flava , and Pseudokeronopsis carnea ) (Figs.…”

“…Gene family expansion is widespread during the genomic evolution of nearly all major phyla of eukaryotes, including ciliates [ 22 , 23 , 26 ]. Furthermore, it is often associated with the adaptation of organisms to variable environments [ 27 , 28 ].…”

“…With the rapid development of high-throughput sequencing technologies, genomic sequencing and comparison analyses of ciliates have become effective methods to provide insights into above questions. However, despite the high number of morphospecies found in hypotrichs [ 8 , 17 ], very little genomic data (publicly available for six species of hypotrichs) is available until now, primarily due to difficulties of bulk cultivation in laboratory conditions [ 18 – 22 ].…”

A supernumerary synthetic chromosome inKomagataella phaffiias a repository for extraneous genetic material

“…Hence, we adopted the term “nano” chromosomes for our constructs. Telomere-capped gene-sized DNA molecules in the macronucleus of some single-celled ciliates were also called nanochromosomes, but lack centromeres and do not segregate [31]. In S. cerevisiae , which has highly efficient HR-based DSB-repair mechanisms, “yeast artificial chromosomes” were developed as vehicles for Mb-sized segments of foreign DNA and used early in the human genome project and for generating transgenic animals [32].…”