Unveiling an ancient whole-genome duplication event in Stentor, the model unicellular eukaryotes

Whole-genome duplication (WGD) events are widespread across eukaryotes and have played a significant role in moulding the genetic architectures of diverse organisms. In the present study, the newly sequenced genome of a giant ciliated protist, Stentor roeselii, provides an opportunity for the analysis of the collinearity and retention of reciprocal best-hit genes between two Stentor species. As a main result, we have unveiled a previously undetected ancient WGD event shaping the genome of its congener, Stentor coeruleus, a model protist used in cytological and evolutionary studies. Genomes of two congeners, S. coeruleus and S. roeselii, are compared and analyzed, revealing that: (i) the former exhibits a much higher retention rate of colinear-gene pairs (28%) than does S. roeselii, and in S. coeruleus, 75% of genes that have a RBH hit in S. roeselii, have paralogs with high amino-acid identity, consistent with a WGD event in the lineage leading to S. coeruleus; (ii) the S. roeselii genome possesses extremely short intergenic regions, implying that the lengths of intergenic regions are under strong selection; (iii) the unique characteristics of introns may have been shaped in the common ancestor of heterotrichs; (iv) gene families that play a role in activities of multiple protein kinases and voltage-gated ion channels expanded rapidly in the ancestor of both taxa, possibly relating to the remarkable regenerative ability in Stentor. This study offers new insights into the evolutionary dynamics of ciliate genomes, with implications for understanding of the processes underlying the evolution of genomic complexity.

SDRAP for annotating scrambled or rearranged genomes

Genomes sometimes undergo large-scale rearrangements. Programmed genome rearrangements in ciliates offer an extreme example, making them a compelling model system to study DNA rearrangements. Currently, available methods for genome annotation are not adequate for highly scrambled genomes. We present a theoretical framework and software implementation for the systematic extraction and analysis of DNA rearrangement annotations from pairs of genome assemblies corresponding to precursor and product versions. The software makes no assumptions about the structure of the rearrangements, and permits the user to select parameters to suit the data. Compared to previous approaches, this work achieves more complete precursor-product mappings, allows for full transparency and reproducibility, and can be adapted to genomic data from different sources.

Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes

Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement, a natural genome editing process that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax, Tetrahymena thermophila, and Paramecium tetraurelia, but only the Oxytricha lineage has a massively scrambled genome, whose assembly during development requires hundreds of thousands of precisely programmed DNA joining events, representing the most complex genome dynamics of any known organism. Here we study the emergence of such complex genomes by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage. This study compares six genomes from three species, the germline and somatic genomes for Euplotes woodruffi, Tetmemena sp., and the model ciliate O. trifallax. We sequenced, assembled, and annotated the germline and somatic genomes of E. woodruffi, which provides an outgroup, and the germline genome of Tetmemena sp. We find that the germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha's: 13.6% of its gene loci require programmed translocations and/or inversions, with some genes requiring hundreds of precise gene editing events during development. This study revealed that the earlier diverged spirotrich, E. woodruffi, also has a scrambled genome, but only roughly half as many loci (7.3%) are scrambled. Furthermore, its scrambled genes are less complex, together supporting the position of Euplotes as a possible evolutionary intermediate in this lineage, in the process of accumulating complex evolutionary genome rearrangements, all of which require extensive repair to assemble functional coding regions. Comparative analysis also reveals that scrambled loci are often associated with local duplications, supporting a gradual model for the origin of complex, scrambled genomes via many small events of DNA duplication and decay.

An extremely streamlined macronuclear genome in the free-living protozoan Fabrea salina

Ciliated protists are among the oldest unicellular organisms with a heterotrophic lifestyle and share a common ancestor with Plantae. Unlike any other eukaryotes, there are two distinct nuclei in ciliates with separate germline and somatic cell functions. Here, we assembled a near-complete macronuclear genome of Fabrea salina, which belongs to one of the oldest clades of ciliates. Its extremely minimized genome (18.35 Mb) is the smallest among all free-living heterotrophic eukaryotes and exhibits typical streamlined genomic features, including high gene density, tiny introns, and shrinkage of gene paralogs. Gene families involved in hypersaline stress resistance, DNA replication proteins, and mitochondrial biogenesis are expanded, and the accumulation of phosphatidic acid may play an important role in resistance to high osmotic pressure. We further investigated the morphological and transcriptomic changes in the macronucleus during sexual reproduction and highlighted the potential contribution of macronuclear residuals to this process. We believe that the minimized genome generated in this study provides novel insights into the genome streamlining theory and will be an ideal model to study the evolution of eukaryotic heterotrophs.

BleTIES: annotation of natural genome editing in ciliates using long read sequencing

SUMMARY

Ciliates are single-celled eukaryotes that eliminate specific, interspersed DNA sequences (internally eliminated sequences, IESs) from their genomes during development. These are challenging to annotate and assemble because IES-containing sequences are typically much less abundant in the cell than those without, and IES sequences themselves often contain repetitive and low-complexity sequences. Long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore have the potential to reconstruct longer IESs than has been possible with short reads but require a different assembly strategy. Here we present BleTIES, a software toolkit for detecting, assembling, and analyzing IESs using mapped long reads.

AVAILABILITY AND IMPLEMENTATION

BleTIES is implemented in Python 3. Source code is available at https://github.com/Swart-lab/bleties (MIT license) and also distributed via Bioconda.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

New contribution to epigenetic studies: Isolation of micronuclei with high purity and DNA integrity in the model ciliated protist, Tetrahymena thermophila

The ciliated protist Tetrahymena thermophila is a well-known model organism with typical nuclear dimorphism containing a somatic macronucleus (MAC) and a germline micronucleus (MIC). The presence in the same cell compartment of two nuclei with distinctly different structural and functional properties provides an ideal model system to explore mechanisms of genome maintenance. Although methods for the isolation of MIC have been available for many years, cross-contamination and DNA degradation remain unresolved. Here, we describe a reliable and quick method to isolate MIC with high purity and DNA integrity in T. thermophila. Different factors are examined to optimize the MIC purification. The MAC contamination ratio in purified MIC is about 0.19% and DNA integrity of purified MIC is maintained. We also establish a more accurate method to detect the contamination rate of nuclei including microscopic observation and PCR detection. This study will facilitate further epigenetic research in Tetrahymena.

The Compact Macronuclear Genome of the Ciliate Halteria grandinella: A Transcriptome-Like Genome with 23,000 Nanochromosomes

How to achieve protein diversity by genome and transcriptome processing is essential for organismal complexity and adaptation. The present work identifies that the macronuclear genome of Halteria grandinella, a cosmopolitan unicellular eukaryote, is composed almost entirely of gene-sized nanochromosomes with extremely short nongenic regions.

How to achieve protein diversity by genome and transcriptome processing is essential for organismal complexity and adaptation. The present work identifies that the macronuclear genome of Halteria grandinella, a cosmopolitan unicellular eukaryote, is composed almost entirely of gene-sized nanochromosomes with extremely short nongenic regions. This challenges our usual understanding of chromosomal structure and suggests the possibility of novel mechvanisms in transcriptional regulation. Comprehensive analysis of multiple data sets reveals that Halteria transcription dynamics are influenced by: (i) nonuniform nanochromosome copy numbers correlated with gene-expression level; (ii) dynamic alterations at both the DNA and RNA levels, including alternative internal eliminated sequence (IES) deletions during macronucleus formation and large-scale alternative splicing in transcript maturation; and (iii) extremely short 5′ and 3′ untranslated regions (UTRs) and universal TATA box-like motifs in the compact 5′ subtelomeric regions of most chromosomes. This study broadens the view of ciliate biology and the evolution of unicellular eukaryotes, and identifies Halteria as one of the most compact known eukaryotic genomes, indicating that complex cell structure does not require complex gene architecture.

New contributions to the phylogeny of the ciliate class Heterotrichea (Protista, Ciliophora): analyses at family-genus level and new evolutionary hypotheses

Heterotrichous ciliates play an important role in aquatic ecosystem energy flow processes and many are model organisms for research in cytology, regenerative biology, and toxicology. In the present study, we combine both morphological and molecular data to infer phylogenetic relationships at family-genus level and propose new evolutionary hypotheses for the class Heterotrichea. The main results include: (1) 96 new ribosomal DNA sequences from 36 populations, representing eight families and 13 genera, including three poorly annotated genera, Folliculinopsis, Ampullofolliculina and Linostomella; (2) the earliest-branching families are Spirostomidae in single-gene trees and Peritromidae in the concatenated tree, but the family Peritromidae probably represents the basal lineage based on its possession of many "primitive" morphological characters; (3) some findings in molecular trees are not supported by morphological evidence, such as the family Blepharismidae is one of the most recent branches and the relationship between Fabreidae and Folliculinidae is very close; (4) the systematic positions of Condylostomatidae, Climacostomidae, and Gruberiidae remain uncertain based either on morphological or molecular data; and (5) the monophyly of each genus included in the present study is supported by the molecular phylogenetic trees, except for Blepharisma in the SSU rDNA tree and Folliculina in the ITS1-5.8S-ITS2 tree.

SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping

Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Postzygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. Although many high-quality somatic genomes have been assembled, a high-quality germline genome assembly is difficult to obtain due to its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline, SIGAR (Split-read Inference of Genome Architecture and Rearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short DNA sequencing reads. As a proof of principle, 93% of rearrangement junctions identified by SIGAR in the ciliate Oxytricha trifallax were validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, including Ichthyophthirius multifilii, a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences, and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements.