A free-living protist that lacks canonical eukaryotic DNA replication and segregation systems

Abstract

Cells must replicate and segregate their DNA with precision. In eukaryotes, these processes are part of a regulated cell-cycle that begins at S-phase with the replication of DNA and ends after M-phase. Previous studies showed that these processes were present in the last eukaryotic common ancestor and the core parts of their molecular systems are conserved across eukaryotic diversity. However, some unicellular parasites, such as the metamonad Giardia intestinalis, have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a high-quality draft genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. We found that parasitic and free-living metamonads harbor a conspicuously incomplete set of canonical proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, completely lacking the origin recognition complex, Cdc6 and other replisome components, most structural kinetochore subunits including the Ndc80 complex, as well as several canonical cell-cycle checkpoint proteins. Carpediemonas is the first eukaryote known to have lost this large suite of conserved complexes, suggesting that it has a highly unusual cell cycle and that unlike any other known eukaryote, it must rely on a novel set of mechanisms to carry out these fundamental processes.

High quality genome assembly of the amitochondriate eukaryote Monocercomonoides exilis

“…Repeat analysis using RepeatModeler suggested that around 45.97 % of the new genome assembly is represented by various types of repeats ( Table 2 ), higher than the initially reported 37–38 % [ 5, 16 ] and consistent with the size increase of the assembly. In metamonads, the percentage of repetitive elements varies from 4 % in Carpediemonas frisia up to approximately 67 % in Trichomonas vaginalis [ 16 ], placing the genome of M. exilis on an average measure of repetitive elements-content. Yet, the relative composition of repetitive elements is very different to other metamonads, containing the highest percentage of unclassified repeats ( Table 2 ) [ 16 ].…”

“…In metamonads, the percentage of repetitive elements varies from 4 % in Carpediemonas frisia up to approximately 67 % in Trichomonas vaginalis [ 16 ], placing the genome of M. exilis on an average measure of repetitive elements-content. Yet, the relative composition of repetitive elements is very different to other metamonads, containing the highest percentage of unclassified repeats ( Table 2 ) [ 16 ]. While these could represent some new types of repeats, we hypothesise that some of the unclassified repeats may be misidentified and may represent highly expanded protein families in the genome of M. exilis, such as protein tyrosine kinases, which tend to overlap with unclassified repeats ( Fig.…”

“…Long-read sequencing technologies like Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have recently been very helpful in improving genome assemblies of several model and non-model organisms [8][9][10]. ONT has been successfully used for generating draft genome assemblies of plants [11,12], metazoans [13,14], fungi [15] and even protists [9,16], and it consistently produced much more contiguous assemblies. The main drawback of long-read sequencing remains the consensus accuracy, however, recent improvements in sequencing chemistry as well as base-calling algorithms for ONT improved this issue.…”

Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata

“…Query protein sequences for individual subunits from each ESCRT sub-complex from various pan-eukaryotic representatives were obtained and aligned using MUSCLE v3. 8.31 (Additional Material 24-Supplementary Table 4 ) [ 45 , 69 – 83 ]. Resulting alignments were used to generate Hidden Markov Models using the hmmbuild option available through the HMMER 3.1.b1 package and HMMER searches into all Fornicata genomes and transcriptomes using the hmmsearch tool with an e-value cutoff set to 0.01 [ 84 ].…”

Genomic survey maps differences in the molecular complement of vesicle formation machinery between Giardia intestinalis assemblages

“…While these are much lower than what is typically expected of a eukaryotic genome from animal, plant, or fungal lineages (i.e., 85-95%), low BUSCO scores in Giardia are a drawback of limited inclusion of diverse protist lineages within the eukaryote_odb10 database. In general, metamonad lineages are highly divergent in their sequences and ancestrally lack many of the proteins present in model eukaryotes, and therefore all suffer from poor BUSCO scores [42][43][44]. Instead of using these as absolute measures, BUSCO scores were evaluated against those published for other Giardia assemblies.…”