A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data

Wang, Guangying; Wang, Su; Chai, Xiaocui; Zhang, Jing; Yang, Wentao; Jiang, Chuanqi; Chen, Kai; Miao, Wei; Xiong, Jie

doi:10.1016/j.csbj.2021.04.007

Cited by 14 publications

(11 citation statements)

References 19 publications

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“…Nevertheless, even with long‐read sequencing, repeat‐rich genomes yielded more fragmented assemblies (Sevim et al, 2019). While tools have been developed specially for improved scaffolding of large, repeat‐rich eukaryotic genomes (Gao et al, 2016; Miga et al, 2020; Wang et al, 2021), several long‐read metagenomic data sets already exist (Corrêa et al, 2020; Kasmanas et al, 2021; Nata'ala et al, 2022). Since short reads tend to assemble into shorter contigs compared to long reads, short‐read sequencing can influence the accuracy of gene predictions by not covering a gene's total length (Pearman et al, 2020), and single‐copy genes may not provide a realistic measure of the completeness of complex organisms such as eukaryotes.…”

Section: Discussionmentioning

confidence: 99%

“…For instance, the human reference genome is the most accurate vertebrate genome but still lacks the characterization of some chromosomes (Miga et al, 2020;Nurk et al, 2022). A study by Wang and collaborators (Wang et al, 2021), proposed a strategy for the complete assembly of two ciliates. Both studies suggest that high coverage and ultra-long nanopore sequencing may yield a better assembly of genomes.…”

Section: Discussionmentioning

confidence: 99%

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Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes

Saraiva

Bartholomäus

Toscan

et al. 2023

Molecular Ecology Resources

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As most eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recovering Prokaryotic genomes have become common in genome biology, few studies have tackled the recovery of eukaryotic genomes from metagenomes.This study assessed the reconstruction of microbial eukaryotic genomes using 6000 metagenomes from terrestrial and some transition environments using the EukRep pipeline. Only 215 metagenomic libraries yielded eukaryotic bins. From a total of 447 eukaryotic bins recovered 197 were classified at the phylum level. Streptophytes and fungi were the most represented clades with 83 and 73 bins, respectively. More than 78% of the obtained eukaryotic bins were recovered from samples whose biomes were classified as host-associated, aquatic, and anthropogenic terrestrial. However, only 93 bins were taxonomically assigned at the genus level and 17 bins at the species level. Completeness and contamination estimates were obtained for a total of 193 bins and consisted of 44.64% (σ = 27.41%) and 3.97% (σ = 6.53%), respectively.Micromonas commoda was the most frequent taxon found while Saccharomyces cerevisiae presented the highest completeness, probably because more reference genomes are available. Current measures of completeness are based on the presence of single-copy genes. However, mapping of the contigs from the recovered eukaryotic bins to the chromosomes of the reference genomes showed many gaps, suggesting that completeness measures should also include chromosome coverage. Recovering eukaryotic genomes will benefit significantly from long-read sequencing, development of tools for dealing with repeat-rich genomes, and improved reference genomes databases.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes

Saraiva

Bartholomäus

Toscan

et al. 2023

Molecular Ecology Resources

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“…However, later cytochemical experiments to measure the ratio of DNA content between the MAC and MIC (23:1 at G1 phase) suggested that the amount of MAC DNA is sufficient for only 45 haploid units (Doerder & Debault, 1975; Woodard et al, 1972), based on the assumption of little difference in size between MAC and MIC genomes. However, the current version of the assembled MIC genome (157 Mb) is approximately 1.5 times larger than the MAC genome (103 Mb) (Hamilton et al, 2016; Wang, Wang, et al, 2021), corresponding to approximately 70 copies of MAC chromosomes at G1 phase. In the present study, we quantified 15 of the 180 non‐rDNA MAC chromosomes and obtained an average copy number at G1 phase of approximately 90 (Figure 2).…”

Section: Discussionmentioning

confidence: 99%

“…(103 × 90.9)/(23 × 2) ≈ 204 Mb. To resolve this discrepancy, MIC genome assembly needs to be refined using long‐read sequencing technology, as was done for MAC genome assembly (Sheng et al, 2020; Wang, Wang, et al, 2021), because the current version of the assembled MIC genome contains many gaps that are likely caused by repetitive sequences (Hamilton et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

“…The T . thermophila MIC contains five pairs of large metacentric chromosomes (Hamilton et al, 2016); in contrast, the most recent complete genome assembly showed that the mature polyploid MAC is composed of 181 acentric chromosomes, including one highly amplified rDNA minichromosome (Sheng et al, 2020; Wang, Wang, et al, 2021). MAC chromosomes differentiate from MIC chromosomes during sexual conjugation via chromosome fragmentation, deletion of internal eliminated sequences (IES), and polyploidization (Orias et al, 2011).…”

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Absolute quantification of chromosome copy numbers in the polyploid macronucleus of Tetrahymena thermophila at the single‐cell level

Zhou

Mochizuki

et al. 2022

J Eukaryotic Microbiology

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AMITOSIS is a simple type of cell division in which nuclear genetic materials are distributed to daughter cells in the absence of a mitotic spindle. This process occurs not only in primitive eukaryotes such as ciliates and amoeba (Gicquaud & Tremblay, 1991;Prescott, 1994) but also in a wide variety of higher eukaryotic organisms, including plants, insects, fish, and mammals (Miller, 1980;Nagata & Ma, 2004;Nakahara, 1917;Wang et al., 2010). Furthermore, recent studies indicate that amitosis has an important role in tumorigenesis and in the regeneration of tissue-specific stem cells

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Tetrahymena

Cole¹

2022

Encyclopedia of Life Sciences

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The Tetrahymena genus is composed of mostly free‐living ciliated protozoa that have helped researchers gain insight into fundamental problems of cell biology. As all ciliates, Tetrahymena contain separate germline and somatic nuclei known as the micronucleus and macronucleus, respectively. The macronucleus is derived from a copy of the micronucleus through a process that involves extensive whole‐genome rearrangement and that is under intensive study. Tetrahymena thermophila can be readily manipulated using the tools of genetics, molecular biology, cell biology and biochemistry. Recently, next‐generation, whole‐genome sequencing has made possible the identification of previously unidentified genes responsible for a rich gallery of mutant phenotypes. Notable discoveries made using Tetrahymena include the structure of telomeres and telomerase, self‐splicing RNA, the first microtubular motor, and the link between histone acetylation and gene regulation. The approximately 104 Megabase macronuclear genome of T. thermophila has been sequenced and annotated; the micronuclear genome has been sequenced as well. Key Concepts Tetrahymena are large, complex eukaryotic cells well‐suited both for university research and for the undergraduate teaching‐laboratory. Tetrahymena, have been studied for nearly a century and have been the source of numerous ground‐breaking discoveries. Applying modern tools of genomics, proteomics, and next‐generation, whole‐genome sequencing has ushered in a new era of research to such topics as the assembly of basal bodies and cilia, pattern formation, novel roles for small ribonucleic acids ( RNAs ), membrane trafficking, secretion, phagocytosis, pinocytosis, cytoskeletal motility and chromosome dynamics including studies on the origins of deoxyribonucleic acid ( DNA ) replication, telomere synthesis, meiosis, recombination, apoptosis and the regulation of gene expression through epigenetic chromatin marking. Tetrahymena offer special insights into cell biological processes due to their many original and extraordinary capabilities including the use of a unique genetic code, novel twists on metabolism and protein trafficking, self‐splicing RNA, programmed genome rearrangement involved in genome surveillance, cortical patterning and cellular regeneration. Tetrahymena exhibit both conserved and evolutionarily divergent solutions to fundamental cell biological problems.

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A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data

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Cited by 14 publications

References 19 publications

Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes

Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes

Absolute quantification of chromosome copy numbers in the polyploid macronucleus of Tetrahymena thermophila at the single‐cell level

Tetrahymena

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