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. 2020 Apr;214(4):769-780.
doi: 10.1534/genetics.119.303018. Epub 2020 Feb 28.

Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization

Anastasia A Teterina  1   2 , John H Willis  1 , Patrick C Phillips  3
Affiliations

Chromosome-Level Assembly of the Caenorhabditis remanei Genome Reveals Conserved Patterns of Nematode Genome Organization

Anastasia A Teterina et al. Genetics. 2020 Apr.

Abstract

The nematode Caenorhabditis elegans is one of the key model systems in biology, including possessing the first fully assembled animal genome. Whereas C. elegans is a self-reproducing hermaphrodite with fairly limited within-population variation, its relative C. remanei is an outcrossing species with much more extensive genetic variation, making it an ideal parallel model system for evolutionary genetic investigations. Here, we greatly improve on previous assemblies by generating a chromosome-level assembly of the entire C. remanei genome (124.8 Mb of total size) using long-read sequencing and chromatin conformation capture data. Like other fully assembled genomes in the genus, we find that the C. remanei genome displays a high degree of synteny with C. elegans despite multiple within-chromosome rearrangements. Both genomes have high gene density in central regions of chromosomes relative to chromosome ends and the opposite pattern for the accumulation of repetitive elements. C. elegans and C. remanei also show similar patterns of interchromosome interactions, with the central regions of chromosomes appearing to interact with one another more than the distal ends. The new C. remanei genome presented here greatly augments the use of the Caenorhabditis as a platform for comparative genomics and serves as a basis for molecular population genetics within this highly diverse species.

Keywords: Caenorhabditis elegans; Caenorhabditis remanei; chromosome-level assembly; comparative genomics.

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Figures

Figure 1
Figure 1
Gene synteny plot of the 9247 one-to-one orthologs of C. elegans (the top row) and C. remanei (the bottom row). The lines connect locations of the orthologs on the C. elegans and C. remanei reference genomes. Teal lines represent genes in the same orientation, whereas orange lines show genes in an inverted orientation.
Figure 2
Figure 2
Genomic landscape of genetic elements for C. elegans and C. remanei. Vertical dashed lines show the boundaries of the central domain. Colored lines represent the smoothed means of the fraction of repetitive DNA (gray), exons (orange), and introns (purple) calculated from 100-kb windows. Shaded areas show 95% C.I.s of the mean.
Figure 3
Figure 3
Genome landscape of median distances in Hi-C read pairs in C. elegans and C. remanei samples. (A) Distributions of distances between paired reads of cis-chromosome interactions. The vertical dashed lines show the boundaries of the central domain. Medians are estimated per 100-kb windows, with the gray lines representing the smoothed means of the values. The differences between values for C. elegans and C. remanei are due to the library size selection for Illumina sequencing in these two Hi-C experiments, and so only the relative patterns and not the absolute values are relevant here. (B) Trans-chromosome interactions in C. elegans and C. remanei. Lines represent contacts between 100-kb windows. For the C. elegans data set, only contacts with > 200 pairs of reads are shown; for the C. remanei data set, only contacts with > 100 pairs of reads are shown (the C. remanei Hi-C data set is two times smaller than the C. elegans data set). These filters emphasize differences in interaction density/location; the actual total number of interactions is approximately the same for all chromosomes.
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