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. 2019 Aug 1;8(8):giz089.
doi: 10.1093/gigascience/giz089.

A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata

Qin Liu  1 , Yunhai Guo  1 , Yi Zhang  1 , Wei Hu  1   2 , Yuanyuan Li  1 , Dan Zhu  1 , Zhengbin Zhou  1 , Jiatong Wu  1 , Nansheng Chen  3   4   5 , Xiao-Nong Zhou  1
Affiliations

A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata

Qin Liu et al. Gigascience. .

Abstract

Background: Triatoma rubrofasciata is a widespread pathogen vector for Chagas disease, an illness that affects approximately 7 million people worldwide. Despite its importance to human health, its evolutionary origin has not been conclusively determined. A reference genome for T. rubrofasciata is not yet available.

Finding: We have sequenced the genome of a female individual with T. rubrofasciatausing a single molecular DNA sequencing technology (i.e., PacBio Sequel platform) and have successfully reconstructed a whole-genome (680-Mb) assembly that covers 90% of the nuclear genome (757 Mb). Through Hi-C analysis, we have reconstructed full-length chromosomes of this female individual that has 13 unique chromosomes (2n = 24 = 22 + X1 + X2) with a contig N50 of 2.72 Mb and a scaffold N50 of 50.7 Mb. This genome has achieved a high base-level accuracy of 99.99%. This platinum-grade genome assembly has 12,691 annotated protein-coding genes. More than 95.1% of BUSCO genes were single-copy completed, indicating a high level of completeness of the genome.

Conclusion: The platinum-grade genome assembly and its annotation provide valuable information for future in-depth comparative genomics studies, including sexual determination analysis in T. rubrofasciata and the pathogenesis of Chagas disease.

Keywords: Triatoma rubrofasciata; Hi-C; Iso-Seq; PacBio Sequel platform; RNA-Seq; chromosomal-level assembly; comparative genomics.

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Figures

Figure 1:
Figure 1:
Dorsal (left) and ventral (right) views of a female Triatoma rubrofasciata.
Figure 2:
Figure 2:
The plot of the read length distribution/ratio of the subreads.
Figure 3:
Figure 3:
17-mer depth distribution for genome size estimation analysis of Triatoma rubrofasciata.
Figure 4:
Figure 4:
DNA interaction heatmap generated in Hi-C analysis (resolution: 500 Kb).
Figure 5:
Figure 5:
Genome assembly comparison of Triatoma rubrofasciata with other sequenced insect genomes (Apis mellifera, Acyrthosiphon pisum, Cimex lectularius, Culex quinquefasciatus, Drosophila melanogaster, Gerris buenoi, Glossina palpalis, Halyomorpha halys, Heliconius melpomene, Homalodisca vitripennis, Oncopeltus fasciatus, Rhodnius prolixus). The x- and y-axes represent the contig and scaffold N50s, respectively. The genomes with both contig and scaffold N50s less than 2M are hignlighted in black.
Figure 6:
Figure 6:
Length distribution comparison on total gene, CDS, exon, and intron of annotated gene models of Triatoma rubrofasciata with other closely related insect species. Length distribution of total gene (A), CDS (B), exon (C), and intron (D) was compared to those of Rhodnius prolixus, Halyomorpha halys, Oncopeltus fasciatus, Cimex lectularius, and Drosophila melanogaster.
Figure 7:
Figure 7:
Phylogenetic analysis of T. rubrofasciata with other insect species. The estimated species divergence time (million years ago) and the 95% confidential intervals are labeled at each branch site. The divergence used for time recalibration is illuminated as red dots in the tree.
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References

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