Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host - PubMed (original) (raw)

doi: 10.1038/ncomms12845.

Sen Wang 2 3, Yingfeng Luo 2, Lihua Xiao 4, Xuenong Luo 1, Shenghan Gao 2, Yongxi Dou 1, Huangkai Zhang 2 3, Aijiang Guo 1, Qingshu Meng 2, Junling Hou 1, Bing Zhang 5, Shaohua Zhang 1, Meng Yang 2, Xuelian Meng 1, Hailiang Mei 2, Hui Li 1, Zilong He 2, Xueliang Zhu 1, Xinyu Tan 2, Xing-Quan Zhu 1, Jun Yu 2, Jianping Cai 1, Guan Zhu 6, Songnian Hu 2, Xuepeng Cai 1

Affiliations

Comparative genomics reveals adaptive evolution of Asian tapeworm in switching to a new intermediate host

Shuai Wang et al. Nat Commun. 2016.

Erratum in

Abstract

Taenia saginata, Taenia solium and Taenia asiatica (beef, pork and Asian tapeworms, respectively) are parasitic flatworms of major public health and food safety importance. Among them, T. asiatica is a newly recognized species that split from T. saginata via an intermediate host switch ∼1.14 Myr ago. Here we report the 169- and 168-Mb draft genomes of T. saginata and T. asiatica. Comparative analysis reveals that high rates of gene duplications and functional diversifications might have partially driven the divergence between T. asiatica and T. saginata. We observe accelerated evolutionary rates, adaptive evolutions in homeostasis regulation, tegument maintenance and lipid uptakes, and differential/specialized gene family expansions in T. asiatica that may favour its hepatotropism in the new intermediate host. We also identify potential targets for developing diagnostic or intervention tools against human tapeworms. These data provide new insights into the evolution of Taenia parasites, particularly the recent speciation of T. asiatica.

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Figures

Figure 1

Figure 1. Unique intron features in the tapeworm genomes.

(a) Bimodal length distributions of short introns in tapeworms (T. asiatica, T. saginata, T. solium and E. multilocularis) and monogenean G. salaris in comparison with the unimodal distributions in the fluke S. mansoni and the free-living flatworm S. mediterranea. (b) Preferential distributions of peak-1 and peak-2 introns toward 3′-end and middle regions of genes, respectively. The curves show the relationship between intron densities and relative positions from the 5′-ends of genes. (c) Peak-2 intron-containing genes are highly enriched to certain functional groups (shown for T. asiatica, by two-sided Fisher's exact test). (d) Length preference of introns flanking small exons (<400 bp; shown for T. asiatica). The minimal mean length of (5′ or 3′) introns flanking small exons that have a specific length (<400 bp) is 370 bp in T. asiatica.

Figure 2

Figure 2. Homologues and synteny between T. asiatica and related tapeworms.

(a) Homologous genes shared between T. asiatica and other tapeworms (that is, T. saginata, T. solium, E. multicularis and H. microstoma). (b) Gene block linkages between T. asiatica and T. saginata. The collinear gene blocks determined by MCScan between genome scaffolds (>1 Mb) represent 7,212 and 7,201 genes for T. asiatica and T. saginata, respectively.

Figure 3

Figure 3. Gene duplications revealed by _K_s analysis.

(a) The percentage of paralogous gene pairs of duplicated genes along with _K_s values are typically L shaped in the T. saginata (Tsa) and T. asiatica (Tas) genomes, indicating the occurrence of continuous gene duplication events and the losses of duplicated genes over the time. (b) Distribution of _K_s values in orthologous genes with peaks indicating the splits between various flatworms T. asiatica (Tas), T. saginata (Tsa), T. solium (Tso), E. granulosus (Egr), E. multilocularis (Emu), S. mansoni (Sma) and S. japanicum (Sja). The grey bar indicates the divergence point between the Taenia and Echinococcus lineages. (c) Extensive duplications of diagnostic antigen gp50 genes in the tapeworm lineage (Taenia, Echinococcus and Hymenolepis). (d) Sequence logo shows the conserved and distinct sequence characteristics of the gp50 sequences from the tapeworms. The sequence logo was generated from 183 sequences aligned at the conserved blocks selected by Gblocks with a less stringent selection (

http://molevol.cmima.csic.es/castresana/Gblocks\_server.html

).

Figure 4

Figure 4. Evolution of gene families in the flatworms and roundworms.

(a) The dynamics of gene family sizes in the genomes of T. saginata, T. asiatica, T. solium, E. granulosus, E. multilocularis, H. microstoma, S. japonicum and S. mansoni. Numbers above and below the branches indicate gene family gains/losses (red) and the expansions/contractions (blue), respectively. (b) Phylogenetic reconstruction clustered low-density lipoprotein receptor (LDLR) genes from T. saginata, T. asiatica and T. solium into four groups, in which group-4 LDLR genes were expanded only in the T. asiatica genome (Supplementary Methods, section 8.8). (c) The expansion of fatty acid desaturases (FADS) in the T. asiatica genome, compared with that in the T. saginata genome (Supplementary Methods, section 8.8).

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