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Differentially expressed homologous genes reveal interspecies differences of Paragonimus proliferus based on transcriptome analysis Cover

Differentially expressed homologous genes reveal interspecies differences of Paragonimus proliferus based on transcriptome analysis

Helminthologia
Volume 57 (2020): Issue 3 (September 2020)
By: S. H. Li,  S. D. Li,  H. J. Li,  J. Y. Li,  J. J. Xu,  G. J. Chang,  L. J. Yang,  W. Q. Wang,  Y. L. Zhang,  Z. Q. Ma,  S. M. He,  W. L. Wang and  H. L. Huang  
Open Access
|Aug 2020

Figures & Tables

Fig. 1

Metacercaria and adult worms stained magenta with hydrochloric acid.A metacercaria isolated from a crab (a), and an adult worm recovered from the lung tissue of a rat (b).
Metacercaria and adult worms stained magenta with hydrochloric acid.A metacercaria isolated from a crab (a), and an adult worm recovered from the lung tissue of a rat (b).

Fig. 2

Sequencing, pretreatment, and annotation of Paragonimus proliferus transcriptome. The transcriptome of adult P. proliferus was sequenced using RNA-Seq (Hi-Seq Illumina X 4000). A total of 119.20 Mb raw reads were obtained, and 89.34 clean reads remained after removing low-quality and adaptor-polluted reads and reads with a high N content. The total number of clean bases, Q20, Q30, and clean reads ratio were 13.40 Gb, 96.85%, 91.23%, and 74.95, respectively. Trinity assembly of the clean reads generated 47,959 transcripts (total length: 22,204,462 bp, mean length: 462 bp, N50: 632 bp, N70: 339 bp, N90: 209 bp, GC content: 47.83%). A total of 29,967 unigenes (total length, 17,089,849 bp; mean length, 570 bp; N50, 826 bp; N70, 446 bp; N90, 249 bp; GC content, 47.36%) were further obtained after clustering and removal of redundant sequences using Tgicl. Finally, a total of 20,669 (68.97%) unigenes were annotated using seven functional databases: NR, 19,994 (66.72%); NT, 11,458 (38.24%); Swiss-Prot, 13,794 (46.03%); KEGG, 14,131 (47.16%); COG, 6,766 (22.58%); Interpro, 12,626 (42.13%); and GO, 9,659 (32.23%).
Sequencing, pretreatment, and annotation of Paragonimus proliferus transcriptome. The transcriptome of adult P. proliferus was sequenced using RNA-Seq (Hi-Seq Illumina X 4000). A total of 119.20 Mb raw reads were obtained, and 89.34 clean reads remained after removing low-quality and adaptor-polluted reads and reads with a high N content. The total number of clean bases, Q20, Q30, and clean reads ratio were 13.40 Gb, 96.85%, 91.23%, and 74.95, respectively. Trinity assembly of the clean reads generated 47,959 transcripts (total length: 22,204,462 bp, mean length: 462 bp, N50: 632 bp, N70: 339 bp, N90: 209 bp, GC content: 47.83%). A total of 29,967 unigenes (total length, 17,089,849 bp; mean length, 570 bp; N50, 826 bp; N70, 446 bp; N90, 249 bp; GC content, 47.36%) were further obtained after clustering and removal of redundant sequences using Tgicl. Finally, a total of 20,669 (68.97%) unigenes were annotated using seven functional databases: NR, 19,994 (66.72%); NT, 11,458 (38.24%); Swiss-Prot, 13,794 (46.03%); KEGG, 14,131 (47.16%); COG, 6,766 (22.58%); Interpro, 12,626 (42.13%); and GO, 9,659 (32.23%).

Fig. 3

Species distribution of annotated unigenes in the Paragonimus proliferus transcriptome. A total of 26.25%, 22.36%, 20.83%, and 3.7% of the annotated unigenes belonged to the genera and species Opisthorchis viverrini, Culex quinquefasciatus, Clonorchis sinensis, and Halyomorpha halys, respectively, whereas 28.86% belonged to other species.
Species distribution of annotated unigenes in the Paragonimus proliferus transcriptome. A total of 26.25%, 22.36%, 20.83%, and 3.7% of the annotated unigenes belonged to the genera and species Opisthorchis viverrini, Culex quinquefasciatus, Clonorchis sinensis, and Halyomorpha halys, respectively, whereas 28.86% belonged to other species.

Fig. 4

Venn diagram showing homologous genes among comparisons of Paragonimus proliferus vs. Paragonimus skrjabini, Paragonimus kellicotti,Paragonimus miyazakii, or Paragonimus westermani.
Venn diagram showing homologous genes among comparisons of Paragonimus proliferus vs. Paragonimus skrjabini, Paragonimus kellicotti,Paragonimus miyazakii, or Paragonimus westermani.

Fig. 5

Changes in expression of differentially expressed homologous genes between Paragonimus proliferus and four other common Paragonimus species. A total of 3950/5622 (70.26 %), 1049/1084 (96.77 %), 388/473 (82.03 %), and 189/214 (88.32 %) genes were expressed at lower levels in P. proliferus compared to Paragonimus kellicotti, Paragonimus skrjabini, Paragonimus westermani, and Paragonimus miyazakii, respectively.
Changes in expression of differentially expressed homologous genes between Paragonimus proliferus and four other common Paragonimus species. A total of 3950/5622 (70.26 %), 1049/1084 (96.77 %), 388/473 (82.03 %), and 189/214 (88.32 %) genes were expressed at lower levels in P. proliferus compared to Paragonimus kellicotti, Paragonimus skrjabini, Paragonimus westermani, and Paragonimus miyazakii, respectively.

Fig. 6

Forty-two Gene Ontology (GO) terms significantly enriched by differentially expressed homologous genes (P < 0.05).Eight genes were assigned to cellular components (CC), 10 to biological processes (BP), and 14 to molecular functions (MF).
Forty-two Gene Ontology (GO) terms significantly enriched by differentially expressed homologous genes (P < 0.05).Eight genes were assigned to cellular components (CC), 10 to biological processes (BP), and 14 to molecular functions (MF).

Fig. 7

Venn diagram showing 49 core genes identified from the 8192 differentially expressed homologous genes.
Venn diagram showing 49 core genes identified from the 8192 differentially expressed homologous genes.

Fig. 8

Fifty-eight Gene Ontology (GO) terms (11 cellular components [CC], 21 biological processes [BP], and 26 molecular functions [MF]) enriched by core genes. Four BP (phosphate-containing compound metabolic process, organophosphate metabolic process, phosphorus metabolic process, and carbohydrate derivative metabolic process) and three MF (phosphotransferase activity/alcohol group as acceptor, kinase activity, and transferase activity/transferring phosphorus-containing groups) were significantly enriched at P < 0.05.
Fifty-eight Gene Ontology (GO) terms (11 cellular components [CC], 21 biological processes [BP], and 26 molecular functions [MF]) enriched by core genes. Four BP (phosphate-containing compound metabolic process, organophosphate metabolic process, phosphorus metabolic process, and carbohydrate derivative metabolic process) and three MF (phosphotransferase activity/alcohol group as acceptor, kinase activity, and transferase activity/transferring phosphorus-containing groups) were significantly enriched at P < 0.05.

Top 13 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways significantly enriched by differentially expressed homologous genes (P < 0_05)_

PathwaysInvolving genesP valuePathway IDLevel 2
Bladder cancer80.006593ko05219Cancers: Specific types
Melanoma90.02046ko05218Cancers: Specific types
Thyroid cancer90.03693ko05216Cancers: Specific types
Pyruvate metabolism200.03104ko00620Carbohydrate metabolism
Bile secretion140.04864ko04976Digestive system
Aldosterone-sodium reabsorption regulated120.002475ko04960Excretory system
Primary immunodeficiency60.02711ko05340Immune diseases
Terpenoid backbone biosynthesis100.03597ko00900Metabolism of terpenoids and polyketides
DNA replication170.01765ko03030Replication and repair
FoxO signaling pathway240.0109ko04068Signal transduction
TGF-beta signaling pathway150.01839ko04350Signal transduction
VEGF signaling pathway110.03018ko04370Signal transduction
mTOR signaling pathway130.03336ko04150Signal transduction

Annotation information for the 16 core genes_

Gene-IDDatabaseAnnotated IDDescription
TR11359|c0_g1KEGGsmm:Smp_137080multidrug resistance protein; K05658 ATP-binding cassette, subfamily B (MDR/TAP), member 1 [EC:3.6.3.44]
TR12766|c0_g1KEGGoas:101108295tubulin alpha-3 chain; K07374 tubulin alpha
TR16634|c0_g1KEGGsmm:Smp_164960phosphatidylinositol-45-bisphosphate 3-kinase catalytic subunit alpha PI3K; K00922 phosphatidylinositol-4,5-bisphosphate 3-kinase [EC:2.7.1.153]
TR17957|c0_g1KEGGfab:101816860WASF2; WAS protein family, member 2; K05748 WAS protein family, member 2
TR89500|c0_g1KEGGsmm:Smp_159120family C48 unassigned peptidase (C48 family); K08596 sentrin-specific protease 7 [EC:3.4.22.68]
TR10230|c0_g1NRgi|358340450|dbj|GAA48338.1|retrovirus-related Pol polyprotein from transposon opus [Clonorchis sinensis]
TR11281|c0_g1NRgi|358253292|dbj|GAA52762.1|serine/threonine-protein phosphatase 2A regulatory subunit B′′ subunit alpha [Clonorchis sinensis]
TR15039|c0_g2NRgi|684389238|ref|XP_009169318.1|hypothetical protein T265_05919 [Opisthorchis viverrini] >gi|663050934|gb|KER26939.1| hypothetical protein T265_05919 [Opisthorchis viverrini]
TR18101|c0_g1NRgi|684372571|ref|XP_009164145.1|hypothetical protein T265_01791 [Opisthorchis viverrini] >gi|663056274|gb|KER32181.1| hypothetical protein T265_01791 [Opisthorchis viverrini]
TR22019|c0_g1NRgi|358337500|dbj|GAA32515.2|cell wall protein Awa1p [Clonorchis sinensis]
TR18820|c0_g1SwissProtsp|Q64640|ADK_RATAdenosine kinase OS=Rattus norvegicus GN=Adk PE=1 SV=3
TR18976|c0_g1SwissProtsp|Q9D6Z1|NOP56_MOUSENucleolar protein 56 OS=Mus musculus GN=Nop56 PE=1 SV=2
TR20969|c0_g1SwissProtsp|Q5EB30|ODF3A_XENTROuter dense fiber protein 3 OS=Xenopus tropicalis GN=odf3 PE=2 SV=1
TR21606|c0_g1SwissProtsp|Q9P2D7|DYH1_HUMANDynein heavy chain 1, axonemal OS=Homo sapiens GN=DNAH1 PE=2 SV=4
TR275|c0_g1SwissProtsp|Q6DTY7|F264_MOUSE6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4 OS=Mus musculus GN=Pfkfb4 PE=2 SV=4
TR50927|c0_g1SwissProtsp|Q3UM45|PP1R7_MOUSEProtein phosphatase 1 regulatory subunit 7 OS=Mus musculus GN=Ppp1r7 PE=1 SV=2

Top 28 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways significantly enriched by core genes (P < 0_05)_

PathwayPathway IDLevel 2PvalueInvolving DEHGs
Choline metabolism in cancerko05231Cancers: Overview0.004227PI3K;WASF2
MicroRNAs in cancerko05206Cancers: Overview0.01585PI3K;MRP
Melanomako05218Cancers: Specific types0.02688PI3K
Acute myeloid leukemiako05221Cancers: Specific types0.0292PI3K
Non-small cell lung cancerko05223Cancers: Specific types0.03013PI3K
Pancreatic cancerko05212Cancers: Specific types0.03338PI3K
Endometrial cancerko05213Cancers: Specific types0.04168PI3K
Chronic myeloid leukemiako05220Cancers: Specific types0.04397PI3K
Colorectal cancerko05210Cancers: Specific types0.04718PI3K
Fructose and mannose metabolismko00051Carbohydrate metabolism0.04352PFK-2/FBPase2
Apoptosisko04210Cell growth and death0.03661PI3K
Carbohydrate digestion and absorptionko04973Digestive system0.0292PI3K
Type II diabetes mellitusko04930Endocrine and metabolic diseases0.02781PI3K
Regulation of lipolysis in adipocytesko04923Endocrine system0.03292PI3K
Thyroid hormone signaling pathwayko04919Endocrine system0.03431PI3K;PFK-2/FBPase2
Prolactin signaling pathwayko04917Endocrine system0.03754PI3K
Aldosterone-regulated sodium reabsorptionko04960Excretory system0.03013PI3K
Fc gamma R-mediated phagocytosisko04666Immune system0.005578PI3K;WASF2
Toll-like receptor signaling pathwayko04620Immune system0.02641PI3K
Fc epsilon RI signaling pathwayko04664Immune system0.03477PI3K
B cell receptor signaling pathwayko04662Immune system0.03754PI3K
Bacterial invasion of epithelial cellsko05100Infectious diseases: Bacterial0.02904PI3K;WASF2
Chagas disease (American trypanosomiasis)ko05142Infectious diseases: Parasitic0.04214PI3K
ABC transportersko02010Membrane transport0.0426MRP
AMPK signaling pathwayko04152Signal transduction0.007408PI3K;PFK-2/FBPase2
Jak-STAT signaling pathwayko04630Signal transduction0.03615PI3K
VEGF signaling pathwayko04370Signal transduction0.03846PI3K
mTOR signaling pathwayko04150Signal transduction0.04901PI3K
DOI: https://doi.org/10.2478/helm-2020-0029 | Journal eISSN: 1336-9083 | Journal ISSN: 0440-6605
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Language: English
Page range: 196 - 210
Submitted on: Nov 8, 2019
Accepted on: Apr 1, 2020
Published on: Aug 5, 2020
Published by: Slovak Academy of Sciences, Mathematical Institute
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
Keywords:
transcriptome,
homologous genes,
interspecies differences
Related subjects:
Life sciences,
Zoology,
Ecology,
Life sciences, other,
Medicine,
Clinical medicine,
Microbiology, virology and infection epidemiology

© 2020 S. H. Li, S. D. Li, H. J. Li, J. Y. Li, J. J. Xu, G. J. Chang, L. J. Yang, W. Q. Wang, Y. L. Zhang, Z. Q. Ma, S. M. He, W. L. Wang, H. L. Huang, published by Slovak Academy of Sciences, Mathematical Institute
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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