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Phylogenetic study of Baylisascaris schroederi isolated from Qinling subspecies of giant panda in China based on combined nuclear 5.8S and the second internal transcribed spacer (ITS-2) ribosomal DNA sequences

Abstract The nuclear ribosomal DNA (rDNA) region spanning 5.8S rDNA and the second internal transcribed spacer (ITS-2) of Baylisascaris schroederi isolated from the Qinling subspecies of giant panda in Shaanxi Province, China were amplified and sequenced. Sequence variations in the two rDNA regions...

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Published in:Parasitology international 2012-09, Vol.61 (3), p.497-500
Main Authors: Zhao, Guang-Hui, Li, Hong-Mei, Ryan, Una M, Cong, Mei-Mei, Hu, Bing, Gao, Man, Ren, Wan-Xin, Wang, Xing-Ye, Zhang, Shui-Ping, Lin, Qing, Zhu, Xing-Quan, Yu, San-Ke
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description Abstract The nuclear ribosomal DNA (rDNA) region spanning 5.8S rDNA and the second internal transcribed spacer (ITS-2) of Baylisascaris schroederi isolated from the Qinling subspecies of giant panda in Shaanxi Province, China were amplified and sequenced. Sequence variations in the two rDNA regions within B. schroederi and among species in the family Ascarididae were examined. The lengths of B. schroederi 5.8S and ITS-2 rDNA sequences were 156 bp and 327 bp, respectively, and no nucleotide variation was found in these two rDNA regions among the 20 B. schroederi samples examined, and these ITS-2 sequences were identical to that of B. schroederi isolated from giant panda in Sichuan province, China. The inter-species differences in 5.8S and ITS-2 rDNA sequences among members of the family Ascarididae were 0–1.3% and 0–17.7%, respectively. Phylogenetic relationships among species in the Ascarididae were re-constructed by Bayesian inference (Bayes), maximum parsimony (MP), and maximum likelihood (ML) analyses, based on combined sequences of 5.8S and ITS-2 rDNA. All B. schroederi samples clustered together and sistered to B. transfuga with high posterior probabilities/bootstrap values, which further confirmed that nematodes isolated from the Qinling subspecies of giant panda in Shaanxi Province, China represent B. schroederi . Because of the large number of ambiguously aligned sequence positions (difficulty of inferring homology by positions), ITS-2 sequence alone is likely unsuitable for phylogenetic analyses at the family level, but the combined 5.8S and ITS-2 rDNA sequences provide alternative genetic markers for the identification of B. schroederi and for phylogenetic analysis of parasites in the family Ascarididae.
doi_str_mv 10.1016/j.parint.2012.02.009
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Sequence variations in the two rDNA regions within B. schroederi and among species in the family Ascarididae were examined. The lengths of B. schroederi 5.8S and ITS-2 rDNA sequences were 156 bp and 327 bp, respectively, and no nucleotide variation was found in these two rDNA regions among the 20 B. schroederi samples examined, and these ITS-2 sequences were identical to that of B. schroederi isolated from giant panda in Sichuan province, China. The inter-species differences in 5.8S and ITS-2 rDNA sequences among members of the family Ascarididae were 0–1.3% and 0–17.7%, respectively. Phylogenetic relationships among species in the Ascarididae were re-constructed by Bayesian inference (Bayes), maximum parsimony (MP), and maximum likelihood (ML) analyses, based on combined sequences of 5.8S and ITS-2 rDNA. All B. schroederi samples clustered together and sistered to B. transfuga with high posterior probabilities/bootstrap values, which further confirmed that nematodes isolated from the Qinling subspecies of giant panda in Shaanxi Province, China represent B. schroederi . Because of the large number of ambiguously aligned sequence positions (difficulty of inferring homology by positions), ITS-2 sequence alone is likely unsuitable for phylogenetic analyses at the family level, but the combined 5.8S and ITS-2 rDNA sequences provide alternative genetic markers for the identification of B. schroederi and for phylogenetic analysis of parasites in the family Ascarididae.</description><identifier>ISSN: 1383-5769</identifier><identifier>EISSN: 1873-0329</identifier><identifier>DOI: 10.1016/j.parint.2012.02.009</identifier><identifier>PMID: 22402105</identifier><language>eng</language><publisher>Netherlands: Elsevier Ireland Ltd</publisher><subject>5.8S rDNA ; Ailuropoda melanoleuca ; Animals ; Ascarididae ; Ascaridoidea - genetics ; Ascaridoidea - isolation &amp; purification ; Bayes Theorem ; Bayesian theory ; Baylisascaris ; Baylisascaris schroederi ; China ; DNA, Helminth - genetics ; DNA, Ribosomal Spacer - genetics ; Female ; Gastroenterology and Hepatology ; Genetic Markers ; Genetic Variation ; Giant panda ; Infectious Disease ; internal transcribed spacers ; ITS-2 rDNA ; Male ; parasites ; parasitology ; Phylogeny ; Qinling subspecies ; ribosomal DNA ; Sequence Alignment ; Sequence Analysis, DNA ; Ursidae - parasitology</subject><ispartof>Parasitology international, 2012-09, Vol.61 (3), p.497-500</ispartof><rights>Elsevier Ireland Ltd</rights><rights>2012 Elsevier Ireland Ltd</rights><rights>Copyright © 2012 Elsevier Ireland Ltd. 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Sequence variations in the two rDNA regions within B. schroederi and among species in the family Ascarididae were examined. The lengths of B. schroederi 5.8S and ITS-2 rDNA sequences were 156 bp and 327 bp, respectively, and no nucleotide variation was found in these two rDNA regions among the 20 B. schroederi samples examined, and these ITS-2 sequences were identical to that of B. schroederi isolated from giant panda in Sichuan province, China. The inter-species differences in 5.8S and ITS-2 rDNA sequences among members of the family Ascarididae were 0–1.3% and 0–17.7%, respectively. Phylogenetic relationships among species in the Ascarididae were re-constructed by Bayesian inference (Bayes), maximum parsimony (MP), and maximum likelihood (ML) analyses, based on combined sequences of 5.8S and ITS-2 rDNA. 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Li, Hong-Mei ; Ryan, Una M ; Cong, Mei-Mei ; Hu, Bing ; Gao, Man ; Ren, Wan-Xin ; Wang, Xing-Ye ; Zhang, Shui-Ping ; Lin, Qing ; Zhu, Xing-Quan ; Yu, San-Ke</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c465t-f064d0ef2e7cbd5e3b60ec26d538887f2ee92d18928765e43ba76bbe9291c8963</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>5.8S rDNA</topic><topic>Ailuropoda melanoleuca</topic><topic>Animals</topic><topic>Ascarididae</topic><topic>Ascaridoidea - genetics</topic><topic>Ascaridoidea - isolation &amp; purification</topic><topic>Bayes Theorem</topic><topic>Bayesian theory</topic><topic>Baylisascaris</topic><topic>Baylisascaris schroederi</topic><topic>China</topic><topic>DNA, Helminth - genetics</topic><topic>DNA, Ribosomal Spacer - genetics</topic><topic>Female</topic><topic>Gastroenterology and Hepatology</topic><topic>Genetic Markers</topic><topic>Genetic Variation</topic><topic>Giant panda</topic><topic>Infectious Disease</topic><topic>internal transcribed spacers</topic><topic>ITS-2 rDNA</topic><topic>Male</topic><topic>parasites</topic><topic>parasitology</topic><topic>Phylogeny</topic><topic>Qinling subspecies</topic><topic>ribosomal DNA</topic><topic>Sequence Alignment</topic><topic>Sequence Analysis, DNA</topic><topic>Ursidae - parasitology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhao, Guang-Hui</creatorcontrib><creatorcontrib>Li, Hong-Mei</creatorcontrib><creatorcontrib>Ryan, Una M</creatorcontrib><creatorcontrib>Cong, Mei-Mei</creatorcontrib><creatorcontrib>Hu, Bing</creatorcontrib><creatorcontrib>Gao, Man</creatorcontrib><creatorcontrib>Ren, Wan-Xin</creatorcontrib><creatorcontrib>Wang, Xing-Ye</creatorcontrib><creatorcontrib>Zhang, Shui-Ping</creatorcontrib><creatorcontrib>Lin, Qing</creatorcontrib><creatorcontrib>Zhu, Xing-Quan</creatorcontrib><creatorcontrib>Yu, San-Ke</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Parasitology international</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhao, Guang-Hui</au><au>Li, Hong-Mei</au><au>Ryan, Una M</au><au>Cong, Mei-Mei</au><au>Hu, Bing</au><au>Gao, Man</au><au>Ren, Wan-Xin</au><au>Wang, Xing-Ye</au><au>Zhang, Shui-Ping</au><au>Lin, Qing</au><au>Zhu, Xing-Quan</au><au>Yu, San-Ke</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Phylogenetic study of Baylisascaris schroederi isolated from Qinling subspecies of giant panda in China based on combined nuclear 5.8S and the second internal transcribed spacer (ITS-2) ribosomal DNA sequences</atitle><jtitle>Parasitology international</jtitle><addtitle>Parasitol Int</addtitle><date>2012-09-01</date><risdate>2012</risdate><volume>61</volume><issue>3</issue><spage>497</spage><epage>500</epage><pages>497-500</pages><issn>1383-5769</issn><eissn>1873-0329</eissn><abstract>Abstract The nuclear ribosomal DNA (rDNA) region spanning 5.8S rDNA and the second internal transcribed spacer (ITS-2) of Baylisascaris schroederi isolated from the Qinling subspecies of giant panda in Shaanxi Province, China were amplified and sequenced. Sequence variations in the two rDNA regions within B. schroederi and among species in the family Ascarididae were examined. The lengths of B. schroederi 5.8S and ITS-2 rDNA sequences were 156 bp and 327 bp, respectively, and no nucleotide variation was found in these two rDNA regions among the 20 B. schroederi samples examined, and these ITS-2 sequences were identical to that of B. schroederi isolated from giant panda in Sichuan province, China. The inter-species differences in 5.8S and ITS-2 rDNA sequences among members of the family Ascarididae were 0–1.3% and 0–17.7%, respectively. Phylogenetic relationships among species in the Ascarididae were re-constructed by Bayesian inference (Bayes), maximum parsimony (MP), and maximum likelihood (ML) analyses, based on combined sequences of 5.8S and ITS-2 rDNA. All B. schroederi samples clustered together and sistered to B. transfuga with high posterior probabilities/bootstrap values, which further confirmed that nematodes isolated from the Qinling subspecies of giant panda in Shaanxi Province, China represent B. schroederi . Because of the large number of ambiguously aligned sequence positions (difficulty of inferring homology by positions), ITS-2 sequence alone is likely unsuitable for phylogenetic analyses at the family level, but the combined 5.8S and ITS-2 rDNA sequences provide alternative genetic markers for the identification of B. schroederi and for phylogenetic analysis of parasites in the family Ascarididae.</abstract><cop>Netherlands</cop><pub>Elsevier Ireland Ltd</pub><pmid>22402105</pmid><doi>10.1016/j.parint.2012.02.009</doi><tpages>4</tpages></addata></record>
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ispartof Parasitology international, 2012-09, Vol.61 (3), p.497-500
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1873-0329
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source ScienceDirect Journals
subjects 5.8S rDNA
Ailuropoda melanoleuca
Animals
Ascarididae
Ascaridoidea - genetics
Ascaridoidea - isolation & purification
Bayes Theorem
Bayesian theory
Baylisascaris
Baylisascaris schroederi
China
DNA, Helminth - genetics
DNA, Ribosomal Spacer - genetics
Female
Gastroenterology and Hepatology
Genetic Markers
Genetic Variation
Giant panda
Infectious Disease
internal transcribed spacers
ITS-2 rDNA
Male
parasites
parasitology
Phylogeny
Qinling subspecies
ribosomal DNA
Sequence Alignment
Sequence Analysis, DNA
Ursidae - parasitology
title Phylogenetic study of Baylisascaris schroederi isolated from Qinling subspecies of giant panda in China based on combined nuclear 5.8S and the second internal transcribed spacer (ITS-2) ribosomal DNA sequences
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