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Avoidance and Potential Remedy Solutions of Chimeras in Reconstructing the Phylogeny of Aphids Using the 16S rRNA Gene of Buchnera: A Case in Lachninae (Hemiptera).

Chen R, Wang Z, Chen J, Qiao GX - Int J Mol Sci (2015)

Bottom Line: Thus, chimeric sequences may lead to the discovery of non-existent endosymbiont species and mislead Buchnera-based phylogenetic analysis that lead to false conclusions.In this study, a high probability (6.49%) of chimeric sequence occurrence was found in the amplified 16S rRNA gene sequences of endosymbionts from aphid species in the subfamily Lachninae.Thus, our study strongly suggests that using appropriate methods to detect chimeric 16S rRNA sequences may avoid some false conclusions in endosymbiont-based aphid research.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. chrui11@live.cn.

ABSTRACT
It is known that PCR amplification of highly homologous genes from complex DNA mixtures can generate a significant proportion of chimeric sequences. The 16S rRNA gene is not only widely used in estimating the species diversity of endosymbionts in aphids but also used to explore the co-diversification of aphids and their endosymbionts. Thus, chimeric sequences may lead to the discovery of non-existent endosymbiont species and mislead Buchnera-based phylogenetic analysis that lead to false conclusions. In this study, a high probability (6.49%) of chimeric sequence occurrence was found in the amplified 16S rRNA gene sequences of endosymbionts from aphid species in the subfamily Lachninae. These chimeras are hybrid products of multiple parent sequences from the dominant species of endosymbionts in each corresponding host. It is difficult to identify the chimeric sequences of a new or unidentified species due to the high variability of their main parent, Buchnera aphidicola, and because the chimeric sequences can confuse the phylogenetic analysis of 16S rRNA gene sequences. These chimeras present a challenge to Buchnera-based phylogenetic research in aphids. Thus, our study strongly suggests that using appropriate methods to detect chimeric 16S rRNA sequences may avoid some false conclusions in endosymbiont-based aphid research.

No MeSH data available.


Related in: MedlinePlus

The maximum likelihood (ML) phylogenetic tree inferred from data-set I (without chimeric sequences). Buchnera sequences are represented by the names of their host species. The sequences obtained from this study are underlined. The nodes are marked by their ML bootstrap values. The bar represents 4% of sequence change with regard to the likelihood distance. The underlined species are with chimeric sequences.
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ijms-16-20152-f002: The maximum likelihood (ML) phylogenetic tree inferred from data-set I (without chimeric sequences). Buchnera sequences are represented by the names of their host species. The sequences obtained from this study are underlined. The nodes are marked by their ML bootstrap values. The bar represents 4% of sequence change with regard to the likelihood distance. The underlined species are with chimeric sequences.

Mentions: The results of the analyses of these two data sets indicated that the 16S sequences of Buchnera clustered into five clades (red, yellow, violet, green, and gray clade in Figure 2 and Figure 3). Tree topologies were very different for data-set II (with chimeric sequences) (Figure 3) and data-set I (Figure 2). The violet clade (= Lachninae) is monophyletic and forms the sister group of the green clade in Figure 2, while it is a “basal” paraphyletic assemblage in Figure 3. The species Tetraneura caerulescens (non-chimeric sequence) falls into the green clade in Figure 2, while in Figure 3 it is remote from this clade. All chimeric sequences fell into the in group, except for the chimeric sequence from Lachnus siniquercus (Figure 3). According to the results of the SH test, the difference between the phylogenetic trees constructed by data-sets I and II was significant because the p value was <0.05. Thus, chimeric sequences can confuse the phylogenetic structure of Buchnera based on strict host correlation. We also emphasize that the ML bootstrap values are higher in data-set I than in data-set II.


Avoidance and Potential Remedy Solutions of Chimeras in Reconstructing the Phylogeny of Aphids Using the 16S rRNA Gene of Buchnera: A Case in Lachninae (Hemiptera).

Chen R, Wang Z, Chen J, Qiao GX - Int J Mol Sci (2015)

The maximum likelihood (ML) phylogenetic tree inferred from data-set I (without chimeric sequences). Buchnera sequences are represented by the names of their host species. The sequences obtained from this study are underlined. The nodes are marked by their ML bootstrap values. The bar represents 4% of sequence change with regard to the likelihood distance. The underlined species are with chimeric sequences.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4613194&req=5

ijms-16-20152-f002: The maximum likelihood (ML) phylogenetic tree inferred from data-set I (without chimeric sequences). Buchnera sequences are represented by the names of their host species. The sequences obtained from this study are underlined. The nodes are marked by their ML bootstrap values. The bar represents 4% of sequence change with regard to the likelihood distance. The underlined species are with chimeric sequences.
Mentions: The results of the analyses of these two data sets indicated that the 16S sequences of Buchnera clustered into five clades (red, yellow, violet, green, and gray clade in Figure 2 and Figure 3). Tree topologies were very different for data-set II (with chimeric sequences) (Figure 3) and data-set I (Figure 2). The violet clade (= Lachninae) is monophyletic and forms the sister group of the green clade in Figure 2, while it is a “basal” paraphyletic assemblage in Figure 3. The species Tetraneura caerulescens (non-chimeric sequence) falls into the green clade in Figure 2, while in Figure 3 it is remote from this clade. All chimeric sequences fell into the in group, except for the chimeric sequence from Lachnus siniquercus (Figure 3). According to the results of the SH test, the difference between the phylogenetic trees constructed by data-sets I and II was significant because the p value was <0.05. Thus, chimeric sequences can confuse the phylogenetic structure of Buchnera based on strict host correlation. We also emphasize that the ML bootstrap values are higher in data-set I than in data-set II.

Bottom Line: Thus, chimeric sequences may lead to the discovery of non-existent endosymbiont species and mislead Buchnera-based phylogenetic analysis that lead to false conclusions.In this study, a high probability (6.49%) of chimeric sequence occurrence was found in the amplified 16S rRNA gene sequences of endosymbionts from aphid species in the subfamily Lachninae.Thus, our study strongly suggests that using appropriate methods to detect chimeric 16S rRNA sequences may avoid some false conclusions in endosymbiont-based aphid research.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. chrui11@live.cn.

ABSTRACT
It is known that PCR amplification of highly homologous genes from complex DNA mixtures can generate a significant proportion of chimeric sequences. The 16S rRNA gene is not only widely used in estimating the species diversity of endosymbionts in aphids but also used to explore the co-diversification of aphids and their endosymbionts. Thus, chimeric sequences may lead to the discovery of non-existent endosymbiont species and mislead Buchnera-based phylogenetic analysis that lead to false conclusions. In this study, a high probability (6.49%) of chimeric sequence occurrence was found in the amplified 16S rRNA gene sequences of endosymbionts from aphid species in the subfamily Lachninae. These chimeras are hybrid products of multiple parent sequences from the dominant species of endosymbionts in each corresponding host. It is difficult to identify the chimeric sequences of a new or unidentified species due to the high variability of their main parent, Buchnera aphidicola, and because the chimeric sequences can confuse the phylogenetic analysis of 16S rRNA gene sequences. These chimeras present a challenge to Buchnera-based phylogenetic research in aphids. Thus, our study strongly suggests that using appropriate methods to detect chimeric 16S rRNA sequences may avoid some false conclusions in endosymbiont-based aphid research.

No MeSH data available.


Related in: MedlinePlus