Computational protocol: Nitrogen hurdle of host alternation for a polyphagous aphid and the associated changes of endosymbionts

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Protocol publication

[…] Partial 16S rRNA gene sequences of S. symbiotica were obtained from a range of aphids (GenBank accession numbers see ), and partial sequences of 16S rRNA gene from E. coli was used as the outgroup. All sequences obtained were aligned using MEGA6 and trimmed using the option of automated in TRIMAL v.1.2. The neighbor-joining phylogeny tree was reconstructed by MEGA6 with default settings with 1000 bootsrapped replicates. [...] Raw data of developmental time, survival rate, longevity, and fecundity of M. persicae on different plants were analyzed by basic run of TWOSEX-MSChart, the computer program for the age-stage, two-sex life table analysis modified for parthenogenetic aphid (available at http://140.120.197.173/Ecology//Download/TWOSEX-MSChart.rar). The intrinsic rate of increase (r) was also obtained by using the program, TWOSEX-MSChart. Then 100,000 bootstrap replicates were used to calculate SEs of all estimates of life-table and population parameters and pair-wise comparison of these parameters with 1000 bootstrap replicates was conducted.Adult weight, endosymbiont abundance, individual amino acid concentrations, TAAs concentrations, EAAs concentrations and proportion of EAAs were checked for normal distribution using the Kolmogorov-Smirnov test before further analysis. These data were analyzed by one-way ANOVA with Tukey’s HSD test using IBM SPSS Statistics package v. 19.0 (SPSS Inc., Chicago, IL, USA). The variation among the body width of M. persicae adult, trichome spacing of tobacco and eggplant leaves was also analyzed by one-way ANOVA with Tukey’s HSD test using SPSS 19.0. Individual amino acid concentrations in different plant exudates were transformed to mol %, which were further analyzed via multiple-dimensional principal component analysis (PCA) using SAS Version 9.1. The variations among the amino acid composition profiles were based on first two principal components analysis. Each spot in the PCA plot represented individual sample, and distances among the spot groups showed the variation level of amino acid profiles among different treatments. A P < 0.05 was taken as statistical significance for all analyses. […]

Pipeline specifications

Software tools MEGA, trimAl, SPSS
Applications Miscellaneous, Phylogenetics
Organisms Myzus persicae, Solanum melongena, Nicotiana tabacum, Spinacia oleracea
Chemicals Nitrogen