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2.
Figure 1

Figure 1. Species distribution of homology search of unigenes against the Nr database.. From: Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis.

The species distribution is shown as a percentage of the total homologous sequences in the NCBI Nr protein database with an E-value<10−5.

Shang-Wei Li, et al. PLoS One. 2012;7(11):e47401.
3.
Figure 8

Figure 8. Differentially expressed genes (DEGs) between the different developmental phases of RLF.. From: Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis.

This figure shows the number of upregulated (red) and downregulated (green) genes in each pairwise comparison of eggs, 3rd instar larvae, pupae, and adults.

Shang-Wei Li, et al. PLoS One. 2012;7(11):e47401.
4.
Figure 2

Figure 2. Gene ontology classification of the unigenes.. From: Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis.

A total of 8,838 unigenes were annotated by three categories: biological process, cellular component, and molecular function. The left and right y-axes denote separately the percent and number of genes in the category.

Shang-Wei Li, et al. PLoS One. 2012;7(11):e47401.
5.
Figure 6

Figure 6. Phylogenetic tree of carboxylesterases from Cnaphalocrocis medinalis (Cm) and Bombyx mori (Bm).. From: Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis.

The tree was constructed from the multiple alignments using MEGA 5.0 software and generated with 1,000 bootstrap trials using the neighbor-joining method. The numbers indicate the bootstrap confidence values obtained for each node after 1,000 repetitions.

Shang-Wei Li, et al. PLoS One. 2012;7(11):e47401.
6.
Figure 5

Figure 5. Phylogenetic tree of glutathione S-transferases from Cnaphalocrocis medinalis (Cm) and Bombyx mori (Bm).. From: Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis.

The tree was constructed from the multiple alignments using MEGA 5.0 software and generated with 1,000 bootstrap trials using the neighbor-joining method. The numbers indicate the bootstrap confidence values obtained for each node after 1,000 repetitions.

Shang-Wei Li, et al. PLoS One. 2012;7(11):e47401.
7.
Figure 4

Figure 4. Phylogenetic tree of cytochrome P450s from Cnaphalocrocis medinalis (Cm) and Bombyx mori (Bm).. From: Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis.

The tree was constructed from the multiple alignments using MEGA 5.0 software and generated with 1,000 bootstrap trials using the neighbor-joining method. The numbers indicate the bootstrap confidence values obtained for each node after 1,000 repetitions.

Shang-Wei Li, et al. PLoS One. 2012;7(11):e47401.
8.
Figure 10

Figure 10. Genes related to sex differences.. From: Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis.

A: Gene expression analysis from DGE data. The fold changes in gene expression were calculated as the log2 ratio of females (TPM) to males (TPM). B: qRT-PCR analysis of gene expression. This figure shows the fold change of differential expression for 12 genes (Vg, VgR, YP4, HSP19.8, TSD, GST, CarE7, Tra2, CYP6CV1, PBP, OBP2, and SFP) in females compared with male adults.

Shang-Wei Li, et al. PLoS One. 2012;7(11):e47401.
9.
Figure 9

Figure 9. Genes in flight muscles from adult RLF.. From: Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis.

A: Gene expression analysis from DGE data. The fold changes in gene expression were calculated as the log2 ratio of adults (TPM) to 3rd instar larvae (TPM). B: qRT-PCR analysis of gene expression. This figure shows the fold change of differential expression for 10 genes (Fln, Mlc1, Mlc2, Unc89, PMY, mPMY, Tm2, TpnC, TpnT, Tm1, and Kettin) in adults compared with 3rd instar larvae.

Shang-Wei Li, et al. PLoS One. 2012;7(11):e47401.
10.
Figure 7

Figure 7. An unrooted consensus tree of annotated OBP proteins among C. medinalis and other Lepidopteran insects.. From: Transcriptome and Gene Expression Analysis of the Rice Leaf Folder, Cnaphalocrosis medinalis.

This tree was constructed from the multiple alignments using MEGA 5.0 software, generated with 1,000 bootstrap trials using the neighbor-joining method, and presented with a cut-off value of 10%. For most OBPs, names are presented as a three-letter code (first letter of genus followed by first two letters of species name) followed by the GenBank accession number in the parenthesis at the end of each branch. The insect species are indicated by colored markers. Atra, Amyelois transitella; Bmor, Bombyx mori; Cmed, Cnaphalocrocis medinalis; Csup, Chilo suppressalis; Dind, Diaphania indica; Hvir, Heliothis virescens; Ldis, Lymantria dispar; Msex, Manduca sexta; Pxyl, Plutella xylostella; Sfru, Spodoptera frugiperda.

Shang-Wei Li, et al. PLoS One. 2012;7(11):e47401.

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