Adaptive evolution of the symbiotic gene is not correlated with shifts of rhizobial specificity in the genus -0

<p><b>Copyright information:</b></p><p>Taken from "Adaptive evolution of the symbiotic gene is not correlated with shifts of rhizobial specificity in the genus "</p><p>http://www.biomedcentral.com/1471-2148/7/210</p><p>BMC Evolutionary Biology 2007;7():210-210.</p><p>Published online 6 Nov 2007</p><p>PMCID:PMC2247475.</p><p></p>ction of ancestral states is from ref. [13]. The numbered branch labels indicate branch where most likely shifts in rhizobial specificity occurred. B. Phylogram with branch lengths estimated with the codon model (model M8). The numbered branches are those used for testing positive selection (1–5: same as in Figure 1A; 6: noticed for having an unexpected length). Asterisks indicate branches with an significantly higher than in the rest of the tree. The scale for branch length represents 0.1 nucleotide substitution per codon

Adaptive evolution of the symbiotic gene is not correlated with shifts of rhizobial specificity in the genus -1

<p><b>Copyright information:</b></p><p>Taken from "Adaptive evolution of the symbiotic gene is not correlated with shifts of rhizobial specificity in the genus "</p><p>http://www.biomedcentral.com/1471-2148/7/210</p><p>BMC Evolutionary Biology 2007;7():210-210.</p><p>Published online 6 Nov 2007</p><p>PMCID:PMC2247475.</p><p></p>s reference sequence, two sites have been inserted between sites 240 and 241 and are not numbered in this figure. GAP: the positions 330 to 342 are missing and the numbering jumps from 329 to 343. The dotted line represents = 1. Arrowheads: candidate sites for positive selection. Shaded frames: LRRs (solvent-exposed β sheets are marked by darker frames)

Primer pairs, PCR conditions, and peptide nucleic acid clamps affect fungal diversity assessment from plant root tissues

High-throughput sequencing has become a prominent tool to assess plant-associated microbial diversity. Still, some technical challenges remain in characterising these communities, notably due to plant and fungal DNA co-amplification. Fungal-specific primers, Peptide Nucleic Acid (PNA) clamps, or adjusting PCR conditions are approaches to limit plant DNA contamination. However, a systematic comparison of these factors and their interactions, which could limit plant DNA contamination in the study of plant mycobiota, is still lacking. Here, three primers targeting the ITS2 region were evaluated alone or in combination with PNA clamps both on nettle (Urtica dioica) root DNA and a mock community. PNA clamps did not improve the richness or diversity of the fungal communities but increased the number of fungal reads. Among the tested factors, the most significant was the primer pair. Specifically, the 5.8S-Fun/ITS4-Fun pair exhibited a higher OTU richness but fewer fungal reads. Our study demonstrates that the choice of primers is critical for limiting plant and fungal DNA co-amplification. PNA clamps increase the number of fungal reads when ITS2 is targeted but do not result in higher fungal diversity recovery at high sequencing depth. At lower read depths, PNA clamps might enhance microbial diversity quantification for primer pairs lacking fungal specificity.</p

Galaxy9-[F__ORFs]

Fasta format file containing contigs with ORFS used in the study. Contigs were a subset of denovo assembly of the transcriptome reads obtained for this study. The raw reads are available from SRA (see original publication for accession numbers

Additional file 1 of Whole-genome sequencing and comparative genomics reveal candidate genes associated with quality traits in Dioscorea alata

Supplementary Material 1

RAM63_reverse_500k

RAM63_reverse_500

De novo assembly Chloroplast of Dioscorea rotundata

The software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Dioscorea elephantipes (EF380353.1

De novo assembly Chloroplast of Digitaria excilis

The software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Pennisetum glaucu

Description of the bait design.

<p>Orange lines represent the durum wheat genome, with the targeted SNP in brackets. Bait sequences are represented in grey. The number of SNPs targeted by each type of bait is specified.</p

De novo assembly Chloroplast of Cenchrus americanus

The software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Zea may