UPGMA dendrogram of the genetic relationships among seven buffalo breeds.

<p>The dendrogram was generated using the Nei similarity coefficient based on 69 polymorphic primer pairs.</p

EuKaryotic orthologous group (KOG) classification.

<p>Approximately 15,813 of the 86,017 unigenes with NR hits were grouped into 25 KOG classifications.</p

Frequency of classified repeat types of SSRs.

<p>The most abundant dinucleotide and trinucleotide motifs were AC/GT and AGC/CTG.</p

Pathway assignment based on the Kyoto Encyclopedia of Genes and Genomes (KEGG).

<p>(<b>A</b>) Classification based on cellular processes categories, (<b>B</b>) Classification based on environmental information processing categories, (<b>C</b>) Classification based on genetic information processing categories, (<b>D</b>) Classification based on human diseases categories, (<b>E</b>) Classification based on metabolism categories, and (<b>F</b>) Classification based on organismal systems categories.</p

Characteristics of the results of homology search for swamp buffalo unigenes.

<p>(<b>A</b>) Venn diagram of BLAST hits for unigenes against protein databases (E-value ≤1.0e-05). Numbers in the circles indicate the number of unigenes annotated by single or multiple databases, (<b>B</b>) E-value distribution of BLAST hits for each unique sequence (E-value ≤1.0e-05). (<b>C</b>) Identity distribution of BLAST hits for each sequence. (<b>D</b>) Species distribution of the top BLAST hits for the assembled unigenes (E-value ≤1.0e-05).</p

Gene ontology (GO) classification of assembled unigenes.

<p>A total of 14,439 unigenes with significant similarity in NR protein databases were assigned to GO classifications.</p

Flowchart of <i>de novo</i> assemble in swamp buffalo transcriptome and SSR discovery.

<p>Flowchart of <i>de novo</i> assemble in swamp buffalo transcriptome and SSR discovery.</p

Data files used in the paper

A zip file including data sets and input files for various analysis methods

mtDNA Haplotype Sequence Alignment

Swamp type and river type haplotype alignments. These data were used to generate Fig.S1

input file for skyline plot anlaysis

This is an example input file for skyline plot ananlysi