Identification of Rubber Tree Aquaporin Genes

The deduced amino acids of HbAQPs available in the NCBI GenBank were used as queries to search the available RRIM600 genome and our in-house RY7-33-97 genome for rubber tree homologs. Sequences with an E-value of less than 1e⁻⁵ in the tBlastn search [61 (link)] were selected for further analyses. The gene structures were firstly predicted using GeneMark.hmm [62 (link)], and the gene models were further validated with ESTs and raw RNA sequencing reads available at GenBank. The exon-intron structures of AQP genes detected in the laticifer transcriptome were also confirmed by aligning the cloned cDNAs to the corresponding gene sequences. Gene structures were displayed using GSDS [63 (link)]. Homology search for nucleotides or Sanger ESTs was performed using Blastn, and sequences with an identity of more than 98 % were taken into account. RNA sequencing reads were mapped using Bowtie 2 [64 (link)] with default parameters, and mapped read number of more than one was counted as expressed. Unless specific statements, the tools used in this study were performed with default parameters.