Transcriptome characterisation and simple sequence repeat marker discovery in the seagrass Posidonia oceanica

Abstract

Posidonia oceanica is an endemic seagrass in the Mediterranean Sea, where it provides important ecosystem services and sustains a rich and diverse ecosystem. P. oceanica meadows extend from the surface to 40 meters depth. With the aim of boosting research in this iconic species, we generated a comprehensive RNA-Seq data set for P. oceanica by sequencing specimens collected at two depths and two times during the day. With this approach we attempted to capture the transcriptional diversity associated with change in light and other depth-related environmental factors. Using this extensive data set we generated gene predictions and identified an extensive catalogue of potential Simple Sequence Repeats (SSR) markers. The data generated here will open new avenues for the analysis of population genetic features and functional variation in P. oceanica. In total, 79,235 contigs were obtained by the assembly of 70,453,120 paired end reads. 43,711 contigs were successfully annotated. A total of 17,436 SSR were identified within 13,912 contigs.

Heat‐stress induced flowering can be a potential adaptive response to ocean warming for the iconic seagrass Posidonia oceanica

“…The newly assembled transcriptome was combined with three previously published P. oceanica transcriptomes using Trinity to generate a comprehensive and representative transcriptome of the species. A whole description of methods and bioinformatic analysis of these three de novo assemblies can be found elsewhere (D'Esposito et al, ; Entrambasaguas et al, ; Marín‐Guirao et al, ). In order to remove intra‐assembly redundancy, each individual assembly was firstly processed by cd‐hit‐est v4.6.7 (Huang, Niu, Gao, Fu, & Li, ) with 100% identity to remove identical contigs with a word size of 10.…”

“…A whole description of methods and bioinformatic analysis of these three de novo assemblies can be found elsewhere (D'Esposito et al, 2016;Entrambasaguas et al, 2017;Marín-Guirao et al, 2017). In order to remove intra-assembly redundancy, each individual assembly was firstly processed by cd-hit-est v4.6.7 (Huang, Niu, Gao, Fu, & Li, 2010) with 100% identity to remove identical contigs with a word size of 10.…”

Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L.

“…Libraries of cDNA from control and heat-treated deep and shallow P. oceanica meadow stands (six replicates each) were used to analyze retrotransposon expression. As reference, we used an available de novo transcriptome of P. oceanica (obtained using leaves of plants from a meadow located in Stareso, Corse, France [48] to which were added the retrotransposon sequences [38].…”

“…The expression of the 180 LTR-retrotransposon fragments was analyzed using Illumina cDNA libraries of P. oceanica, obtained from leaves of plants taken from shallow or deep meadow stands in south-eastern coast of Spain [39], publicly available in the SRA database (see Materials and Methods). Mapping was performed on a sequence set composed of gene sequences of P. oceanica [48] (see Materials and Methods) and of the 180 retrotransposon fragments. Expression data are reported in Supplementary file #1.…”

“…Although two actin-and two tubulin-encoding transcripts were highly expressed, as expected, the majority of both tubulin and actin genes were expressed at medium level (between 5 and 30 mapped reads x million, Figure 3). In order to establish the extent of the expression level of retrotransposon-related sequences, the transcription of different copies of actin-and tubulin-encoding genes, identified in the transcriptome of P. oceanica [48], was concurrently measured. The transcript abundance of 10 actin-and 22 tubulin-encoding genes in leaves of plants of shallow Posidonia meadow stands is reported in Figure 3.…”