Transcriptome Assembly and Comparison of an Allotetraploid Weed Species, Annual Bluegrass, with its Two Diploid Progenitor Species, Poa supina Schrad and Poa infirma Kunth

Annual bluegrass (Poa annua L.) is one of the most widespread weed species in this world. As a young allotetraploid, P. annua has occupied diverse environments from Antarctic area to subtropical regions. To unveil the evolutionary mystery behind P. annua's wide distribution, extensive adaptability and phenotypic plasticity needs collaboration from multiple research scopes from ecology and plant physiology to population genetics and molecular biology. However, the lack of omic data and reference has greatly hampered the study. This is the first comprehensive transcriptome study on Poa species. Total RNA was extracted from P. annua and its two proposed diploid parents, P. supina Schrad and P. infirma Kunth, and sequenced in Illumina Hiseq2000. Optimized, nonredundant transcriptome references were generated for each species using four de novo assemblers (Trinity, Velvet, SOAPdenovo, and CLC Genomics Workbench) and a redundancy‐reducing pipeline (CD‐HIT‐EST and EvidentialGene tr2aacds). Using the constructed transcriptomes together with sequencing reads, we found high similarity in nucleotide sequences and homeologous polymorphisms between P. annua and the two proposed parents. Comparison of chloroplast and mitochondrion genes further confirmed P. infirma as the maternal parent. Less nucleotide percentage differences were observed between P. infirma and infirma homeologs than between P. supina and supina homeologs, indicating a higher nucleotide substitution rates in supina homeologs than in infirma homeologs. Gene ontology (GO) enrichment analysis suggested the more compatible cytoplasmic environment and cellular apparatus for infirma homeologs as the major cause for this phenomenon.