Assembly of sequences of Northern China alligatorweed identifies processes and gene ontologies associated with invasiveness and provides genomic resources for population and gene regulation studies

Biological invasions remain a major global challenge. Alligatorweed (Alternanthera philoxeroides (Mart.) Griseb.), native to South America, has had profound negative effects on ecosystem function and economy in Australia, North America, and Asia. It is an invasive and primarily aquatic plant that, despite a documented lack of genetic diversity, is unusually adaptive - thriving in both aquatic and terrestrial environments. However, genetic resources for studying this invasive plant are limited. Here, we have assembled the transcriptome of alligatorweed using all publicly available cDNA sequences. The resulting assembly produced over 500K contigs with an average length of [~]700 bases and an N50 of >1000 bases and contains over 100K probable gene-coding sequences. Although this assembly is slightly smaller than the previously published assembly developed from just cold-treated shoot tips, the new assembly is slightly more complete with over 95% of the conserved plant genes being represented as full length transcripts, and only 2.3% of these conserved genes being unrepresented compared to 2.7% missing in the earlier assembly. Resources from the PANTHER database were used to annotate all transcripts containing long open reading frames. Comparisons to several plant species identified gene ontologies that were over- and under-represented in the alligatorweed transcriptome including cellular transport and cytoskeletal processes and cell signaling, which could explain the high growth rate and phenotypic plasticity that make alligatorweed particularly invasive. We also sequenced and assembled a genomic database for alligatorweed using only short read technologies. This assembly produced over ten million contigs with an average length of only 300 bases and an N50 of 451 bases. However, 88% of the transcripts were represented among the genomic contigs, indicating that these contigs could serve as a source for regulatory elements for genes previously shown to be differentially expressed under various conditions. Kmer analysis indicated that 22% of the alligatorweed genome was comprised of repetitive elements. A similarity search against the plant repetitive element database indicated that long terminal repeat containing elements including copia- and gypsy-like elements made up the bulk of the transposons present in the alligatorweed genome. Additionally, we assembled and annotated a full-length chloroplast and a partial mitochondrial genome. Combined, these resources provide a source of gene sequences that should be useful for more complete genomic assemblies and for investigating gene structure and function in this particularly adaptable and invasive species. The results will provide an excellent starting point for many different investigations into the biology and ecology of alligatorweed, strengthen our understanding of the invasiveness, biology and ecology of invasive plants, and will help develop a reasonable management strategy to reduce risk and costs of the impacts.