RNA Sequencing Characterizes Transcriptomes Differences in Cold Response Between Northern and Southern Alternanthera philoxeroides and Highlight Adaptations Associated With Northward Expansion.

Wenmin Liu,Dasheng Liu,David Horvath,Peng Li

doi:10.3389/fpls.2019.00024

Abstract

Alternanthera philoxeroides recently expanded its range northwards in China. It is unknown if the range expansion has a genetic and/or epigenetic basis, or merely an environmental basis due to a warming climate. To test these possibilities, we used an RNAseq approach with a common greenhouse design to examine gene expression in individuals from the northern edge and central portion of alligator weed range from China to determine if there were differences in their responses to cold temperatures. We hypothesized that if the recent range expansion was primarily environmental, we would observe few differences or only differences unrelated to low-temperature adaptations. We assembled over 75,000 genes of which over 65,000 had long open reading frames with similarity to sequences from arabidopsis. Differences in expression between northern and southern populations that were both exposed to low temperatures showed similar expression among genes in the C-REPEAT/DRE BINDING FACTOR (CBF) regulon. However, gene set and sub-network enrichment analysis indicated differences in the response of photosynthetic processes and oxidative stress responses were different between the two populations and we relate these differences to cold adaptation. The transcriptome differences in response to cold between the individuals from the two populations is consistent with adaptations potentiating or resulting from selection after expansion into colder environments and may indicate that genetic changes have accompanied the recent northward expansion of A. philoxeroides in China. However, we cannot rule out the possibility of epigenetic changes may have a role in this expansion.

Highlights

Biological invasions are becoming a major global environmental and economic problem (Cohen and Carlton, 1998), and intentional or unintentional human activities have increasingly resulted in the introduction of invasive species far outside their native or naturalized range
A comparison to a list of highly conserved eukaryotic genes using the program Core Eukaryotic Genes Mapping Approach (CEGMA) indicated that over 93% were represented as full length transcripts in the assembly with over 99% represented at least by partial sequences (Table 3)
We have demonstrated there are differences in gene expression associated with response to cold treatments between tested individuals from populations of A. philoxeroides in the central portion of its range in South China and individuals from a population in North China which has recently expanded its range northward

Summary

Introduction

Biological invasions are becoming a major global environmental and economic problem (Cohen and Carlton, 1998), and intentional or unintentional human activities have increasingly resulted in the introduction of invasive species far outside their native or naturalized range. The fact that invasive species are introduced to new areas that differ from their native range provide a valuable insights into how ecological and evolutionary processes are influenced under novel environmental conditions (Sax et al, 2007; Lachmuth et al, 2010). Next-generation sequencing is an ideal tool for examining adaptive responses and genetic differences resulting in range expansion and is uniquely suited for non-model species (Prentis et al, 2010; Stapley et al, 2010; Ekblom and Galindo, 2011; Puzey and Vallejo-Marin, 2014). Sequence evidence of adaptation during the invasion process is currently scant for most invasive plants due to the lack of genomic resources in weedy species (Stewart et al, 2009; Vandepitte et al, 2014)

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