Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica

Abstract

Tetraena mongolica is a xerophytic shrub endemic to desert regions in Inner Mongolia. This species has evolved distinct survival strategies that allow it to adapt to hyper-drought and heterogeneous habitats. Simple sequence repeats (SSRs) may provide a molecular basis in plants for fast adaptation to environmental change. Thus, identifying SSRs and their possible effects on gene behavior has the potential to provide valuable information for studies of adaptation. In this study, we sequenced six individual transcriptomes of T. mongolica from heterogeneous habitats, focused on SSRs located in genes, and identified 811 polymorphic SSRs. Of the identified SSRs, 172, 470, and 76 were located in 5 UTRs, CDSs, and 3 UTRs in 591 transcripts; and AG/CT, AAC/GTT, and AT/AT were the most abundant repeats in each gene region. Functional annotation showed that many of the identified polymorphic SSRs were in genes that were enriched in several GO terms and KEGG pathways, suggesting the functional significance of these genes in the environmental adaptation process. The identification of polymorphic genic SSRs in our study lays a foundation for future studies investigating the contribution of SSRs to regulation of genes in natural populations of T. mongolica and their importance for adaptive evolution of this species.Genes 2020, 11, 322 2 of 13 is a good candidate for studies of plant origin, evolution, and adversity adaptation in such desert regions. Around these topics, a series of fundamental research investigations have been implemented, the results of which are of importance for comprehensively understanding the properties of T. mongolica. This pioneering work includes the studies of systematic, geographic, and taxonomic aspects [7-9]; morphology and anatomy [10][11][12]; physiological ecology [13][14][15][16]; chemometrics and biochemistry [17,18]; population genetics [5]; conservation biology [19][20][21]; abiotic stress response [3]; and medicinal phytochemistry [22,23]. In recent decades, the plant has suffered from serious habitat destruction in size and has even disappeared, leading to the general decline of the species and making the survival of T. mongolica much harder than before [24]. Correspondingly, one consideration for the ongoing survival of the species that has been paid much attention recently is an apparent decrease in genetic diversity due to loss of demographics, inbreeding depression, stochastic events, and other factors [5,24]. However, contrary to the assumption of diversity loss, it has been observed that the species has an intermediate or high level of genetic diversity as detected from analyses of inter-simple sequence repeats and nuclear microsatellites, respectively [5,24]. Therefore, further exploration of these hereditary characteristics and a potential link to adaptation strategies of the species is needed.Genic simple sequence repeats (SSRs) (also called genic microsatellites or expressed sequence tag (EST)-SSRs), a relatively newly established concept, are simple sequence repeats located in ...

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