Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests.

Panthita Ruang-Areerate,Wasitthee Kongkachana,Phakamas Phetchawang,Wirulda Pootakham,Chatree Maknual,Sithichoke Tangphatsornruang,Wijarn Meepol,Darunee Jiumjamrassil,Thippawan Yoocha

doi:10.3390/biology11030383

Panthita Ruang-Areerate, Wasitthee Kongkachana + Show 7 more

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https://doi.org/10.3390/biology11030383

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Abstract

Simple SummaryWe sequenced the complete chloroplast genomes of three Ceriops species (C. decandra, C. zippeliana, and C. tagal) and Avicennia lanata and performed comparative analyses among them. All chloroplast genomes have a circular quadripartite structure containing LSC, SSC, and two IR regions. The rpl32 gene was lost in C. zippeliana, and the infA gene was present in only A. lanata. Comparative genome analysis showed that the IR contraction or expansion events resulted in the differentiation of three genes and pseudogenes. Additionally, repeats and SSRs were identified and compared among them and other relative mangrove species. The phylogenetic analysis strongly supports that C. decandra is evolutionarily closer to C. zippeliana and A. lanata is closer to A. marina. In addition, two primer pairs were developed for species identification unique to the three Ceriops species.Ceriops and Avicennia are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of Ceriops decandra, Ceriops zippeliana, and Ceriops tagal were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas Avicennia lanata was 148,264 bp in length. The gene content and gene order are highly conserved among these species. The chloroplast genome contains 125 genes in A. lanata and 129 genes in Ceriops species. Three duplicate genes (rpl2, rpl23, and trnM-CAU) were found in the IR regions of the three Ceriops species, resulting in expansion of the IR regions. The rpl32 gene was lost in C. zippeliana, whereas the infA gene was present in A. lanata. Short repeats (<40 bp) and a lower number of SSRs were found in A. lanata but not in Ceriops species. The phylogenetic analysis supports that all Ceriops species are clustered in Rhizophoraceae and A. lanata is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the rps7 gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three Ceriops species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in Ceriops and Avicennia species.

Highlights

Mangroves are extremely important plants to coastal ecosystems
We investigated the chloroplast genomes of four mangrove species that are commonly distributed in the middle (Ceriops decandra, C. zippeliana, and C. tagal) and seaward (Avicennia lanata) zones of the coastal region of Southeast Asia to understand the evolutionary relationships under different coastal environments and to identify genetic markers for species identification and candidate genes under selective pressures
The chloroplast genome of A. lanata is compact compared with the three Ceriops species

Summary

Introduction

Mangroves are extremely important plants to coastal ecosystems. They protect shorelines from erosion and provide marine nursery areas and breeding sites for a variety of marine and terrestrial organisms (e.g., fish, crustaceans, reptiles, birds, and mammals) [1,2]. For human beings, they are used for food, fuels, timber, and medicines [1,2]. There are roughly 70 mangrove species in 28 genera in 16–19 families [4,5]. A few mangrove species in the families Rhizophoraceae and Acanthaceae occupy most areas of mangrove forests [6,7]. Mangrove forest areas have been dramatically decreasing due to anthropogenic impacts and climate change [8–10]. A number of whole mangrove genomes have been reported [15–23]

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