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

Abstract

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.

Chromosome‐level genome assembly of Indian mangrove (Ceriops tagal) revealed a genome‐wide duplication event predating the divergence of Rhizophoraceae mangrove species

“…(He et al., 2020) from the Lythraceae family. Although the chloroplast genome assemblies in C. tagal have been reported (Chen et al., 2019; Ruang‐areerate et al., 2022), the information on the nuclear genome sequence is currently not available. Here, we present the first high‐quality, chromosome‐level assembly of the C. tagal genome using the 10× Genomics and chromatin contact mapping (Hi‐C) technologies and report full‐length transcript information obtained from Pacific Biosciences isoform sequencing (Iso‐seq).…”

Characterization of the complete chloroplast genome of Carallia diplopetala (Rhizophoraceae)

“…( 2012 ) and Ruang-areerate et al. ( 2022 ). All sequences were aligned by MAFFT 7.409 (Katoh and Standley 2013 ).…”

“…The following sequences were used: Ceriops tagal NC_061404, Ceriops zippeliana NC_061405, Ceriops decandra NC_061406 (Ruang-areerate et al. 2022 ); Pellacalyx yunnanensis NC_048998 (Zhang et al, 2019 ); Kandelia obovata NC_042718 (Chen et al. 2019 ); Rhizophora stylosa NC_042819 (Li et al.…”

The characteristics of the complete chloroplast genome of Staurogyne concinnula (Hance) O. Kuntze (Acanthaceae)

“… 2017 ), with the chloroplast genome of Avicennia marina (GenBank accession number: MT012822; Ruang-Areerate et al. 2022 ) as the reference. The annotations were manually checked for errors.…”