Lineage‐specific evolution of mangrove plastid genomes

Abstract

Mangroves is an umbrella term for plants located across the tropics and sub-tropics that live in the coastal region, between the sea and the land. All mangroves evolved from terrestrial plants, providing the opportunity to assess convergence, as well as the lineage-specific features, at the genetic level. In this study, we compared chloroplast genomes from 21 mangrove species, covering main phylogenetic clades. We demonstrate that chloroplast gene order, content, and genome size is largely conserved in mangroves. The exceptions are loss of the photosystem I gene psaZ in Acanthus ilicifolius and inversion of the ribosomal protein gene rpl23 in Avicennia germinans. The repeat content of mangrove chloroplast varied between species, but was conserved within species of the same order. Sequence diversity analysis revealed that the IR (invert repeat) region was highly conserved compared to the SC (single-copy) region in most phylogenetic clades, except clade core leptosporangiates (ferns). The ribosomal protein gene rps7 was under positive selection in Kandelia obovato, Rhizophora stylosa, Bruguiera sexangular and Rhizophora mangle, a monophyletic branch of clade fabids, while no evidence of positive selection was found in other mangrove lineages. Taken together, our data suggests that convergent evolutionary dynamics leaves no significant signal on the plastid genome of mangroves. The complete chloroplast genomes provided in this study shed light on the evolution of these important plastids and provides a valuable resource for further research efforts. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Complete chloroplast genome sequences of five Bruguiera species (Rhizophoraceae): comparative analysis and phylogenetic relationships

“…The result of the rps7 gene is consistent with previous findings for many mangrove species and some land plants such as K . obovata , R. stylosa , R. mangle and Ananas comosus (pineapple) ( Redwan, Saidin & Kumar, 2015 ; Han et al, 2020 ). The rps7 gene encoding small ribosomal protein seven is involved in the regulation of chloroplast translation ( Fargo, Boynton & Gillham, 2001 ).…”

“…A total 74 shared plastid protein-coding genes in the five Bruguiera species and four terrestrial plant species, Erythroxylum novogranatense ( ), Ctenolophon englerianus ( ), Averrhoa carambola ( ) and Vitis rotundifolia ( ) ( Table S5 ), were used to investigate selection pressures. Pairwise sequence alignments for each gene between the Bruguiera species and the terrestrial plant species based on the background of different evolutionary clades, including Erythroxylaceae ( E. novogranatense) , Ctenolophonaceae ( C. englerianus ), Oxalidales ( A. carambola ), and Rosids ( Vitis rotundifolia ) ( Han et al, 2020 ) were generated using MUSCLE with default setting in MEGA X ( Edgar, 2004 ; Kumar et al, 2018 ). Gaps between compared sequences were removed before further analysis.…”

Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments

“…In addition, they carry genes mainly involved in photosynthesis, transcription, and translation. Mangrove chloroplast genomes are also observed to be highly conserved ( Han et al., 2020 ). All of the mangrove chloroplast genomes analyzed contained a typical quadripartite structure with IR, LSC, and SSC regions ( Table 4 ).…”

“…Comparative analysis of chloroplast genomes of Nypa fruticans , B. sexangula , Acrostichum aureus , A. ilicifolius , Acrostichum speciosum , R. mangle , Sonneratia hainanensis , Hernandez sonora , Avicennia germinans , and L. littorea , suggests that convergent evolution of mangroves have no effect on chloroplast genomes ( Han et al., 2020 ). Moreover, correlation of chloroplast genome and adaptations could not be established between mangroves and non-mangrove species ( Yang et al., 2019 ), even though the individual gene products of the chloroplast genome may have been complemented in known adaptive responses.…”

“…Photosynthesis I and II, cytochrome b 6/f complex, ATP synthase, and Rubisco along with small and large subunit proteins such as ribosomal protein S (rps) and ribosomal protein L (rpl) are annotated from A. marina chloroplast genome ( Asaf et al., 2021 ). Another ribosomal protein gene, rpl7 from the members of Rhizophoraceae ( R. mangle , B. sexangula , R. stylosa , and K. obovata ) is reported to show signs of positive selection ( Han et al., 2020 ). The basic role of plant ribosomal proteins is in translation but they are also known for their involvement in hormone signaling and developmental processes.…”