Complete chloroplast genomes of 14 mangroves: phylogenetic and genomic comparative analyses

Abstract

<jats:title>Abstract</jats:title><jats:p>Mangroves are main components of an ecosystem which connect land and ocean and is of significant ecological importance. They are found around the world and taxonomically distributed in 17 families. Until now there has been no evolutionary phylogenetic analyses on mangroves based on complete plastome sequences. In order to infer the relationship between mangroves and terrestrial plants at the molecular level, we generated chloroplast genomes of 14 mangrove species from eight families, spanning six orders: Fabales (<jats:italic>Pongamia pinnata</jats:italic>), Lamiales (<jats:italic>Avicennia marina</jats:italic>), Malpighiales (<jats:italic>Excoecaria agallocha</jats:italic>, <jats:italic>Bruguiera sexangula</jats:italic>, <jats:italic>Kandelia obovata</jats:italic>, <jats:italic>Rhizophora stylosa</jats:italic>, <jats:italic>Ceriops tagal</jats:italic>), Malvales (<jats:italic>Hibiscus tiliaceus</jats:italic>, <jats:italic>Heritiera littoralis</jats:italic>, <jats:italic>Thespesia populnea</jats:italic>), Myrtales (<jats:italic>Laguncularia racemose</jats:italic>, <jats:italic>Sonneratia ovata</jats:italic>, <jats:italic>Pemphis acidula</jats:italic>), and Sapindales (<jats:italic>Xylocarpus moluccensis</jats:italic>). The whole-genome length of these chloroplasts is from 149kb to 168kb. They have a conserved structure, with two Inverted Repeat (IRa and IRb, ~25.8kb), a large single-copy region (LSC, ~89.0kb), a short single-copy (SSC, ~18.9kb) region, as well as ~130 genes (85 protein-coding, 37 tRNA, and 8 rRNA). The number of simple sequence repeats (SSRs) varied between mangrove species. Phylogenetic analysis using complete chloroplast genomes of 71 mangrove and land plants, confirmed the previously reported phylogeny within rosids, including the positioning of obscure families such as Linaceae within Malpighiales. Most mangrove chloroplast genes are conserved and we found six genes subjected to positive or neutral selection. Genomic comparison showed IR regions have lower divergence than other regions. Our study firstly reported several plastid genetic resource for mangroves, and the determined evolutionary locations as well as comparative analyses of these species provid insights into the mangrove genetic and phylogenetic research.</jats:p>

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

“…Based on a reference genome-based strategy, the Illumina paired-end reads and B. sexangula (the accession in the project-ID in CNSA ( ) ( Shi et al, 2020 )) were used for assembling the chloroplast genomes of the five Bruguiera species using GetOrganelle ( Jin et al, 2020 ).…”

“…The comparison of whole chloroplast genomes among the Bruguiera species and two close non-mangrove species, Pellacalyx yunnanensis ( ) of Rhizophoraceae and Erythroxylum novogranatense ( ) of Erythroxylaceae, were analyzed to investigate sequence divergence using mVISTA with the Shuffe-LAGAN mode ( Frazer et al, 2004 ). The previously reported chloroplast genome of B. sexangula was used as a reference for comparison ( Shi et al, 2020 ). Furthermore, the junctions and borders of the IR regions were illustrated using IRscope ( Amiryousefi, Hyvönen & Poczai, 2018 ).…”

“…Furthermore, SSRs in the chloroplast genome sequences of the five Bruguiera species and three previously reported mangrove species, Kandelia obavata ( ), Rhizophora x lamarckii ( ) and Rhizophora stylosa ( ), in the family Rhizophoraceae were identified using MISA ( Thiel et al, 2003 ). Minimum repeat number requirements were set to 10 for mono-, five for di-, four for tri-, and three for tetra-, penta- and hexa-nucleotide repeats ( Shi et al, 2020 ). The distance for compound SSRs was ≤100 bp (default).…”

“…Over the past decade, next generation sequencing technologies have been used to generate hundreds of complete chloroplast genomes ( Tangphatsornruang et al, 2010 ; Tangphatsornruang et al, 2011 ; Uthaipaisanwong et al, 2012 ). Recently, a number of complete chloroplast genomes of mangroves in the family Rhizophoraceae were reported ( Li et al, 2019 ; Yang et al, 2019 ; Zhang, Zhong & Yuan, 2019 ; Shi et al, 2020 ; Li et al, 2021 ). These mangrove chloroplast genomes are 160–164 kb in length and consist of all four regions with LSC; ~91–93 kb, SSC; ~16–19 kb and IRs; ~26–27 kb.…”

“…They contain 128–131 genes and have a highly conserved organization and structure. To date, only the chloroplast genomes of B. sexangula and B. gymnorhiza are available ( Shi et al, 2020 ; Li et al, 2021 ). Thus, the chloroplast genome sequences in the genus Bruguiera are limited.…”