Comparative Analysis and Phylogenetic Relationships of <i>Ceriops</i> Species (Rhizophoraceae) and <i>Avicennia lanata</i> (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests
<i>Ceriops</i> and <i>Avicennia</i> are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of <i>Ceriops decandra</i>, <i>Ceriops zippeliana</i>, and <i>Ceriops tagal</i> were assembled...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-02-01
|
| Series: | Biology |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-7737/11/3/383 |
| _version_ | 1797447119919906816 |
|---|---|
| author | Panthita Ruang-areerate Thippawan Yoocha Wasitthee Kongkachana Phakamas Phetchawang Chatree Maknual Wijarn Meepol Darunee Jiumjamrassil Wirulda Pootakham Sithichoke Tangphatsornruang |
| author_facet | Panthita Ruang-areerate Thippawan Yoocha Wasitthee Kongkachana Phakamas Phetchawang Chatree Maknual Wijarn Meepol Darunee Jiumjamrassil Wirulda Pootakham Sithichoke Tangphatsornruang |
| author_sort | Panthita Ruang-areerate |
| collection | DOAJ |
| description | <i>Ceriops</i> and <i>Avicennia</i> are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of <i>Ceriops decandra</i>, <i>Ceriops zippeliana</i>, and <i>Ceriops tagal</i> were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas <i>Avicennia lanata</i> 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 <i>A. lanata</i> and 129 genes in <i>Ceriops</i> species. Three duplicate genes (<i>rpl2</i>, <i>rpl23</i>, and <i>trnM-CAU</i>) were found in the IR regions of the three <i>Ceriops</i> species, resulting in expansion of the IR regions. The <i>rpl32</i> gene was lost in <i>C. zippeliana</i>, whereas the <i>infA</i> gene was present in <i>A. lanata</i>. Short repeats (<40 bp) and a lower number of SSRs were found in <i>A. lanata</i> but not in <i>Ceriops</i> species. The phylogenetic analysis supports that all <i>Ceriops</i> species are clustered in Rhizophoraceae and <i>A. lanata</i> is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the <i>rps7</i> gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three <i>Ceriops</i> species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in <i>Ceriops</i> and <i>Avicennia</i> species. |
| first_indexed | 2024-03-09T13:50:13Z |
| format | Article |
| id | doaj.art-8969bc60a4cc43b4ac0b6d940f0a545d |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-09T13:50:13Z |
| publishDate | 2022-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-8969bc60a4cc43b4ac0b6d940f0a545d2023-11-30T20:51:24ZengMDPI AGBiology2079-77372022-02-0111338310.3390/biology11030383Comparative Analysis and Phylogenetic Relationships of <i>Ceriops</i> Species (Rhizophoraceae) and <i>Avicennia lanata</i> (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove ForestsPanthita Ruang-areerate0Thippawan Yoocha1Wasitthee Kongkachana2Phakamas Phetchawang3Chatree Maknual4Wijarn Meepol5Darunee Jiumjamrassil6Wirulda Pootakham7Sithichoke Tangphatsornruang8National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, ThailandNational Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, ThailandNational Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, ThailandNational Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, ThailandDepartment of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok 10210, ThailandDepartment of Marine and Coastal Resources, Ranong Mangrove Forest Research Center, Tambon Ngao, Muang District, Ranong 85000, ThailandMarine and Coastal Resources Office 5, 199/6 Khanom, Khanom, Nakhon Si Thammarat 80210, ThailandNational Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, ThailandNational Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand<i>Ceriops</i> and <i>Avicennia</i> are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of <i>Ceriops decandra</i>, <i>Ceriops zippeliana</i>, and <i>Ceriops tagal</i> were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas <i>Avicennia lanata</i> 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 <i>A. lanata</i> and 129 genes in <i>Ceriops</i> species. Three duplicate genes (<i>rpl2</i>, <i>rpl23</i>, and <i>trnM-CAU</i>) were found in the IR regions of the three <i>Ceriops</i> species, resulting in expansion of the IR regions. The <i>rpl32</i> gene was lost in <i>C. zippeliana</i>, whereas the <i>infA</i> gene was present in <i>A. lanata</i>. Short repeats (<40 bp) and a lower number of SSRs were found in <i>A. lanata</i> but not in <i>Ceriops</i> species. The phylogenetic analysis supports that all <i>Ceriops</i> species are clustered in Rhizophoraceae and <i>A. lanata</i> is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the <i>rps7</i> gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three <i>Ceriops</i> species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in <i>Ceriops</i> and <i>Avicennia</i> species.https://www.mdpi.com/2079-7737/11/3/383<i>Ceriops</i><i>Avicennia</i>mangrovechloroplast genomeplastidcomparative analysis |
| spellingShingle | Panthita Ruang-areerate Thippawan Yoocha Wasitthee Kongkachana Phakamas Phetchawang Chatree Maknual Wijarn Meepol Darunee Jiumjamrassil Wirulda Pootakham Sithichoke Tangphatsornruang Comparative Analysis and Phylogenetic Relationships of <i>Ceriops</i> Species (Rhizophoraceae) and <i>Avicennia lanata</i> (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests Biology <i>Ceriops</i> <i>Avicennia</i> mangrove chloroplast genome plastid comparative analysis |
| title | Comparative Analysis and Phylogenetic Relationships of <i>Ceriops</i> Species (Rhizophoraceae) and <i>Avicennia lanata</i> (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests |
| title_full | Comparative Analysis and Phylogenetic Relationships of <i>Ceriops</i> Species (Rhizophoraceae) and <i>Avicennia lanata</i> (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests |
| title_fullStr | Comparative Analysis and Phylogenetic Relationships of <i>Ceriops</i> Species (Rhizophoraceae) and <i>Avicennia lanata</i> (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests |
| title_full_unstemmed | Comparative Analysis and Phylogenetic Relationships of <i>Ceriops</i> Species (Rhizophoraceae) and <i>Avicennia lanata</i> (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests |
| title_short | Comparative Analysis and Phylogenetic Relationships of <i>Ceriops</i> Species (Rhizophoraceae) and <i>Avicennia lanata</i> (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests |
| title_sort | comparative analysis and phylogenetic relationships of i ceriops i species rhizophoraceae and i avicennia lanata i acanthaceae insight into the chloroplast genome evolution between middle and seaward zones of mangrove forests |
| topic | <i>Ceriops</i> <i>Avicennia</i> mangrove chloroplast genome plastid comparative analysis |
| url | https://www.mdpi.com/2079-7737/11/3/383 |
| work_keys_str_mv | AT panthitaruangareerate comparativeanalysisandphylogeneticrelationshipsoficeriopsispeciesrhizophoraceaeandiavicennialanataiacanthaceaeinsightintothechloroplastgenomeevolutionbetweenmiddleandseawardzonesofmangroveforests AT thippawanyoocha comparativeanalysisandphylogeneticrelationshipsoficeriopsispeciesrhizophoraceaeandiavicennialanataiacanthaceaeinsightintothechloroplastgenomeevolutionbetweenmiddleandseawardzonesofmangroveforests AT wasittheekongkachana comparativeanalysisandphylogeneticrelationshipsoficeriopsispeciesrhizophoraceaeandiavicennialanataiacanthaceaeinsightintothechloroplastgenomeevolutionbetweenmiddleandseawardzonesofmangroveforests AT phakamasphetchawang comparativeanalysisandphylogeneticrelationshipsoficeriopsispeciesrhizophoraceaeandiavicennialanataiacanthaceaeinsightintothechloroplastgenomeevolutionbetweenmiddleandseawardzonesofmangroveforests AT chatreemaknual comparativeanalysisandphylogeneticrelationshipsoficeriopsispeciesrhizophoraceaeandiavicennialanataiacanthaceaeinsightintothechloroplastgenomeevolutionbetweenmiddleandseawardzonesofmangroveforests AT wijarnmeepol comparativeanalysisandphylogeneticrelationshipsoficeriopsispeciesrhizophoraceaeandiavicennialanataiacanthaceaeinsightintothechloroplastgenomeevolutionbetweenmiddleandseawardzonesofmangroveforests AT daruneejiumjamrassil comparativeanalysisandphylogeneticrelationshipsoficeriopsispeciesrhizophoraceaeandiavicennialanataiacanthaceaeinsightintothechloroplastgenomeevolutionbetweenmiddleandseawardzonesofmangroveforests AT wiruldapootakham comparativeanalysisandphylogeneticrelationshipsoficeriopsispeciesrhizophoraceaeandiavicennialanataiacanthaceaeinsightintothechloroplastgenomeevolutionbetweenmiddleandseawardzonesofmangroveforests AT sithichoketangphatsornruang comparativeanalysisandphylogeneticrelationshipsoficeriopsispeciesrhizophoraceaeandiavicennialanataiacanthaceaeinsightintothechloroplastgenomeevolutionbetweenmiddleandseawardzonesofmangroveforests |