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

2019 ◽  
Author(s):  
Chengcheng Shi ◽  
Kai Han ◽  
Liangwei Li ◽  
Inge Seim ◽  
Simon Ming-Yuen Lee ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Single Copy ◽  
Avicennia Marina ◽  
Terrestrial Plants ◽  
Mangrove Species ◽  
Rhizophora Stylosa ◽  
Comparative Analyses ◽  
Excoecaria Agallocha ◽  
Thespesia Populnea ◽  
Chloroplast Genomes

AbstractMangroves 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 (Pongamia pinnata), Lamiales (Avicennia marina), Malpighiales (Excoecaria agallocha, Bruguiera sexangula, Kandelia obovata, Rhizophora stylosa, Ceriops tagal), Malvales (Hibiscus tiliaceus, Heritiera littoralis, Thespesia populnea), Myrtales (Laguncularia racemose, Sonneratia ovata, Pemphis acidula), and Sapindales (Xylocarpus moluccensis). 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.

scholarly journals Complete Chloroplast Genomes of 14 Mangroves: Phylogenetic and Comparative Genomic Analyses

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Chengcheng Shi ◽  
Kai Han ◽  
Liangwei Li ◽  
Inge Seim ◽  
Simon Ming-Yuen Lee ◽  
...  
Keyword(s):  
Single Copy ◽  
Avicennia Marina ◽  
Comparative Genomic ◽  
Mangrove Species ◽  
Rhizophora Stylosa ◽  
Protein Coding ◽  
Excoecaria Agallocha ◽  
Thespesia Populnea ◽  
Chloroplast Genomes ◽  
Genome Features

Mangroves are a group of plant species that occupy the coastal intertidal zone and are major components of this ecologically important ecosystem. Mangroves belong to about twenty diverse families. Here, we sequenced and assembled chloroplast genomes of 14 mangrove species from eight families spanning five rosid orders and one asterid order: Fabales (Pongamia pinnata), Lamiales (Avicennia marina), Malpighiales (Excoecaria agallocha, Bruguiera sexangula, Kandelia obovata, Rhizophora stylosa, and Ceriops tagal), Malvales (Hibiscus tiliaceus, Heritiera littoralis, and Thespesia populnea), Myrtales (Laguncularia racemosa, Sonneratia ovata, and Pemphis acidula), and Sapindales (Xylocarpus moluccensis). These chloroplast genomes range from 149 kb to 168 kb in length. A conserved structure of two inverted repeats (IRa and IRb, ~25.8 kb), one large single-copy region (LSC, ~89.0 kb), and one short single-copy region (SSC, ~18.9 kb) as well as ~130 genes (85 protein-coding, 37 tRNAs, and 8 rRNAs) was observed. We found the lowest divergence in the IR regions among the four regions. We also identified simple sequence repeats (SSRs), which were found to be variable in numbers. Most chloroplast genes are highly conserved, with only four genes under positive selection or relaxed pressure. Combined with publicly available chloroplast genomes, we carried out phylogenetic analysis and confirmed the previously reported phylogeny within rosids, including the positioning of obscure families in Malpighiales. Our study reports 14 mangrove chloroplast genomes and illustrates their genome features and evolution.

scholarly journals KEANEKARAGAMAN JENIS MANGROVE DI DESA MENDALOK KECAMATAN SUNGAI KUNYIT KABUPATEN MEMPAWAH

2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Syahrul Muharamsyah ◽  
M Sofwan Anwari ◽  
Hafiz Ardian
Keyword(s):  
Mangrove Forest ◽  
Avicennia Marina ◽  
Raw Material ◽  
Mangrove Forests ◽  
Bruguiera Gymnorrhiza ◽  
Mangrove Species ◽  
Rhizophora Stylosa ◽  
Sonneratia Caseolaris ◽  
Rhizophora Apiculata ◽  
Bruguiera Cylindrica

Mangrove forests are unique ecosystems that have ecological, biological and socio-economic functions. The function of mangrove forests on the environment is very important especially in the coastal and oceanic regions. Mangrove forests providers of wood, leaves as raw material for medicines, and natural dye. This study aims to inventory the diversity of species of mangrove vegetation in Mendalok Village, Sungai Kunyit Subdistrict, Mempawah Regency. The benefits of this study are to provide the data on mangrove forest vegetation as basic data for local government and related agencies in efforts to protect and preserve mangrove forests in Mendalok Village, Sungai Kunyit Subdistrict, Mempawah Regency. Inventory the tree in mangrove forest used a line with measured 200 meters. There are 6 lines and the distance between the lines as far as 100 meters. The lines of observation are placed by purposive sampling. The results of research found 11 types of species and consisted of 6 genera. The genera are Avicennia, Bruguiera, Ceriops, Rhizophora, Soneratia and Xylocarpus. The species found were Avicennia alba, Avicennia marina, Bruguiera cylindrica, Bruguiera gymnorrhiza, Bruguiera parviflora, Ceriops decandra, Rhizophora apiculata, Rhizophora mucronata, Rhizophora stylosa, Sonneratia caseolaris, Xylocarpus mollucensis. Diversity of mangrove species in Mendalok Village, Sungai Kunyit Subdistrict, Mempawah Regency was high and should be maintained for conservation and ecotourism area. Keywords : conservation, ecotourism, mangrove, Mendalok Village

The anatomical basis of the link between density and mechanical strength in mangrove branches

2013 ◽  
Vol 40 (4) ◽  
pp. 400 ◽  
Author(s):  
Nadia S. Santini ◽  
Nele Schmitz ◽  
Vicki Bennion ◽  
Catherine E. Lovelock
Keyword(s):  
Mechanical Strength ◽  
Avicennia Marina ◽  
Modulus Of Rupture ◽  
Carbon Gain ◽  
Bruguiera Gymnorrhiza ◽  
Mangrove Species ◽  
Rhizophora Stylosa ◽  
Anatomical Characteristics ◽  
Trade Offs ◽  
Anatomical Basis

Tree branches are important as they support the canopy, which controls photosynthetic carbon gain and determines ecological interactions such as competition with neighbours. Mangrove trees are subject to high wind speeds, strong tidal flows and waves that can damage their branches. The survival and establishment of mangroves partly depend on the structural and mechanical characteristics of their branches. In addition, mangroves are exposed to soils that vary in salinity. Highly saline conditions can increase the tension in the water column, imposing mechanical stresses on the xylem vessels. Here, we investigated how mechanical strength, assessed as the modulus of elasticity (MOE) and the modulus of rupture (MOR), and density relate to the anatomical characteristics of intact mangrove branches from southeast Queensland and whether the mechanical strength of branches varies among mangrove species. Mechanical strength was positively correlated with density of mangrove intact branches. Mechanical strength (MOE) varied among species, with Avicennia marina (Forssk.) Vierh. branches having the highest mechanical strength (2079 ± 176 MPa), and Rhizophora stylosa Griff. and Bruguiera gymnorrhiza (L.) Savigny ex Lam. and Poiret having the lowest mechanical strength (536.8 ± 39.2 MPa in R. stylosa and 554 ± 58.2 MPa in B. gymnorrhiza). High levels of mechanical strength were associated with reductions in xylem vessel lumen area, pith content and bark content, and positively associated with increases in fibre wall thickness. The associations between mechanical strength and anatomical characteristics in mangrove branches suggest trade-offs between mechanical strength and water supply, which are linked to tree growth and survival.

scholarly journals Complete Chloroplast Genomes of Fagus sylvatica L. Reveal Sequence Conservation in the Inverted Repeat and the Presence of Allelic Variation in NUPTs

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1357
Author(s):  
Bartosz Ulaszewski ◽  
Joanna Meger ◽  
Bagdevi Mishra ◽  
Marco Thines ◽  
Jarosław Burczyk
Keyword(s):  
Fagus Sylvatica ◽  
Inverted Repeat ◽  
Allelic Variation ◽  
Phylogenetic Analyses ◽  
Geographic Distance ◽  
European Beech ◽  
Single Copy ◽  
Chloroplast Genomes ◽  
Efficient Suppression ◽  
Broadleaved Tree Species

Growing amounts of genomic data and more efficient assembly tools advance organelle genomics at an unprecedented scale. Genomic resources are increasingly used for phylogenetic analyses of many plant species, but are less frequently used to investigate within-species variability and phylogeography. In this study, we investigated genetic diversity of Fagus sylvatica, an important broadleaved tree species of European forests, based on complete chloroplast genomes of 18 individuals sampled widely across the species distribution. Our results confirm the hypothesis of a low cpDNA diversity in European beech. The chloroplast genome size was remarkably stable (158,428 ± 37 bp). The polymorphic markers, 12 microsatellites (SSR), four SNPs and one indel, were found only in the single copy regions, while inverted repeat regions were monomorphic both in terms of length and sequence, suggesting highly efficient suppression of mutation. The within-individual analysis of polymorphisms showed >9k of markers which were proportionally present in gene and non-gene areas. However, an investigation of the frequency of alternate alleles revealed that the source of this diversity originated likely from nuclear-encoded plastome remnants (NUPTs). Phylogeographic and Mantel correlation analysis based on the complete chloroplast genomes exhibited clustering of individuals according to geographic distance in the first distance class, suggesting that the novel markers and in particular the cpSSRs could provide a more detailed picture of beech population structure in Central Europe.

scholarly journals Complete chloroplast genome sequences of Dioscorea: Characterization, genomic resources, and phylogenetic analyses

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e6032 ◽  
Author(s):  
Zhenyu Zhao ◽  
Xin Wang ◽  
Yi Yu ◽  
Subo Yuan ◽  
Dan Jiang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Genomic Resources ◽  
Chloroplast Genomes ◽  
The Family ◽  
Small Single Copy

Dioscorea L., the largest genus of the family Dioscoreaceae with over 600 species, is not only an important food but also a medicinal plant. The identification and classification of Dioscorea L. is a rather difficult task. In this study, we sequenced five Dioscorea chloroplast genomes, and analyzed with four other chloroplast genomes of Dioscorea species from GenBank. The Dioscorea chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted repeats separated by a large single-copy region, and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined, and the rapidly evolving chloroplast genome regions (trnK-trnQ, trnS-trnG, trnC-petN, trnE-trnT, petG-trnW-trnP, ndhF, trnL-rpl32, and ycf1) were detected. Phylogenetic relationships of Dioscorea inferred from chloroplast genomes obtained high support even in shortest internodes. Thus, chloroplast genome sequences provide potential molecular markers and genomic resources for phylogeny and species identification.

scholarly journals Percentage of Mangrove Canopy Cover and Mollusks Abundance in Benoa Bay Mangrove Ecosystem

2021 ◽  
Vol 5 (3) ◽  
pp. 105
Author(s):  
Shintani Asri Tinambunan ◽  
Nyoman Dati Pertami ◽  
Ni Made Ernawati
Keyword(s):  
Canopy Cover ◽  
Avicennia Marina ◽  
Mangrove Ecosystem ◽  
Line Transect ◽  
Hemispherical Photography ◽  
Bruguiera Gymnorrhiza ◽  
Mangrove Species ◽  
Rhizophora Stylosa ◽  
Rhizophora Apiculata ◽  
The Relationship

This research was conducted to determine the condition of the mangrove ecosystem based on its canopy cover and to determine the types of mollusks (Bivalves and Gastropods) associated with the Benoa Bay mangrove ecosystem. Hemispherical photography is a method for observing mangrove canopy cover and line transect method for mollusks. The composition of mangrove species found in the research location were five species, namely Rhizophora stylosa, Rhizophora mucronata, Rhizophora apiculata, Bruguiera gymnorrhiza, and Avicennia marina. The percentage of mangrove canopy cover in the Benoa Bay mangrove ecosystem is in a good category (average = 76.59%). There are eight types of mollusks found in the research location. There are two types of bivalves (Polymesoda bengalensis and Gafrarium pectinatum) and six types of gastropods (Nerita balteata, Nerita picea, Neritina turrita, Pila ampullacea, Cassidula aurisfelis, and Littoraria melanostoma). The relationship between the percentage of mangrove canopy cover and abundance of mollusks in the Benoa Bay mangrove ecosystem is very strong (r) of 0.920. The higher the percentage value of mangrove canopy cover, the higher the mollusks abundance.

scholarly journals The affinity of mangrove species using Association and Cluster Index in North Coast of Jakarta and Segara Anakan of Cilacap, Indonesia

2021 ◽  
Vol 22 (7) ◽  
Author(s):  
Endang Hilmi ◽  
Lilik Kartika Sari ◽  
Tri Nur Cahyo ◽  
Muslih MUSLIH ◽  
Arif Mahdiana ◽  
...  
Keyword(s):  
Avicennia Marina ◽  
North Coast ◽  
Bruguiera Gymnorrhiza ◽  
Mangrove Species ◽  
Association Index ◽  
Rhizophora Stylosa ◽  
Species Association ◽  
Nypa Fruticans ◽  
Cluster Index ◽  
Bruguiera Parviflora

Abstract. Hilmi E, Sari LK, Cahyo TN, Muslih, Mahdiana A, Samudra SR. 2021. The affinity of mangrove species using Association and Cluster Index in North Coast of Jakarta and Segara Anakan of Cilacap, Indonesia. Biodiversitas 22: 2907-2920. The affinity of mangrove species using association and cluster index describe relationship among mangrove species. The species association and clustering explain the degree of utilization of resources and space by mangrove species. The association and cluster also describe specific species adaptation in mangrove ecosystems. This paper was aimed to analyze species affinity using association and clustering index of mangrove species. The association index used Chi-square equation and the clustered index used Euclidian distance analysis. The results showed that (i) mangrove density in Segara Anakan (166-4000 trees ha-1) > North Jakarta (220-1100 trees ha-1). (ii) Nypa fruticans, Avicennia marina, Rhizophora stylosa and Rhizophora apiculata dominated in Segara Anakan of Cilacap, and Rhizophora stylosa and Avicennia marina dominated in North Jakarta (iii) The association index had 12 pairs of negative species association and 17 pairs of positive species association, but most of mangrove vegetations had no association. (iv) mangrove ecosystem in Segara Anakan and North Jakarta had four clusters with Euclidean distance (ED score) 484 to describe cluster between Bruguiera parviflora-Bruguiera sexangula until 76430847 to describe cluster among Bruguiera gymnorrhiza, Bruguiera parviflora, Ceriops decandra, Exoecaria agallocha, Nypa fruticans, Ceriops tagal, Rhizophora stylosa, and Sonneratia caseolaris

scholarly journals Studies on Canopy Parameters of Some Mangroves Along the Coast of Maharashtra

2021 ◽  
Vol 4 (4-5) ◽  
pp. 225-229
Author(s):  
Narendra Kulkarni ◽  
Leela J. Bhosale
Keyword(s):  
Correlation Coefficient ◽  
Canopy Cover ◽  
Avicennia Marina ◽  
Kandelia Candel ◽  
Rhizophora Mucronata ◽  
Mangrove Species ◽  
Aegiceras Corniculatum ◽  
Excoecaria Agallocha ◽  
Sonneratia Alba ◽  
Avicennia Officinalis

Mangrove species, viz., Avicennia officinalis, Avicennia marina var. acutissima, Avicennia marina (dwarf), Rhizophora mucronata, Sonneratia alba, Aegiceras  corniculatum, Kandelia  candel were chosen for measurement of height of the tree and girth or circumference. The sampling was random and at least 50 records were made. The girth is measured by the tape. The measurement of the height is made with the help of abny level. The Tables 1 to 8 records the values for girth, height and canopy cover as well as for correlation coefficient (r). There correlation between girth and canopy in all the species studied however in case of Avicennia officinalis and Aegiceras corniculatum girth and height show more co-relation than girth and C. cover. The positive co-relation observed between girth and canopy is more or less 0.7 except Avicennia marina (dwarf) Excoecaria agallocha and Aegiceras corniculatum. The co-relation is observed in girth and height is difficult to explain. This case is observed in Avicennia officinalis and Aegiceras corniculatum.

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