The first complete chloroplast genome of a major mangrove species <i>Sonneratia alba</i> Sm. and its implications on conservation efforts

Yu, Tianhui; Hinsinger, Damien Daniel; Strijk, Joeri S.; Wee, Alison K. S.

doi:10.1080/23802359.2018.1463828

Cited by 6 publications

(6 citation statements)

References 10 publications

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“…The phylogenetic tree supported the close relationship between Trapa and Sonneratia , which was reported in previous studies (Yu et al 2018 ; Gu et al 2019 ; Sun et al 2020 ). Monophyletic clustering of Trapa was revealed, with the large-fruit Trapa species ( T. kozhevnikoviorum , T. bicornis , and T. natans ) forming a clade closely related to T. maximowiczii with small fruit ( Figure 1 ), suggesting the distinct genetic divergence between the two clades, and the basal classification status of the small-fruit species T. maximowiczii .…”

Section: Resultssupporting

confidence: 86%

The complete chloroplast genome sequence of Trapa kozhevnikoviorum Pshenn. (Lythraceae)

Wagutu

Fan

Wang

et al. 2021

Mitochondrial DNA Part B

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Trapa (Lythraceae) is an economically important aquatic genus used for food and medicine, with wide distribution in Asia, Africa, and Europe. Identification of species, genetic studies and utilization of Trapa are limited by lack of molecular data. Herein, we report the complete chloroplast (cp) genome sequence of a wild species, Trapa kozhevnikoviorum Pshenn. The cp genome size of T. kozhevnikoviorum is 155,545 bp, consisting of a pair of inverted repeat regions (IRa/IRb) of length 24,388 bp, separated by the small single copy (SSC) region of 18,275 bp and a large single copy (LSC) region of 88,494 bp. A total of 113 unique genes, including 79 protein-coding, 30 tRNA, and four rRNA were annotated. Phylogenetic analysis based on 15 whole cp genomes of Lythraceae species supported the monophyletic clustering of Trapa. A cladal relationship among T. kozhevnikoviorum, T. bicornis, and T. natans was revealed.

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Section: Resultssupporting

confidence: 86%

The complete chloroplast genome sequence of Trapa kozhevnikoviorum Pshenn. (Lythraceae)

Wagutu

Fan

Wang

et al. 2021

Mitochondrial DNA Part B

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“…In this study, we aligned the positions of the LSC, IRA, SSC and IRB borders and the adjacent genes among members of mangrove species and found that the studied locations are generally similar to those of all previously reported chloroplast genomes (Jo et al, 2016; Wei et al, 2017; Zhou et al, 2017; Yu et al, 2018). However, in the analyzed species, two copies of the K. obovata rpl22 gene are located in the boundaries of the LSC/IRA junction and IRB region; as the rpl22 gene in the IRB region has no open reading frame that encodes a functional protein, we regarded this gene as a pseudogene.…”

Section: Resultssupporting

confidence: 73%

Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species

Yang

Zhang

Gul

et al. 2019

PeerJ

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As one of the most cold and salt-tolerant mangrove species, Kandelia obovata is widely distributed in China. Here, we report the complete chloroplast genome sequence K. obovata (Rhizophoraceae) obtained via next-generation sequencing, compare the general features of the sampled plastomes of this species to those of other sequenced mangrove species, and perform a phylogenetic analysis based on the protein-coding genes of these plastomes. The complete chloroplast genome of K. obovata is 160,325 bp in size and has a 35.22% GC content. The genome has a typical circular quadripartite structure, with a pair of inverted repeat (IR) regions 26,670 bp in length separating a large single-copy (LSC) region (91,156 bp) and a small single-cope (SSC) region (15,829 bp). The chloroplast genome of K. obovata contains 128 unique genes, including 80 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 2 pseudogenes (ycf1 in the IRA region and rpl22 in the IRB region). In addition, a simple sequence repeat (SSR) analysis found 108 SSR loci in the chloroplast genome of K. obovata, most of which are A/T rich. IR expansion and contraction regions were compared between K. obovata and five related species: two from Malpighiales and three mangrove species from different orders. The mVISTA results indicated that the genome structure, gene order and gene content are highly conserved among the analyzed species. The phylogenetic analysis using 54 common protein-coding genes from the chloroplast genome showed that the plant most closely related to K. obovata is Ceriops tagal of Rhizophoraceae. The results of this study provide useful molecular information about the evolution and molecular biology of these mangrove trees.

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“…The genome-skimming approach is now widely used to reconstruct chloroplasts in angiosperms (Straub et al 2012; Bock et al 2014; Malé et al 2014; Weitemier et al 2014; Mandel et al 2015) and an increasing number of Fagales are available (Alexander and Woeste 2014; El Mujtar et al 2014; Hinsinger and Strijk 2015). Since the first Fagaceae ( C. concinna ; Hinsinger and Strijk 2015), the genome skimming approach has been proven to be useful in many non-model organisms (Kane et al 2012; Nikiforova et al 2013; Curci et al 2016; Yu et al 2018), despite a few disadvantages (Straub et al 2012; Du et al 2015), as genome skimming is a PCR-free method and a higher amount of starting material is required. Moreover, best results require high quality DNA (i.e high molecular weight DNA, usually > 10 kb, with little degradation), which is incompatible with large-scale (i.e.…”

Section: Discussionmentioning

confidence: 99%

Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming

Hinsinger¹,

Strijk²

2019

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The genus Quercus L. contains several of the most economically important species for timber production in the Northern Hemisphere. It was one of the first genera described, but genetic diversity at a global scale within and amongst oak species remains unclear, despite numerous regional or species-specific assessments. To evaluate global plastid diversity in oaks, we sequenced the complete chloroplast of Quercus xanthoclada and compared its sequence with those available from other main taxonomic groups in Quercus. We quantify genomic divergence amongst oaks and performed a sliding window analysis to detect the most variable regions amongst members of the various clades, as well as divergent regions occurring in specific pairs of species. We identified private and shared SNPs amongst oaks species and sections and stress the need for a large global assessment of genetic diversity in this economically and ecologically important genus.

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The first complete chloroplast genome of a major mangrove species Sonneratia alba Sm. and its implications on conservation efforts

Cited by 6 publications

References 10 publications

The complete chloroplast genome sequence of Trapa kozhevnikoviorum Pshenn. (Lythraceae)

The complete chloroplast genome sequence of Trapa kozhevnikoviorum Pshenn. (Lythraceae)

Complete chloroplast genome sequence of the mangrove species Kandelia obovata and comparative analyses with related species

Plastome of Quercus xanthoclada and comparison of genomic diversity amongst selected Quercus species using genome skimming

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