Complete plastome sequencing from<i>Toona</i>(Meliaceae) and phylogenomic analyses within Sapindales

Lin, Nan; Moore, Michael J.; Deng, Tao; Sun, Hang; Yang, Linsen; Sun, Yanxia; Wang, Heng-chang

doi:10.1002/aps3.1040

Cited by 16 publications

(21 citation statements)

References 61 publications

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“…The relationship of families within this order is consistent with a ML tree of Myrtales constructed by Berger and colleagues [17]. Sapindales includes one mangrove Xylocarpus moluccensis , and their positions in this order here support the result in Toona plastid analysis [18]. For Malvales, three mangroves Hibiscus tiliaceus , Heritiera littoralis and Thespesia populnea , together with Huerteales, Brassicales species were clustered as neighbor orders.…”

Section: Resultssupporting

confidence: 85%

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

Shi

Han²,

Li³

et al. 2019

Preprint

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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.

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Section: Resultssupporting

confidence: 85%

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

Shi

Han²,

Li³

et al. 2019

Preprint

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“…A recent phylogenetic study based on plastid rbcL, atpB, and trnL-trnF sequences indicated that Simaroubaceae was sister to Meliaceae, with moderate support (0.98 PP/82 BS), but the position of Sapindaceae could not be resolved with confidence [30]. Using 80 genes of plastomes, Lin et al [31] sister to Rutaceae with strong support (100 BS), but the position of Sapindaceae was still poorly supported (57 BS). In this study, both BI and ML analyses generated a wellresolved phylogeny of the six families of Sapindales.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, Anacardiaceae is among the families of Sapindales, which is known for citrus, maples, lychees, mangos, and cashews [29]. Previous studies have shown that Sapindales is a monophyletic group [30,31]. However, phylogenetic relationships among several families of the order, such as Simaroubaceae, Rutaceae, and Meliaceae, are still not fully resolved [30][31][32].…”

Section: Introductionmentioning

confidence: 99%

“…Previous studies have shown that Sapindales is a monophyletic group [30,31]. However, phylogenetic relationships among several families of the order, such as Simaroubaceae, Rutaceae, and Meliaceae, are still not fully resolved [30][31][32]. e chloroplast (cp) genome is nonrecombinant and uniparental and is more conserved than mitochondrial and nuclear genomes in terms of gene content, organization, and structure [33].…”

Section: Introductionmentioning

confidence: 99%

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Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

Wang

He²,

et al. 2020

BioMed Research International

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Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species widely cultivated in East Asia for producing highly durable lacquer. Here, we sequenced and analyzed the complete chloroplast (cp) genome of T. vernicifluum and reconstructed the phylogeny of Sapindales based on 52 cp genomes of six families. The plastome of T. vernicifluum is 159,571 bp in length, including a pair of inverted repeats (IRs) of 26,511 bp, separated by a large single-copy (LSC) region of 87,475 bp and a small single-copy (SSC) region of 19,074 bp. A total of 126 genes were identified, of which 81 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Forty-nine mononucleotide microsatellites, one dinucleotide microsatellite, two complex microsatellites, and 49 long repeats were determined. Structural differences such as inversion variation in LSC and gene loss in IR were detected across cp genomes of the six genera in Anacardiaceae. Phylogenetic analyses revealed that the genus Toxicodendron is closely related to Pistacia and Rhus. The phylogenetic relationships of the six families in Sapindales were well resolved. Overall, this study providing complete cp genome resources will be beneficial for determining potential molecular markers and evolutionary patterns of T. vernicifluum and its closely related species.

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“…The Meliaceae are a mostly pantropical family in the order of Sapindales and currently comprise 778 species distributed in 51 genera (Freiberg et al, unpublished data). The available molecular phylogenetic reconstructions for Sapindales (consisting of nine families) point to a close relationship of Meliaceae to Rutaceae and Simaroubaceae (e.g., Gadek et al, 1996; Koenen et al, 2015; APG IV, 2016; Muellner‐Riehl et al, 2016; Lin et al, 2018). The most recent studies either support a sister relationship of Meliaceae to Simaroubaceae (Muellner‐Riehl et al, 2016; based on three plastid DNA markers, and including 33 representatives of Meliaceae, 26 Simaroubaceae, and 15 Rutaceae, plus representatives of all other Sapindales families), or Meliaceae being sister to a clade formed by Simaroubaceae and Rutaceae (Lin et al, 2018; based on complete plastomes, four representatives of Meliaceae, one Simaroubaceae, 13 Rutaceae, a few samples from three other Sapindales families).…”

Section: Introductionmentioning

confidence: 99%

Evolution of reproductive traits in the mahagony family (Meliaceae)

Gama

Muellner‐Riehl

Demarco

et al. 2020

J of Sytematics Evolution

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Meliaceae are a mostly pantropical family in the Sapindales, bearing flowers typically provided with a staminal tube, formed by filaments that are fused partially or totally. Nevertheless, several genera of subfamily Cedreloideae have free stamens, which may be adnate to an androgynophore in some taxa. The fact that the family exhibits a wide diversity of floral and fruit features, as well as of sexual systems and pollination syndromes, presents interesting questions on the evolutionary processes that might have taken place during its history. In this study, we analyzed the distribution of 20 reproductive morphological traits of Meliaceae, upon an available molecular phylogenetic framework, using 31 terminals from the family's two main clades (Cedreloideae and Melioideae), plus six Simaroubaceae taxa as outgroup. We aimed to identify and/or confirm synapomorphies for clades within the family and to develop hypotheses on floral evolution and sexual systems in the group. Our reconstruction suggests that the ancestor of Meliaceae was possibly provided with united stamens and unisexual flowers in dioecious individuals, with a subsequent change to free stamens and monoecy in the ancestor of Cedreloideae. Most characters studied show some degree of homoplasy, but some are unique synapomorphies of clades, such as the haplostemonous androecium. An androgynophore defines the Cedrela‐Toona clade. The comparative approach of our study and the evolutionary hypotheses generated herein reveal several aspects demanding further structural investigation, and possible evolutionary pathways of the reproductive structures along with the lineages' diversification, mostly related to the specialization of sexual systems, floral biology, and dispersal strategies.

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Complete plastome sequencing fromToona(Meliaceae) and phylogenomic analyses within Sapindales

Cited by 16 publications

References 61 publications

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

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

Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

Evolution of reproductive traits in the mahagony family (Meliaceae)

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