Exceptional reduction of the plastid genome of saguaro cactus (<i>Carnegiea gigantea</i>): Loss of the <i>ndh</i> gene suite and inverted repeat

Sanderson, Michael J.; Copetti, Dario; Búrquez, Alberto; Bustamante, Enriquena; Charboneau, Joseph L.M.; Eguiarte, Luis E.; Kumar, Sudhir; Lee, Hyun Oh; Lee, Junki; McMahon, Michelle M.; Steele, Kelly P.; Wing, Rod A.; Yang, Tae Jin; Zwickl, Derrick J.; Wojciechowski, Martin F.

doi:10.3732/ajb.1500184

Cited by 125 publications

(141 citation statements)

References 97 publications

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“…squamar i a 23 . This degree of ndh gene degradation is not only observed in heterotrophic organisms, but also in many autotrophic plants, including Orchidaceae 57,58 , Geraniaceae 59 and Cactaceae 60 . Kim et al .…”

Section: Discussionmentioning

confidence: 93%

Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

Zhou

Chen

et al. 2017

Sci Rep

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Numerous variations are known to occur in the chloroplast genomes of parasitic plants. We determined the complete chloroplast genome sequences of two hemiparasitic species, Taxillus chinensis and T. sutchuenensis, using Illumina and PacBio sequencing technologies. These species are the first members of the family Loranthaceae to be sequenced. The complete chloroplast genomes of T. chinensis and T. sutchuenensis comprise circular 121,363 and 122,562 bp-long molecules with quadripartite structures, respectively. Compared with the chloroplast genomes of Nicotiana tabacum and Osyris alba, all ndh genes as well as three ribosomal protein genes, seven tRNA genes, four ycf genes, and the infA gene of these two species have been lost. The results of the maximum likelihood and neighbor-joining phylogenetic trees strongly support the theory that Loranthaceae and Viscaceae are monophyletic clades. This research reveals the effect of a parasitic lifestyle on the chloroplast structure and genome content of T. chinensis and T. sutchuenensis, and enhances our understanding of the discrepancies in terms of assembly results between Illumina and PacBio.

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Section: Discussionmentioning

confidence: 93%

Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

Zhou

Chen

et al. 2017

Sci Rep

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“…Our two-sided Mann–Whitney test also indicated that ndh genes play an important role in IR/SSC junction stability. The loss of the full set of 11 plastid ndh genes has been reported in diverse photosynthetic seed plants, such as gnetophytes (Braukmann et al, 2009; Wu et al, 2009, 2011), orchids (Chang et al, 2006; Wu et al, 2010; Pan et al, 2012; Lin et al, 2015), pines (Braukmann et al, 2009; Wu et al, 2013), slender naiads (Peredo et al, 2013), and saguaros (Sanderson et al, 2015). With the exception of pines and saguaros, which have only one IR copy, all lineages mentioned above have expanded their IRs to include some genes (i.e., ycf1 , rpl32 , trnL , rps15 , psaC , or ccsA ) that are usually situated in the SSC regions of seed plant plastomes.…”

Section: Discussionmentioning

confidence: 99%

The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots

et al. 2017

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Orchidaceae (orchids) is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome) and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented. In this study, we compared 53 orchid plastomes, including four newly sequenced ones, that represent four remote genera: Dendrobium, Goodyera, Paphiopedilum, and Vanilla. These differ from one another not only in their lengths of inverted repeats and small single copy regions but also in their retention of ndh genes. Comparative analyses of the plastomes revealed that the expansion of inverted repeats in Paphiopedilum and Vanilla is associated with a loss of ndh genes. In orchid plastomes, mutational hotspots are genus specific. After having carefully examined the data, we propose that the three loci 5′trnK-rps16, trnS-trnG, and rps16-trnQ might be powerful markers for genera within Epidendroideae, and clpP-psbB and rps16-trnQ might be markers for genera within Cypripedioideae. After analyses of a partitioned dataset, we found that our plastid phylogenomic trees were congruent in a topology where two one-stamened subfamilies (i.e., Epidendroideae and Orchidoideae) were sisters to a multi-stamened subfamily (i.e., Cypripedioideae) rather than to the other one-stamened subfamily (Vanilloideae), suggesting that the living one-stamened orchids are paraphyletic.

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“…27 proposed that the loss of NDH genes led to the expansion/contraction of IRs 27 . It has been documented that independent loss/retention of NDH genes and expansion/contraction of IRs are largely responsible for the variation of plastomes in different orchid genera 26, 27 and many other species, such as gnetophytes 30–32 , pines 30, 33 , slender naiad 34 , and saguaro 35 . However, our study demonstrated that neither NDH genes loss/retention nor the expansion/contraction of IRs accounted for the most important role in the variation of Dendrobium plastome sizes (Table S1).…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots

Zhitao

Zhu

Pan

et al. 2017

Sci Rep

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Dendrobium is one of the largest genera in Orchidaceae, comprising about 800–1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published. Except for their differences in NDH genes, these plastomes shared identical gene content and order. Comparative analyses revealed that the variation in size of Dendroubium plastomes was associated with dramatically changed length of InDels. Furthermore, ten loci were identified as the top-ten mutational hotspots, whose sequence variability was almost unchanged with more than 10 plastomes sampled, suggesting that they may be powerful markers for Dendrobium species. In addition, primer pairs of 47 polymorphic microsatellites were developed. After assessing the mean BS values of all combinations derived from the top-ten hotspots, we recommend that the combination of five hotspots—trnT-trnL, rpl32-trnL, clpP-psbB, trnL intron, and rps16-trnQ—should be used in the phylogenetic and identification studies of Dendrobium.

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Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat

Cited by 125 publications

References 97 publications

Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

Gene losses and partial deletion of small single-copy regions of the chloroplast genomes of two hemiparasitic Taxillus species

The Complete Plastome Sequences of Four Orchid Species: Insights into the Evolution of the Orchidaceae and the Utility of Plastomic Mutational Hotspots

Comparative analysis of Dendrobium plastomes and utility of plastomic mutational hotspots

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