Genetic and evolutionary analyses of plastomes of the subfamily Cactoideae (Cactaceae) indicate relaxed protein biosynthesis and tRNA import from cytosol

Silva, Gleyson Morais da; Lopes, Amanda de Santana; Pacheco, Túlio Gomes; Machado, Kleiton Lima de Godoy; Silva, Carolina; Oliveira, José Daniel de; Baura, Valter A.; Balsanelli, Eduardo; Souza, Emanuel Maltempi de; Pedrosa, Fábio de Oliveira; Rogalski, Marcelo

doi:10.1007/s40415-020-00689-2

Cited by 11 publications

(15 citation statements)

References 103 publications

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“…Massive loss of tRNA genes has previously been reported in some parasitic plants [14]; however, this loss is rare in nonparasitic plants. In the cactus family, the loss of trnV-UAC has been reported recently in species of the subfamily Cactoideae [45]. Additionally, abnormal loss of three essential tRNA genes (trnA-UGC, trnV-UAC, and trnV-GAC) has previously been found in Melocactus glaucescens Buining & Brederoo [46].…”

Section: Changes In Genomic Characteristics and Gene Contentmentioning

confidence: 90%

Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae)

Zuo

Qin

et al. 2023

BMC Plant Biol

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Background The cactus family (Cactaceae) has been reported to have evolved a minimal photosynthetic plastome size, with the loss of inverted-repeat (IR) regions and NDH gene suites. However, there are very limited genomic data on the family, especially Cereoideae, the largest subfamily of cacti. Results In the present study, we assembled and annotated 35 plastomes, 33 of which were representatives of Cereoideae, alongside 2 previously published plastomes. We analyzed the organelle genomes of 35 genera in the subfamily. These plastomes have variations rarely observed in those of other angiosperms, including size differences (with ~ 30 kb between the shortest and longest), dramatic dynamic changes in IR boundaries, frequent plastome inversions, and rearrangements. These results suggested that cacti have the most complex plastome evolution among angiosperms. Conclusion These results provide unique insight into the dynamic evolutionary history of Cereoideae plastomes and refine current knowledge of the relationships within the subfamily.

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Section: Changes In Genomic Characteristics and Gene Contentmentioning

confidence: 90%

Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae)

Zuo

Qin

et al. 2023

BMC Plant Biol

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“…The NAD(P)H-dehydrogenase complex is known to be the most affected by losses and pseudogenizations (Sanderson et al 2015;Solórzano et al 2019;Silva et al 2021). Accordingly, in this study we observed that five subunits were lost, ndhA, ndhE, ndhG, ndhI, and ndhK, and ndhB, ndhC, ndhD, ndhF, ndhH, and ndhJ were pseudogenized in D. bahiensis and M. ernestii.…”

Section: Plastid Genes Of Discocactus Bahiensis and Melocactusmentioning

confidence: 49%

“…In Caryophyllales, significant gene losses have been reported for Droseraceae and Molluginaceae (Nevill et al 2019;Yao et al 2019). Carnegiea gigantea and species of the genera Mammillaria and Rhipsalis (Cactoideae, Cactaceae) also presented significant gene losses (Sanderson et al 2015;Solórzano et al 2019;Oulo et al 2020;Silva et al 2021). Unlike Cactoideae, the subfamily Opuntioideae did not have such drastic gene losses, although presenting alterations of the IRs after duplication of genes previously positioned in the SSC region (Köhler et al 2020).…”

Section: Plastid Genes Of Discocactus Bahiensis and Melocactusmentioning

confidence: 98%

“…Nevertheless, D. bahiensis and M. ernestii lost nine genes. Thus, gene losses are common in the Cactaceae family, especially in the subfamily Cactoideae, affecting mainly the ndh complex (Sanderson et al 2015;Solórzano et al 2019;Silva et al 2021), as in other groups (Kim et al 2015;Lin et al 2015).…”

Section: Plastid Genes Of Discocactus Bahiensis and Melocactusmentioning

confidence: 99%

“…In R. baccifera, five NAD (P) H-dehydrogenase complex subunits were found, with ndhD designated as functional gene (Oulo et al 2020). In R. teres, six NAD (P) H-dehydrogenase complex subunits were found, with ndhJ annotated as a functional gene (Silva et al 2021). Carnegiea gigantea, also part of Cactoideae, lost nine of the 11 subunits of the ndh complex, with the remaining two subunits being pseudogenized.…”

Section: Plastid Genes Of Discocactus Bahiensis and Melocactusmentioning

confidence: 99%

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Assembling the puzzle: Complete chloroplast genome sequences of Discocactus bahiensis Britton & Rose and Melocactus ernestii Vaupel (Cactaceae) and their evolutionary significance

et al. 2021

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Discocactus and Melocactus are representatives of Core Cactoideae II BCT clade (Browningieae, Cereeae and Trichocereeae clade) and consist of 14 and 50 species, respectively. Both genera occur in South America, but Melocactus distribution extends through Central America and the West Indies. Although the Cactaceae family stands out for having highly rearranged plastomes, with particular gene organization, small or divergent inverted repeats (IRs) and IR loss, the plastome variation in the BCT clade is unknown. In this study, we assembled plastomes of Discocactus bahiensis and Melocactus ernestii and compared them with other available plastomes of Cactoideae (Carnegiea gigantea, and species of the genera Mammillaria and Rhipsalis) as well as with canonical plastomes of members of the order Caryophyllales (Portulaca oleracea and Spinacea oleracea). The plastomes of D. bahiensis (128,733-bp) and M. ernestii (130,703-bp) showed a quadripartite structure with 17 rearrangements when compared to those of P. oleracea and S. oleracea. Thus, twenty-eight genes were transferred from the LSC (large single copy) region to the IRs and 12 genes from the IRs to the LSC or SSC (small single copy) regions. Twenty-seven syntenic blocks were identified, evidencing a large number of rearrangements within the subfamily Cactoideae. These rearrangements could not be explained by the absence of IR regions nor the number of repeats. By comparing plastomes of D. bahiensis and M. ernestii, we propose new regions for phylogenetic inferences for the subfamily Cactoideae, for Discocactus and Melocactus, and for related groups.

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Highly degenerate plastomes in two hemiparasitic dwarf mistletoes: Arceuthobium chinense and A. pini (Viscaceae)

Guo

Zhang

Fan

et al. 2021

Planta

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Genetic and evolutionary analyses of plastomes of the subfamily Cactoideae (Cactaceae) indicate relaxed protein biosynthesis and tRNA import from cytosol

Cited by 11 publications

References 103 publications

Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae)

Plastome variations reveal the distinct evolutionary scenarios of plastomes in the subfamily Cereoideae (Cactaceae)

Assembling the puzzle: Complete chloroplast genome sequences of Discocactus bahiensis Britton & Rose and Melocactus ernestii Vaupel (Cactaceae) and their evolutionary significance

Highly degenerate plastomes in two hemiparasitic dwarf mistletoes: Arceuthobium chinense and A. pini (Viscaceae)

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