Loss of the Acetyl-CoA Carboxylase (accD) Gene in Poales

Harris, Mark E.; Meyer, Georg; Vandergon, Thomas L.; Vandergon, Virginia Oberholzer

doi:10.1007/s11105-012-0461-3

Cited by 45 publications

(37 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…All genes here reported as pseudogenes in the O. quimilo plastome (accD, rpl16, rps16, ycf1 and ycf2) have also been reported as pseudogenes in the Mammillaria plastomes (Solórzano et al 2019), while the accD was described as a pseudogene in Carnegia gigantea (Sanderson et al 2015). Pseudogenization of these genes has been repeatedly reported across different angiosperm lineages, such as Malpighiales, Campanulales, Ericales, Poales, Solanales, Geraniales, Santalales and Myrtales (Harris et al 2013;Haberle et al 2008;Fajardo et al 2013;Weng et al 2013;Bedoya et al 2019;Cui et al 2019;Machado et al 2017). Even though these genes have been identified with essential functions beyond photosynthesis and retained in the plastome of most embryophytes (Drescher et al, 2000;Kuroda and Maliga, 2003;Kode et al, 2005;Kikuchi et al, 2013;Parker et al, 2014;Dong et al, 2015), there are several other plants where these genes are missing from the chloroplast genome (Kim, 2004;Magee et al, 2010;Lei et al, 2016;Graham et al, 2017).…”

Section: Insights From Chloroplast Genome Assemblies In Opuntioideae supporting

confidence: 55%

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Köhler

Reginato

et al. 2020

Preprint

View full text Add to dashboard Cite

Chloroplast genomes (plastomes) are frequently treated as highly conserved among land plants. However, many lineages of vascular plants have experienced extensive structural rearrangements, including inversions and modifications to the size and content of genes. Cacti are one of these lineages, containing the smallest plastome known for an obligately photosynthetic angiosperm, including the loss of one copy of the inverted repeat (~25 kb) and the ndh genes suite, but only a few cacti from the subfamily Cactoideae have been sufficiently characterized. Here, we investigated the variation of plastome sequences across the second-major lineage of the Cactaceae, the subfamily Opuntioideae, to address 1) how variable is the content and arrangement of chloroplast genome sequences across the subfamily, and 2) how phylogenetically informative are the plastome sequences for resolving major relationships among the clades of Opuntioideae. Our de novo assembly of the Opuntia quimilo plastome recovered an organelle of 150,347 bp in length with both copies of the inverted repeats and the presence of all the ndh genes suite. An expansion of the large single copy unit and a reduction of the small single copy was observed, including translocations and inversion of genes as well as the putative pseudogenization of numerous loci. Comparative analyses among all clades within Opuntioideae suggested that plastome structure and content vary across taxa of this subfamily, with putative independent losses of the ndh gene suite and pseudogenization of genes across disparate lineages, further demonstrating the dynamic nature of plastomes in Cactaceae. Our plastome dataset was robust in determining relationships among major clades and subclades within Opuntioideae, resolving three tribes with high support: Cylindropuntieae, Tephrocacteae and Opuntieae. A plastome-wide survey for highly informative phylogenetic markers revealed previously unused regions for future use in Sanger-based studies, presenting a valuable dataset with primers designed for continued evolutionary studies across Cactaceae. These results bring new insights into the evolution of plastomes in cacti, suggesting that further analyses should be carried out to address how ecological drivers, physiological constraints and morphological traits of cacti may be related with the common rearrangements in plastomes that have been reported across the family.

show abstract

Section: Insights From Chloroplast Genome Assemblies In Opuntioideae supporting

confidence: 55%

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Köhler

Reginato

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The differing degrees of plastomic acc D fragmentation in the single Pelargonium clades (fig. 3) resemble observations in lineages of Poales (Harris et al. 2013), Oleaceae (Lee et al.…”

Section: Discussionsupporting

confidence: 82%

Genus-wide screening reveals four distinct types of structural plastid genome organization in Pelargonium (Geraniaceae)

Röschenbleck

Wicke

Weinl³

et al. 2016

Genome Biol Evol

View full text Add to dashboard Cite

Geraniaceae are known for their unusual plastid genomes (plastomes), with the genus Pelargonium being most conspicuous with regard to plastome size and gene organization as judged by the sequenced plastomes of P. x hortorum and P. alternans. However, the hybrid origin of P. x hortorum and the uncertain phylogenetic position of P. alternans obscure the events that led to these extraordinary plastomes. Here, we examine all plastid reconfiguration hotspots for 60 Pelargonium species across all subgenera using a PCR and sequencing approach. Our reconstruction of the rearrangement history revealed four distinct plastome types. The ancestral plastome configuration in the two subgenera Magnipetala and Pelargonium is consistent with that of the P. alternans plastome, whereas that of the subgenus Parvulipetala deviates from this organization by one synapomorphic inversion in the trnNGUU–ndhF region. The plastome of P. x hortorum resembles those of one group of the subgenus Paucisignata, but differs from a second group by another inversion in the psaI–psaJ region. The number of microstructural changes and amount of repetitive DNA are generally elevated in all inverted regions. Nucleotide substitution rates correlate positively with the number of indels in all regions across the different subgenera. We also observed lineage- and species-specific changes in the gene content, including gene duplications and fragmentations. For example, the plastid rbcL–psaI region of Pelargonium contains a highly variable accD-like region. Our results suggest alternative evolutionary paths under possibly changing modes of plastid transmission and indicate the non-functionalization of the plastid accD gene in Pelargonium.

show abstract

“…polysticta plastome, six protein-coding genes have been differentially lost in asterid lineages (Table 5). Three of these that have been pseudogenized or deleted outside of the asterids are: infA (lost in many rosids and other angiosperm lineages [84]), rpl23 ( Spinacia [85] and several gymnosperms [33]), and accD (many Poales families [86]). Both accD and rpl23 were found to be essential for Nicotiana [87], [88] and rpl23 was suggested to be replaced by a nuclear homologue in Spinacia [85].…”

Section: Resultsmentioning

confidence: 99%

Complete Plastid Genome Sequence of the Basal Asterid Ardisia polysticta Miq. and Comparative Analyses of Asterid Plastid Genomes

Kuo

2013

PLoS ONE

View full text Add to dashboard Cite

Ardisia is a basal asterid genus well known for its medicinal values and has the potential for development of novel phytopharmaceuticals. In this genus of nearly 500 species, many ornamental species are commonly grown worldwide and some have become invasive species that caused ecological problems. As there is no completed plastid genome (plastome) sequence in related taxa, we sequenced and characterized the plastome of Ardisia polysticta to find plastid markers of potential utility for phylogenetic analyses at low taxonomic levels. The complete A. polysticta plastome is 156,506 bp in length and has gene content and organization typical of most asterids and other angiosperms. We identified seven intergenic regions as potentially informative markers with resolution for interspecific relationships. Additionally, we characterized the diversity of asterid plastomes with respect to GC content, plastome organization, gene content, and repetitive sequences through comparative analyses. The results demonstrated that the genome organizations near the boundaries between inverted repeats (IRs) and single-copy regions (SCs) are polymorphic. The boundary organization found in Ardisia appears to be the most common type among asterids, while six other types are also found in various asterid lineages. In general, the repetitive sequences in genic regions tend to be more conserved, whereas those in noncoding regions are usually lineage-specific. Finally, we inferred the whole-plastome phylogeny with the available asterid sequences. With the improvement in taxon sampling of asterid orders and families, our result highlights the uncertainty of the position of Gentianales within euasterids I.

show abstract

Loss of the Acetyl-CoA Carboxylase (accD) Gene in Poales

Cited by 45 publications

References 60 publications

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Genus-wide screening reveals four distinct types of structural plastid genome organization in Pelargonium (Geraniaceae)

Complete Plastid Genome Sequence of the Basal Asterid Ardisia polysticta Miq. and Comparative Analyses of Asterid Plastid Genomes

Contact Info

Product

Resources

About