Molecular Phylogeny ofAstragalussect.Ammodendron(Fabaceae) Inferred from Chloroplastycf1 Gene

Dastpak, A; Osaloo, Shahrokh Kazempour; Maassoumi, Ali Asghar; Safar, Kosar Naderi

doi:10.5735/085.055.0108

Cited by 20 publications

(13 citation statements)

References 24 publications

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“…In previous reports, the gene ycf1 was recommended as core DNA barcode for plants because of the high divergence [68]. Ycf1 gene has been widely applied in plant phylogeny and DNA barcoding studies [69–70].…”

Section: Resultsmentioning

confidence: 99%

Complete chloroplast genome of Camellia japonica genome structures, comparative and phylogenetic analysis

Guo

Liu

2019

PLoS ONE

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Camellia is an economically, ecologically and phylogenetically valuable genus in the family Theaceae. The frequent interspecific hybridization and polyploidization makes this genus phylogenetically and taxonomically under controversial and require detailed investigation. Chloroplast (cp) genome sequences have been used for cpDNA marker development and genetic diversity evaluation. Our research newly sequenced the chloroplast genome of Camellia japonica using Illumina HiSeq X Ten platform, and retrieved five other chloroplast genomes of Camellia previously published for comparative analyses, thereby shedding lights on a deeper understanding of the applicability of chloroplast information. The chloroplast genome sizes ranged in length from 156,607 to 157,166 bp, and their gene structure resembled those of other higher plants. There were four categories of SSRs detected in six Camellia cpDNA sequences, with the lengths ranging from 10 to 17bp. The Camellia species exhibited different evolutionary routes that lhbA and orf188, followed by orf42 and psbZ, were readily lost during evolution. Obvious codon preferences were also shown in almost all protein-coding cpDNA and amino acid sequences. Selection pressure analysis revealed the influence of different environmental pressures on different Camellia chloroplast genomes during long-term evolution. All Camellia species, except C . crapnelliana , presented the identical rate of amplification in the IR region. The datasets obtained from the chloroplast genomes are highly supportive in inferring the phylogenetic relationships of the Camellia taxa, indicating that chloroplast genome can be used for classifying interspecific relationships in this genus.

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Section: Resultsmentioning

confidence: 99%

Complete chloroplast genome of Camellia japonica genome structures, comparative and phylogenetic analysis

Guo

Liu

2019

PLoS ONE

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“…From the top 10 markers ranked in our list, just one (trnK/matK) has been used in more than one phylogenetic study in cacti (Nyffeler 2002;Edwards et al 2005 However, accD intergenic spacers, such as rbcL-accD and accD-psaI, have been much more widely used across disparate groups (Barfuss et al 2005;Miikeda et al 2006;Reginato et al 2010;Sun et al 2012;Michelangeli et al 2012). The ycf1 gene appears to be moderately used (Gernandt et al 2009;Guo et al 2012;Majure et al 2012;Whitten et al 2013;Shi et al 2013;Dastpak et al 2018), and increasingly reported to be a useful marker in phylogenetics inferences (Neubig et al 2009;Neubig and Abbott 2010;Dong et al 2012;Thomson et al 2018), and the most promising plastid DNA barcode of land plants (Dong et al 2015). The petD intron has been used Borsh et al 2009;Worberg et al 2007;Scataglini et al 2013), but in our analysis the entire gene was used (exon + intron) showing phylogenetic utility.…”

Section: Phylogenetically Informative Regionsmentioning

confidence: 92%

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Köhler

Reginato

et al. 2020

Preprint

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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.

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“…However, accD intergenic spacers, such as rbcL-accD and accD-psaI, have been much more widely used across disparate groups (Barfuss et al, 2005;Miikeda et al, 2006;Reginato et al, 2010;Sun et al, 2012;Michelangeli et al, 2013). The ycf1 gene appears to be moderately used (Gernandt et al, 2009;Guo et al, 2012;Majure et al, 2012;Shi et al, 2013;Whitten et al, 2013;Dastpak et al, 2018), and increasingly reported to be a useful marker in phylogenetic inferences (Neubig et al, 2009;Neubig and Abbott, 2010;Dong et al, 2012;Thomson et al, 2018), and the most promising plastid DNA barcode of land plants (Dong et al, 2015). The petD intron has been used (Löhne et al, 2007;Worberg et al, 2007;Borsch et al, 2009;Scataglini et al, 2014), but in our analysis the entire gene was used (exon + intron) showing phylogenetic utility.…”

Section: Phylogenetically Informative Regionsmentioning

confidence: 99%

Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies

et al. 2020

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Plastome Evolution in Opuntioideae (Cactaceae) 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.

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Molecular Phylogeny ofAstragalussect.Ammodendron(Fabaceae) Inferred from Chloroplastycf1 Gene

Cited by 20 publications

References 24 publications

Complete chloroplast genome of Camellia japonica genome structures, comparative and phylogenetic analysis

Complete chloroplast genome of Camellia japonica genome structures, comparative and phylogenetic analysis

Insights into chloroplast genome variation across Opuntioideae (Cactaceae)

Insights Into Chloroplast Genome Evolution Across Opuntioideae (Cactaceae) Reveals Robust Yet Sometimes Conflicting Phylogenetic Topologies

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