Choosing an Approach and an Appropriate Gene for Phylogenetic Analysis

Soltis, Douglas E.; Soltis, Pamela S.

doi:10.1007/978-1-4615-5419-6_1

Cited by 270 publications

(208 citation statements)

References 260 publications

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“…Mitochondrial DNA sequence data have long been an important source of data in animal phylogenetics (e.g., Curole and Kocher 1999), equivalent in importance to the use of plastid DNA data in plant studies (e.g., Soltis and Soltis 1998). The reluctance among botanists to use mitochondrial data has been induced primarily by the pronounced structural diversity of plant mitochondrial genomes, caused at least in part by their ability to recombine (Palmer 1992;Backert et al 1997).…”

Section: Introductionmentioning

confidence: 99%

“…By the time systematists turned to DNA sequence data, the focus on plastid and nuclear genomes already had been established. However, the structural diversity of the mitochondrial genome is generally not a problem for the use of mitochondrial sequence data in phylogenetic reconstruction, and in the past ten years plant systematists have begun exploring the mitochondrial genome as a new source of useful characters (Hiesel et al 1994;Soltis and Soltis 1998). There are several advantages to using mitochondrial data in phylogenetic reconstruction.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Mitochondrial Data in Monocot Phylologenetics

Peterson¹,

Seberg²,

Davis³

et al. 2006

aliso

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Mitochondrial sequences are an important source of data in animal phylogenetics, equivalent in importance to plastid sequences in plants. However, in recent years plant systematists have begun exploring the mitochondrial genome as a source of phylogenetically useful characters. The plant mitochondrial genome is renowned for its variability in size, structure, and gene organization, but this need not be of concern for the application of sequence data in phylogenetics. However, the incorporation of reverse transcribed mitochondrial genes ("processed paralogs") and the recurring transfer of genes from the mitochondrion to the nucleus are evolutionary events that must be taken into account. RNA editing of mitochondrial genes is sometimes considered a problem in phylogenetic reconstruction, but we regard it only as a mechanism that may increase variability at edited sites and change the codon position bias accordingly. Additionally, edited sites may prove a valuable tool in identifying processed paralogs. An overview of genes and sequences used in phylogenetic studies of angiosperms is presented. In the monocots, a large amount of mitochondrial sequence data is being collected together with sequence data from plastid and nuclear genes, thus offering an opportunity to compare data from different genomic compartments. The mitochondrial and plastid data are incongruent when organelle gene trees are reconstructed. Possible reasons for the observed incongruence involve sampling of paralogous sequences and highly divergent substitution rates, potentially leading to longbranch attraction. The above problems are addressed in Acorales, Alismatales, Poales, Liliaceae, the "Anthericum clade" (in Agavaceae), and in some achlorophyllous taxa.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mitochondrial Data in Monocot Phylologenetics

Peterson¹,

Seberg²,

Davis³

et al. 2006

aliso

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show abstract

“…On the other hand, the region (psbA~trnK) amplified by the cp101 primer pair includes the whole matK gene and adjacent regions. This gene has already been proved to have excellent utility on specific classification (Soltis and Soltis, 1998). Furthermore, the amplified region (trnY~trnD) of the cp105 primer pair partially overlapped with a region amplified by one primer pair developed by Demesure et al (1995).…”

Section: Discussionmentioning

confidence: 99%

“…Although conducting whole genome sequencing for each species or individuals can provide sufficient and accurate information, a significant amount of time and funding is required. Because the amount of variation provided by the DNA sequences of ITS (internal transcribed spacer), IGS (intergenic spacer), rbcL (large subunit of ribulose 1,5-bisphosphate carboxylase), and matK (maturase K) in plant phylogeny analysis is often inadequate, these sequences cannot be used to reveal the relationships between some species (Soltis and Soltis, 1998;Selvaraj et al, 2013). Demesure et al (1995) developed universal primers based on conservative sequences of chloroplast genomes from three land plants.…”

Section: Introductionmentioning

confidence: 99%

Development of primer pairs from diverse chloroplast genomes for use in plant phylogenetic research

Yang

Kung

Hu³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Variation in the chloroplast DNA sequence is useful for plant phylogenetic studies. However, the number of variable sequences provided by chloroplast DNA for suggested genes or genomic regions in plant phylogenetic analyses is often inadequate. To identify conserved regions that can be used to design primers and amplify variable sequences for use in plant phylogenetic studies, the complete chloroplast genomic sequences of six plant species (including Oryza sativa, Arabidopsis thaliana, Glycine max, Lotus japonicus, Medicago truncatula, and Phaseolus vulgaris), searched from the taxonomy database of NCBI were investigated. A total of 93 conserved regions, 32 in large single copy and 61 in inverted repeat regions, were identified. A set of five primer pairs were designed according to the conserved sequences located in the psbA~trnK, psbB~psbH, rpl23~trnI, trnR~trnN, and trnY~trnD regions to amplify variable DNA fragments. An additional 18 plant accessions from 14 species were used to validate (2015) their utility. Each of the tested species could be distinguished by length polymorphisms of fragments amplified with the five primer pairs. trnR~trnN and rpl23~trnI amplified fragments specific to monocot and legume species, respectively. Three primer pairs located in the psbA~trnK, psbB~psbH, and trnR~trnN regions were applied to amplify variable DNA sequences for phylogenetic analysis using the maximum parsimony method. The consistent result between taxonomy and phylogenetic analysis on the variable sequences amplified with these three primer pairs was revealed. The five newly developed primer pairs are recommended as tools for use in the identification of plant species and in phylogenetic studies.

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“…According to Johnson and Soltis (1994), Olmstead and Palmer (1994), the rate of nucleotide susbstitution in matK is three times higher than that of the large subunit of Rubisco (rbcL) and six fold higher than the amino acid substitution rate, which significantly presents it as a fast evolving gene. This capacity of matK gene also provides high phylogenetic signal for resolving evolutionary relationships and relatedness among plants at all taxonomic levels (Soltis and Soltis, 1998;.…”

Section: Introductionmentioning

confidence: 99%

Sequence analysis of Maturase K (matK): A chloroplast-encoding gene in some selected pulses

Udensi¹,

Ita²,

Ikpeme³

et al. 2017

Glo Jnl Pure Appl Sci

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The application and utilization of sequence data has been found very informative in the characterization and phylogenetic relationship of different crops species. This study aimed to use bioinformatics tools to characterize the matK gene in some selected legumes with special reference to pigeon pea [cajanus cajan (L.)Millsp] matK sequence as a quarry sequence. Nucleotide and amino acid sequence of matK gene of 10 legumes were retrieved from NCBI database and analysed for homology, physiochemical properties, motifs, GC content as well as phylogenetic relationships. Results showed that the nucleotide and amino acid sequence lengths of this gene among the selected legumes differs. Its nucleotide length varied between 631-1580bp, while the amino acids sequence varied between 21 and 509 residues. P. tetragonolobus matK and C. cajan matK sequences had percentage identity of 88% while V. sativa had the lowest percentage identity of 70%. G.tomentella and P. tetragonolobus matK sequence shared the same percentage similarity of 91% with C.cajan while V. sativa had the least (78%) with C.cajan. The motif predicted were tyrosine kinase phosphorylation site, N-myristoylation site, N-glycosylation site, protein kinase phosphorylation site, casein kinase II phosphorylation site and cAMP-and -cGMP dependent protein kinase phosphorylation site. However, microbodies C-terminal targeting site was only predicted in the amino acid sequence of matK gene of P. sativum and C.cajan. Phylogenetically, two major clades were revealed with P.sativum, V.sativa, and C. arientinum matK gene sequence in clade A and matK gene sequence of P.tetragonolobus, C. cajan, G. tomentella, P.vulgaris, V.unguiculata, V. angularis and V. radiate in clade B. It showed that clade A diverged from the ancestry legume approximately 39MYA while legume sequences in clade B diverged from the ancestor about 57MYA. GC content of the nucleotide sequence of matK gene of V. sativa was highest (31.37%) with the range in the selected legume varying between 7.29%-31.37%. The secondary structure of amino acids sequence of matK gene in the selected legume revealed the alpha helix (34.14%-41.27%), extended strand (11.56%-20.99%) and random coil (39.48%-51.76%). The major domain architecture found in the amino acid sequence were single and double types. Implicitly, though maturase K gene sequences in the selected legumes differ in lengths physiochemical properties, GC content and motif. The result of this study revealed that C.cajan matK gene sequences is closely related to that of P. tetragonolobus but distant to V. unguiculata as well as P. vulgaris.

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Choosing an Approach and an Appropriate Gene for Phylogenetic Analysis

Cited by 270 publications

References 260 publications

Mitochondrial Data in Monocot Phylologenetics

Mitochondrial Data in Monocot Phylologenetics

Development of primer pairs from diverse chloroplast genomes for use in plant phylogenetic research

Sequence analysis of Maturase K (matK): A chloroplast-encoding gene in some selected pulses

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