Effectiveness of the DNA barcoding approach for closely related conifers discrimination: A case study of the Pinus mugo complex

Celiński, Konrad; Kijak, Hanna; Wojnicka-Półtorak, Aleksandra; Buczkowska, Katarzyna; Sokołowska, Joanna; Chudzińska, Ewa

doi:10.1016/j.crvi.2017.06.002

Cited by 25 publications

(29 citation statements)

References 48 publications

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“…In agreement with DNA barcode studies [25][26][27], we find that the chloroplast matK and psbA-trnH loci represent optimal genetic barcodes for distinguishing limber from whitebark pine. Indeed, matK and the psbA-trnH spacer were identified as a particularly informative combination for distinguishing pine species [26]. A PsiI digest of the psbA-trnH spacer that remains uncut would suggest that the needles belong to whitebark pine, and a BsmAI digest of matK (Figure 2, upper and middle panels) could verify this.…”

Section: Discussionsupporting

confidence: 88%

An Economical Approach to Distinguish Genetically Needles of Limber from Whitebark Pine

Alongi

Hansen

Laufenberg

et al. 2019

Forests

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Whitebark pine is difficult to distinguish from limber pine when seed cones are not present. This is often the case because of young stand age, growth at environmental extremes, or harvesting by vertebrate species. Developing an economical genetic identification tool that distinguishes non-cone-bearing limber from whitebark pine, therefore, could aid many kinds of research on these species. Phylogenetic studies involving limber and whitebark pine suggest that chloroplast DNA sequences differ between these species. We therefore wanted to identify chloroplast loci that could differentiate limber from whitebark pine trees by taking an economical approach involving restriction-site analysis. We generated chloroplast DNA barcode sequences sampled from limber and whitebark pine trees that we identified using attached seed cones. We searched for nucleotide differences associated with restriction endonuclease recognition sites. Our analyses revealed that matK and the psbA-trnH spacer each readily amplified and harbored multiple DNA-sequence differences between limber and whitebark pine. The matK coding sequence of whitebark pine has a BsmAI restriction site not found in limber pine. The psbA-trnH spacer of limber pine has two PsiI restriction sites, neither of which is found in whitebark pine. DNA-sequence and restriction-site analysis of the psbA-trnH spacer from 111 trees showed complete congruence between visually and genetically identified limber (n = 68) and whitebark (n = 43) pine trees. We conclude that restriction site analysis of the chloroplast psbA-trnH spacer and matK involves both minimal technical expertize and research funds. These findings should be of value to foresters interested in species identification and distribution modeling, as well as the analysis of fossil pine pollen, given that gymnosperms transmit chloroplast DNA paternally.

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Section: Discussionsupporting

confidence: 88%

An Economical Approach to Distinguish Genetically Needles of Limber from Whitebark Pine

Alongi

Hansen

Laufenberg

et al. 2019

Forests

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“…However, in order to settle this matter definitely, molecular screening of the hybrid individuals of the swarms is necessary, preferably using DNA markers. Recent data by Celiński et al (2017) indicate that neither chloroplast nor mitochondrial genomes harbour the potential for discrimination between P. mugo and P. uliginosa. The latter is supposed to evolve as the product of ancient hybridization between P. sylvestris and the taxa from P. mugo complex (Christensen, 1987).…”

Section: Discussionmentioning

confidence: 99%

“…The latter is supposed to evolve as the product of ancient hybridization between P. sylvestris and the taxa from P. mugo complex (Christensen, 1987). Therefore, highly challenging remains the need to involve into screening of these hybrids the nuclear genome (Celiński et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Pollen fertility and seed viability of putative hybrid swarms of Pinus sylvestris and Pinus mugo in Slovakia

et al. 2019

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Generally acknowledged reduction of the interspecific hybrid fertility was utilized in evaluation of the putative hybrid swarms of Scots pine (Pinus sylvestris L.) and mountain dwarf pine (P. mugo Turra) viability under field conditions. Pollen viability and seed quality of the trees from the four contact zones of P. sylvestris and P. mugo in Slovakia were compared with the corresponding characteristics of the pure populations of these species from three reference localities. Pollen germination percentage was comparable in contact zones and control populations of the species. Statistically significant differences between the parent and hybrid groups were detected in pollen tube length only. In general, pollen tubes of the pure species populations were longer than those in contact zones. At the cone level, the individuals from contact zones possessed shorter cones than the trees of pure species populations P. mugo and P. sylvestris. This was paralleled by a lower number of seeds per cone in contact zones and higher amount of seeds per cone in the P. mugo population. Striking differences between individuals of the contact zones and reference populations were revealed also in germination potentials of their seeds. Significantly higher proportions of germinating seeds was found in the reference populations of P. mugo and P. sylvestris than in their contact zones. Contrary to seed quality parameters mentioned above, the fractions of filled but non-germinating seeds and amounts of empty seeds were higher in contact zones than in the parental species populations, indicating higher frequency occurrence of abortive embryogenesis in the former. The lower fertility characteristics of the individuals from contact zones indicate their hybrid nature.

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“…The ycf1 region seems particularly interesting in this respect for Asparagales. Several studies show that this region has a high discriminatory power and much more potential than universal barcodes, including for species other than Dracaena [37,68,69].…”

Section: Genome Comparative Analysis and Identification Of Divergent mentioning

confidence: 99%

“…Comparative analysis of complete chloroplast genomes (cp) not only allows advanced phylogenetic reconstruction [35,36], but also allows them to be used as barcode supercodes to distinguish and identify different taxa. This approach can be very useful especially in the study of closely related or recently divergent species [37].…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome Sequence and Phylogenetic Inference of the Canary Islands Dragon Tree (Dracaena draco L.)

Celiński

Kijak

Wiland-Szymańska

2020

Forests

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Dracaena draco, which belongs to the genus Dracaena, is an endemic succulent of the Canary Islands. Although it is one of the most popular and widely grown ornamental plants in the world, little is known about its genomic variability. Next generation sequencing, especially in combination with advanced bioinformatics analysis, is a new standard in taxonomic and phylogenetic research. Therefore, in this study, the complete D. draco chloroplast genome (cp) was sequenced and analyzed in order to provide new genomic information and to elucidate phylogenetic relationships, particularly within the genus Dracaena. The D. draco chloroplast genome is 155,422 bp, total guanine-cytosine (GC) content is 37.6%, and it has a typical quadripartite plastid genome structure with four separate regions, including one large single copy region of 83,942 bp length and one small single copy region of 18,472 bp length, separated by two inverted repeat regions, each 26,504 bp in length. One hundred and thirty-two genes were identified, 86 of which are protein-coding genes, 38 are transfer RNAs, and eight are ribosomal RNAs. Seventy-seven simple sequence repeats were also detected. Comparative analysis of the sequence data of various members of Asparagales revealed mutational hotspots potentially useful for their genetic identification. Phylogenetic inference based on 16 complete chloroplast genomes of Asparagales strongly suggested that Dracaena species form one monophyletic group, and that close relationships exist between D. draco, D. cochinchinensis and D. cambodiana. This study provides new and valuable data for further taxonomic, evolutionary and phylogenetic studies within the Dracaena genus.

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Effectiveness of the DNA barcoding approach for closely related conifers discrimination: A case study of the Pinus mugo complex

Cited by 25 publications

References 48 publications

An Economical Approach to Distinguish Genetically Needles of Limber from Whitebark Pine

An Economical Approach to Distinguish Genetically Needles of Limber from Whitebark Pine

Pollen fertility and seed viability of putative hybrid swarms of Pinus sylvestris and Pinus mugo in Slovakia

Complete Chloroplast Genome Sequence and Phylogenetic Inference of the Canary Islands Dragon Tree (Dracaena draco L.)

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