Sequences of rDNA internal transcribed spacers from the chloroplast DNA of 26 bryophytes: properties and phylogenetic utility

Samigullin, Tahir H.; Valiejo-Roman, K. M.; Troitsky, A. V.; Bobrova, V. K.; Filin, V. R.; Martin, William; Antonov, A. S.

doi:10.1016/s0014-5793(97)01600-1

Cited by 27 publications

(15 citation statements)

References 21 publications

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“…700 nt of non-coding DNA plus the 4.5S, 5S, and trnR genes were spanned by the two amplicons. Length variation of the three spacers ranged between 62 and 238 nt in bryophytes (Samigullin et al 1998, no sequence lengths mentioned in Samigullin et al 2002). In contrast to the conserved 16 and 23S genes, the cpITS showed considerable length variability across bryophytes (Samigullin et al 2002) and vascular plants (Goremykin et al 1996), including several rather long but yet phylogenetically informative indels.…”

Section: Plastid Ribosomal Dna (16s 23s Cpits)mentioning

confidence: 95%

“…It includes an operon of the 23S, 4.5S, and 5S rRNA genes plus in most plastid genomes a cotranscribed trnR ACG gene downstream of 5S (e.g. Samigullin et al 1998), as well as the 16S rRNA gene separated from this operon.…”

Section: Plastid Ribosomal Dna (16s 23s Cpits)mentioning

confidence: 99%

“…Whereas the ITS1 and 2 of the nuclear rDNA became one of the most popular markers ( Fig. 2; see below), the respective plastid counterparts cpITS2 and 3 plus the 5S-trnR spacer ('cpITS4') were only used by Samigullin et al (1998Samigullin et al ( , 2002. They amplified the respective region in two parts, using two unnamed primers published by Goremykin et al (1996) for cpITS2−3 and newly designed primers (cpITS4F/cpITS4R) for cpITS4.…”

Section: Plastid Ribosomal Dna (16s 23s Cpits)mentioning

confidence: 99%

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20,000 species and five key markers: The status of molecular bryophyte phylogenetics

Stech¹,

Quandt²

2014

Phytotaxa

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A number of reviews have accompanied and monitored the progress of molecular phylogenetic research on bryophytes, focusing on the publication record itself, bryophyte phylogeny and systematics in the molecular era, as well as the evolution and phylogenetic utility of markers from different genomes. However, none of the recent reviews include a detailed characterization of all molecular markers used in bryophyte phylogenetics. Here we provide an overview of the history and current state of marker utilization, including coding and non-coding sequence markers from all three genomes as well as fingerprinting approaches. The molecular architecture and evolutionary peculiarities, as well as practical aspects such as amplification and sequencing strategies, are outlined for the DNA sequence markers, with a focus on the most commonly employed regions. Their phylogenetic utility and potential for solving some of the remaining, pressing questions in bryophyte phylogeny, as well as their suitability for molecular species identification by DNA barcoding, are discussed.

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Section: Plastid Ribosomal Dna (16s 23s Cpits)mentioning

confidence: 95%

Section: Plastid Ribosomal Dna (16s 23s Cpits)mentioning

confidence: 99%

Section: Plastid Ribosomal Dna (16s 23s Cpits)mentioning

confidence: 99%

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20,000 species and five key markers: The status of molecular bryophyte phylogenetics

Stech¹,

Quandt²

2014

Phytotaxa

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“…from its own family Mitteniaceae, distributed in the South America and Australasia. However, recent data based on DNA analysis (Beckert & al., 1999(Beckert & al., , 2001Samigullin & al., 1998) show close relationshi ps of Schistostega with Dicranales (Fissidentaceae, Dicranaceae, Ditrichaceae) whereas Mittenia has double peristome and obviously is very distant evolutionary from mosses with single perisome; Buck & Goffinet (2000) placed Mittenia close to Rhizogoniaceae.…”

Section: Introductionmentioning

confidence: 99%

On the zoochory of Schistostega pennata (Schistostegaceae, Musci)

Ignatov

Ignatova

2001

Arctoa, a jornal of bryology

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The spores of Schistostega pennata (Hedw.) Web. et Mohr have sticky surface and can not be freely dispersed by wind in fresh state. Also spore surface ornamentation is very similar to that of Splachnum, Tetraplodon and Aplodon, genera strictly adapted to entomochory; this allows to suggest the adaptation to zoochory in Schistostega. Other evidences of zoochory in Schistostega are based on its recent rapid expansion in some parts of Central Russia, on habitat peculiarities, and on some other parallels in morphology with Splachnaceae. The possible dispersal agents are discussed (birds, mammals, insects, spiders, etc.), but no one of them can be chosen as the main one, at least in the forests of Central Russia. ÐåçþìåÑïîðû Schistostega pennata (Hedw.) Web. et Mohr èìåþò ëèïêóþ ïîâåðõíîñòü è â ñâåaeåì ñîñòîÿíèè íå ìîãóò ðàñïðîñòðàíÿòüñÿ âåòðîì. Îðíàìåíòàöèÿ ïîâåðõíîñòè ñïîð âåñüìà ñõîäíà ñ òàêîâîé Splachnum, Tetraplodon è Aplodon, ðîäîâ, äëÿ êîòîðûõ ïîêàçàíà èñêëþ÷èòåëüíàÿ àäàïòàöèÿ ê ýíòîìîõîðíîìó ðàñïðîñòðàíåíèþ ñïîð. Ýòî äàåò âîçìîaeíîñòü ïðåäïîëîaeèòü çîîõîðèþ êàê îñíîâíîé ñïîñîá ðàñïðîñòðàíåíèÿ äèàñïîð ó Schistostega. Äîïîëíèòåëüíûìè îñíîâàíèÿìè äëÿ òàêîãî çàêëþ÷åíèÿ ÿâëÿþòñÿ äàííûå î íåäàâíåì áûñòðîì ðàññåëåíèè Schistostega â Öåíòðàëüíîé Ðîññèè, îñîáåííîñòÿõ åå ýêîëîãèè, à òàêaeå ïðî÷èõ îáùèõ ñî Splachnaceae ìîðôîëîãè÷åñêèõ ïðèçíàêàõ. Âîçìîaeíûìè ïåðåíîñ÷èêàìè äèàñïîð ìîãóò áûòü ðàçíûå aeèâîòíûå (ïòèöû, çâåðè, íàñåêîìûå, ïàóêîîáðàçíûå è äð.), íî âûÿâèòü ãëàâíîãî ðàñïðîñòðàíèòåëÿ ñïîð â ëåñàõ Öåíòðàëüíîé Ðîññèè íå óäàëîñü.

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“…ITS sequences have been used successfully in studying phylogenetic and genomic relationships of plants at lower taxonomic levels and the ITS regions are therefore valuable in more discrete phylogenetic separation of closely related species, recognition of new species, determination of conspecificity between isolates, discrimination within a species, and differentiation between species and subspecies (Samigullina et al, 1998;Aktas et al, 2007;Song et al, 2012). I T S a n i n t e r e s t i n g s u b j e c t f o r evolutionary/phylogenetic investigations, that which are found on either side of 5.8S rRNA gene and are described as ITS1 and ITS2.…”

Section: Introductionmentioning

confidence: 99%

The Phylogenetic Relationship Among Varieties of Lansium domesticum Correa Based on ITS rDNA Sequences

Hanum¹,

Kasiamdari²,

Santosa³

et al. 2015

IJBiotech

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Lansium domesticum Corr. with vernacular name in Indonesian duku has been reported containing therapeutic bioactive compounds, and some of these compounds shown to be potent antitumor, anticancer, antimalaria, antimelanogenesis, antibacteria, and antimutagenic activities. This plant is commonly known as duku, kokosan and langsat by the local community in Indonesia. The morphological appearance of all varieties is nearly the same, and identifi cation of the varieties is very diffi cult for growers. Variation of DNA sequences of the ITS (Internal transcribed spacer) region can be used as a molecular character to determine the phylogenetic relationship of different varieties of L. domesticum. The aims of this study were to determine taxonomy status of duku, kokosan, and langsat, also phylogenetic relationship among varieties of L. domesticum based on ITS rDNA sequencing. DNA was isolated from leaves of plant and then amplifi ed using F1 and R1 primers. Nucleotide sequences were identifi ed using Sequence Scanner Software Programm version 1.0, nucleotide sequences from 18S, ITS1, 5.8S, ITS2 and 26S region, that has been mergered using EditSeq and SegMan in software Suite for Sequence Analysis DNASTAR Lasergene DM version 3.0.25. The results of study showed that DNA fragments ranging in size from 782-810 bp. Different pattern of DNA fragments indicated polymorphism among duku, kokosan, and langsat. Based on the results of the ITS rDNA sequencing and phylogenetic tree analysis. It was determined that Lansium and Aglaia are a separated genus with the similarity index value of 0.98. Duku, kokosan and langsat were divided into two cluster, namely cluster kokosan-langsat and cluster duku with the similarity index value of 0.996.

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Sequences of rDNA internal transcribed spacers from the chloroplast DNA of 26 bryophytes: properties and phylogenetic utility

Cited by 27 publications

References 21 publications

20,000 species and five key markers: The status of molecular bryophyte phylogenetics

20,000 species and five key markers: The status of molecular bryophyte phylogenetics

On the zoochory of Schistostega pennata (Schistostegaceae, Musci)

The Phylogenetic Relationship Among Varieties of Lansium domesticum Correa Based on ITS rDNA Sequences

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