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Xin-Yu Zhu Mark W Chase Yin-Long Qiu Hong-Zhi Kong David L Dilcher Jian-Hua Li Zhi-Duan Chen 《BMC evolutionary biology》2007,7(1):217
Background
Rosids are a major clade in the angiosperms containing 13 orders and about one-third of angiosperm species. Recent molecular analyses recognized two major groups (i.e., fabids with seven orders and malvids with three orders). However, phylogenetic relationships within the two groups and among fabids, malvids, and potentially basal rosids including Geraniales, Myrtales, and Crossosomatales remain to be resolved with more data and a broader taxon sampling. In this study, we obtained DNA sequences of the mitochondrial matR gene from 174 species representing 72 families of putative rosids and examined phylogenetic relationships and phylogenetic utility of matR in rosids. We also inferred phylogenetic relationships within the "rosid clade" based on a combined data set of 91 taxa and four genes including matR, two plastid genes (rbcL, atpB), and one nuclear gene (18S rDNA). 相似文献3.
A. V. Seliverstov E. A. Lysenko V. A. Lyubetsky 《Russian Journal of Plant Physiology》2009,56(6):838-845
Plastome is thought to be a very conservative part of plant genome but little is known about the evolution of plastome promoters.
It was previously shown that one light-regulated promoter (LRPpsbD) is highly conserved in different flowering plant species and in black pine. We have undertaken search and demonstrated that
gene ndhF is located in a plastome region that rarely underwent substantial rearrangements in terrestrial plants. However, alignment
of sequences upstream ndhF suggests that promoters of this gene underwent comparatively rapid evolution in flowering plants. Probably, the ancestor
of two basal Magnoliophyta branches (magnoliids and eudicotyledons) had the promoter PA-ndhF, which was substituted with other promoters—PB-ndhF and PC-ndhF—in some phylogenetic lineages of dicots. We failed to reveal conservative sequences with potential promoters of −10/−35 type
upstream ndhF genes of monocotyledonous plants, including nine representatives of the grass family (Poaceae). Multiple alignments of sequences
from related taxa showed that the predicted ndhF promoters (A–C) underwent frequent mutations and these mutations are not only nucleotide substitutions but also small insertions
and deletions. Thus, we can assume that at least some plastome promoters evolve rapidly. 相似文献
4.
Hyosig Won 《Journal of Plant Biology》2009,52(5):411-416
Recent phylogenetic research suggests that Malvaceae s.l. comprises formerly Tiliaceae, Byttneriaceae, Bombacaceae, and Sterculiaceae.
Corchoropsis is traditionally included in Tiliaceae or Sterculiaceae and is distributed in China, Korea, and Japan. One to three species
have been recognized for this genus. Phylogenetic relationships among the Malvacean taxa have been intensively studied with
molecular data, and the evolution of their morphological characteristics has been re-interpreted accordingly. However, no
Corchoropsis species have been included for their phylogenetic position. Here, three chloroplast coding regions—rbcL, atpB, and ndhF, from Corchoropsis psilocarpa and Corchoropsis crenata—were amplified and sequenced, then compared with other Malvacean taxa. This analysis of the three plastid gene sequences
now places Corchoropsis species in Dombeyoideae, as previously proposed by Takeda (Bull Misc Inform Kew 365, 1912), Tang (Cathaya 4:131–150, 1992), and Bayer and Kubitzki (2003). Within Dombeyoideae, Corchoropsis forms a strongly supported sister relationship with the Dombeya–Ruizia clade. 相似文献
5.
Fujii N 《Journal of plant research》2007,120(4):491-500
Phylogeographic analyses using chloroplast DNA (cpDNA) variation were performed for Pedicularis ser. Gloriosae (Orobanchaceae). Eighty-one plants of 18 populations of 6 species (P. gloriosa, P. iwatensis, P. nipponica, P. ochiaiana, P. sceptrum-carolinum and P. grandiflora) were analyzed. Fifteen distinct haplotypes were identified based on six cpDNA regions: the intergenic spacer between the
trnT and trnL 3′exon, trnL 3′exon-trnF, atpB-rbcL, accD–psaI, the rpl16 intron and the trnK region (including the matK gene). Via phylogenetic analyses of the haplotypes, two continental species, P. sceptrum-carolinum and P. grandiflora, were placed at the most ancestral position in the trees. The former species is widely distributed in the Eurasian continent,
and the latter is distributed in Far East Asia. Two robust major cpDNA clades (clades I and II) were revealed in the Japanese
archipelago, although the statistical values of monophyly of these clades were weak. Clade I included the haplotypes (A-1,
A-2, B-1, B-2 and J) of three species (P. gloriosa, P. iwatensis and P. ochiaiana), and Clade II included seven haplotypes (C-D, E-1, E-2 and F-H) of P. nipponica. These results suggest that this series originated on the Eurasian continent and that subsequently populations at the eastern
edge of the continent differentiated into the two Japanese lineages.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
6.
T. P. Tourova A. V. Korshunova E. M. Mikhailova D. Sh. Sokolova A. B. Poltaraus T. N. Nazina 《Microbiology》2010,79(3):356-369
The primary structures of the genes encoding the β-subunits of a type II topoisomerase (gyrase, gyrB) and a type IV topoisomerase (parE) were determined for 15 strains of thermophilic bacteria of the genus Geobacillus. The obtained sequences were used for analysis of the phylogenetic similarity between members of this genus. Comparison of
the phylogenetic trees of geobacilli constructed on the basis of the 16S rRNA, gyrB, and parE gene sequences demonstrated that the level of genetic distance between the sequences of the genes encoding the β-subunits
of type II topoisomerases significantly exceeded the values obtained by comparative analysis of the 16S rRNA gene sequences
of Geobacillus strains. It was shown that, unlike the 16S rRNA gene analysis, comparative analysis of the gyrB and parE gene sequences provided a more precise determination of the phylogenetic position of bacteria at the species level. The data
obtained suggest the possibility of using the genes encoding the β-subunits of type II topoisomerases as phylogenetic markers
for determination of the species structure of geobacilli. 相似文献
7.
Iain Darbyshire 《Kew Bulletin》2008,63(2):261-268
Summary Three new species are described in Barleria L. sect. Stellatohirta M. Balkwill from tropical Africa: B. aristata from south-central Tanzania, B. aenea from south-western Tanzania and northeast Zambia, and B. purpureotincta from south-western Zambia. Their affinities and conservation status are discussed. 相似文献
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Junya Ono Jean W. H. Yong Koji Takayama Mohd Nazre Bin Saleh Alison K. S. Wee Takeshi Asakawa Orlex Baylen Yllano Severino G. SalmoIII Monica Suleiman Nguyen Xuan Tung Khin Khin Soe Sankararamasubramanian Halasya Meenakshisundaram Yasuyuki Watano Edward L. Webb Tadashi Kajita 《Conservation Genetics》2016,17(5):1137-1144
Bruguiera hainesii (Rhizophoraceae) is one of the two Critically Endangered mangrove species listed in the IUCN Red List of Threatened Species. Although the species is vulnerable to extinction, its genetic diversity and the evolutionary relationships with other Bruguiera species are not well understood. Also, intermediate morphological characters imply that the species might be of hybrid origin. To clarify the genetic relationship between B. hainesii and other Bruguiera species, we conducted molecular analyses including all six Bruguiera species using DNA sequences of two nuclear genes (CesA and UNK) and three chloroplast regions (intergenic spacer regions of trnL-trnF, trnS-trnG and atpB-rbcL). For nuclear DNA markers, all nine B. hainesii samples from five populations were heterozygous at both loci, with one allele was shared with B. cylindrica, and the other with B. gymnorhiza. For chloroplast DNA markers, the two haplotypes found in B. hainesii were shared only by B. cylindrica. These results suggested that B. hainesii is a hybrid between B. cylindrica as the maternal parent and B. gymnorhiza as the paternal one. Furthermore, chloroplast DNA haplotypes found in B. hainesii suggest that hybridization has occurred independently in regions where the distribution ranges of the parental species meet. As the IUCN Red List of Threatened Species currently excludes hybrids (except for apomictic plant hybrids), the conservation status of B. hainesii should be reconsidered. 相似文献
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Partial gyrB sequences (>1 kb) were obtained from 34 type strains of the genus Amycolatopsis. Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships
within the genus. The use of gyrB sequence analysis as an alternative to DNA–DNA hybridization was also assessed for distinguishing closely related species.
The gyrB based phylogeny mostly confirmed the conventional 16S rRNA gene-based phylogeny and thus provides additional support for
certain of these 16S rRNA gene-based phylogenetic groupings. Although pairwise gyrB sequence similarity cannot be used to predict the DNA relatedness between type strains, the gyrB genetic distance can be used as a means to assess quickly whether an isolate is likely to represent a new species in the
genus Amycolatopsis. In particular a genetic distance of >0.02 between two Amycolatopsis strains (based on a 315 bp variable region of the gyrB gene) is proposed to provide a good indication that they belong to different species (and that polyphasic taxonomic characterization
of the unknown strain is worth undertaking).
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
The GenBank accession numbers for the gyrB gene sequences obtained in this study are shown in Table 1. 相似文献
11.
Stefanie Kimbacher Ingrid Gerstl Branko Velimirov Sylvia Hagemann 《Molecular genetics and genomics : MGG》2009,282(2):165-172
P transposons belong to the eukaryotic DNA transposons, which are transposed by a cut and paste mechanism using a P-element-coded transposase. They have been detected in Drosophila, and reside as single copies and stable homologous sequences in many vertebrate species. We present the P elements Pcin1, Pcin2 and Pcin3 from Ciona intestinalis, a species of the most primitive chordates, and compare them with those from Ciona savignyi. They showed typical DNA transposon structures, namely terminal inverted repeats and target site duplications. The coding
region of Pcin1 consisted of 13 small exons that could be translated into a P-transposon-homologous protein. C. intestinalis and C. savignyi displayed nearly the same phenotype. However, their P elements were highly divergent and the assumed P transposase from C. intestinalis was more closely related to the transposase from Drosophila melanogaster than to the transposase of C. savignyi. The present study showed that P elements with typical features of transposable DNA elements may be found already at the base of the chordate lineage.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
12.
Association between bacteria Photorhabdus and their nematode hosts Heterorhabditis represents one of the emerging models in symbiosis studies. In this study, we isolated the bacterial symbionts of the nematode
Heterorhabditis georgiana. Using gyrB sequences for phylogenetic analysis, these strains were shown to be part of the species of Photorhbdus luminescens but with clear separation from currently recognized subspecies. Physiological properties and DNA–DNA hybridization profiles
also supported the phylogenetic relationship of these strains. Therefore, a new subspecies, Photorhabdus luminescens subsp. kleinii subsp. nov., is proposed with the type strain KMD37T (=DSM 23513 =ATCC =NRRL B-59419). 相似文献
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Studying rhizobia in the root nodules of Sphaerophysa salsula (Pall.) DC in the northwest of China, we obtained five strains classified as genus Rhizobium on the basis of their 16S rRNA gene sequences. The sequence similarity of strain CCNWQTX14T with the most related species was 99.0%. Further phylogenetic analysis of housekeeping genes (recA and atpD) suggested the five strains comprised a novel lineage within Rhizobium. The nifH and nodD gene sequences of CCNWQTX14T were phylogenetically closely related with those of Sinorhizobium kummerowiae and R. sphaerophysae, respectively. The five strains isolated from different places were also distinct from related Rhizobium species using ERIC fingerprint profiles. The DNA–DNA hybridization value was 41.8% between CCNWQTX14T and Rhizobium sphaerophysae CCNWGS0238T. Our novel strains were only able to form effective nodules on its original host Sphaerophysa salsula. Our data showed that the five Rhizobium strains formed a unique genomic species, for which a novel species Rhizobium
helanshanense sp. nov. is proposed. The type strain is CCNWQTX14T (=ACCC 16237T =HAMBI 3083T). 相似文献
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Phylogenetic relations within the genus Gordonia were analyzed using partial gyrB and secA1 gene sequences of 23 type species in comparison with those of 16S rRNA gene. The gyrB and secA1 phylogenies showed agreement with that constructed using 16S rRNA gene sequences. The degrees of divergence of the gyrB and secA1 genes were approximately 3.4 and 1.7 times greater, respectively, than that of 16S rRNA gene. The gyrB gene showed more discriminatory power than either the secA1 or 16S rRNA gene, facilitating clear differentiation of any two Gordonia species using gyrB gene analysis. Our data indicate that gyrB and secA1 gene sequences are useful as markers for phylogenetic study and identification at the species level of the genus Gordonia. 相似文献
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Acosta MJ Marchal JA Martínez S Puerma E Bullejos M la de Guardia RD Sánchez A 《Genetica》2007,130(1):43-51
The satellite DNA Msat-160 has been previously characterized in several species of the genus Microtus. Here we present the characterization of Msat-160 from Chionomys nivalis, a species with a very primitive karyotype. As in other Microtus species analyzed, C. nivalis Msat-160 is AT rich, has a monomer length of 160 bp, is undermethylated and is mainly located in all the pericentromeric
heterochromatin of all autosomes and the X chromosome, but is completely absent from the Y chromosome. Hence, our results
support the hypothesis that Msat-160 was initially distributed in the pericentromeric heterochromatin of all autosomes and
the X chromosome. The taxonomic status of the genus Chionomys in relation to the genus Microtus is a very interesting issue, so we constructed phylogenetic dendrograms using Msat-160 sequences from several Microtus species. Although the results were not informative about this issue, the presence of Msat-160 in C. nivalis and Microtus species suggested that both genera are closely related and that this satellite DNA was present in the common ancestor. Studies
of Msat-160 in different arvicoline species could help to determine the origin of this satellite and, perhaps, to establish
the phylogenetic relationships of some arvicoline groups. 相似文献
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Nouioui I Ghodhbane-Gtari F Beauchemin NJ Tisa LS Gtari M 《Antonie van Leeuwenhoek》2011,100(4):579-587
To construct an evolutionary hypothesis for the genus Frankia, gyrB (encoding gyrase B), nifH (encoding nitrogenase reductase) and glnII (encoding glutamine synthetase II) gene sequences were considered for 38 strains. The overall clustering pattern among
Frankia strains based on the three analyzed sequences varied among themselves and with the previously established 16S rRNA gene phylogeny
and they did not reliably reflect clear evolution of the four discerned Frankia clusters (1, 2, 3 and 4). Based on concatenated gyrB, nifH and glnII, robust phylogenetic trees were observed with the three treeing methods (Maximum Likelihood, Parsimony and Neighbor-Joining)
and supported by strong bootstrap and posterior probability values (>75%) for overall branching. Cluster 4 (non-infective
and/or non-nitrogen-fixing Frankia) was positioned at a deeper branch followed by cluster 3 (Rhamnaceae and Elaeagnaceae infective Frankia), while cluster 2 represents uncultured Frankia microsymbionts of the Coriariaceae, Datiscaceae, Rosaceae and of Ceanothus sp. (Rhamnaceae); Cluster 1 (Betulaceae, Myricaceae and Casuarinaceae infective Frankia) appears to have diverged more recently. The present study demonstrates the utility of phylogenetic analyses based upon concatenated
gyrB, nifH and glnII sequences to help resolve previously unresolved or poorly resolved nodes and will aid in describing species among the genus
Frankia. 相似文献
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Partial recN gene sequences (>1 kb) were obtained from 35 type strains of the genus Amycolatopsis. Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships
within the genus. The use of recN sequence analysis as an alternative to DNA–DNA hybridization (DDH) for distinguishing closely related species was also assessed.
The recN based phylogeny mostly confirmed the conventional 16S rRNA and gyrB gene-based phylogenies and thus provides further support for these phylogenetic groupings. As is the case for the gyrB gene, pairwise recN sequence similarities cannot be used to predict the DNA relatedness between type strains but the recN genetic distance can be used as a means to assess quickly whether an isolate is likely to represent a new species in the
genus Amycolatopsis. A recN genetic distance of >0.04 between two Amycolatopsis strains is proposed to provide a good indication that they belong to different species (and that polyphasic taxonomic characterization
of the unknown strain is worth undertaking). 相似文献
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Sarawood Sungkaew Atchara Teerawatananon John A. N. Parnell Chris M. A. Stapleton Trevor R. Hodkinson 《Kew Bulletin》2008,63(4):669-673
Summary A new monotypic bamboo genus Phuphanochloa (Poaceae: Bambusoideae) from north-eastern Thailand is described, together with a new species, P. speciosa. 相似文献