Noncoding sequences from the slowly evolving chloroplast inverted repeat in addition to rbcL data do not support gnetalean affinities of angiosperms (original) (raw)

Molecular phylogenies in angiosperm evolution

Molecular biology and evolution, 1993

We have cloned and sequenced cDNAs for the glyceraldehyde-3-phosphate dehydrogenase of glycolysis, gapC, from a bryophyte, a gymnosperm, and three angiosperms. Phylogenetic analyses are presented for these data in the context of other gapC sequences and in parallel with published nucleotide sequences for the chloroplast encoded gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL). Relative-rate tests were performed for these genes in order to assess variation in substitution rate for coding regions, along individual plant lineages studied. The results of both gene analyses suggest that the deepest dichotomy within the angiosperms separates not magnoliids from remaining angiosperms, but monocotyledons from dicotyledons, in sharp contrast to prediction from the Euanthial theory for angiosperm evolution. Furthermore, these chloroplast and nuclear sequence data taken together suggest that the separation of monocotyledonous and dicotyledonous lineages took...

Loss of Different Inverted Repeat Copies from the Chloroplast Genomes of Pinaceae and Cupressophytes and Influence of Heterotachy on the Evaluation of Gymnosperm Phylogeny

Genome Biology and Evolution, 2011

The relationships among the extant five gymnosperm groups-gnetophytes, Pinaceae, non-Pinaceae conifers (cupressophytes), Ginkgo, and cycads-remain equivocal. To clarify this issue, we sequenced the chloroplast genomes (cpDNAs) from two cupressophytes, Cephalotaxus wilsoniana and Taiwania cryptomerioides, and 53 common chloroplast protein-coding genes from another three cupressophytes, Agathis dammara, Nageia nagi, and Sciadopitys verticillata, and a non-Cycadaceae cycad, Bowenia serrulata. Comparative analyses of 11 conifer cpDNAs revealed that Pinaceae and cupressophytes each lost a different copy of inverted repeats (IRs), which contrasts with the view that the same IR has been lost in all conifers. Based on our structural finding, the character of an IR loss no longer conflicts with the ''gnepines'' hypothesis (gnetophytes sister to Pinaceae). Chloroplast phylogenomic analyses of amino acid sequences recovered incongruent topologies using different tree-building methods; however, we demonstrated that high heterotachous genes (genes that have highly different rates in different lineages) contributed to the long-branch attraction (LBA) artifact, resulting in incongruence of phylogenomic estimates. Additionally, amino acid compositions appear more heterogeneous in high than low heterotachous genes among the five gymnosperm groups. Removal of high heterotachous genes alleviated the LBA artifact and yielded congruent and robust tree topologies in which gnetophytes and Pinaceae formed a sister clade to cupressophytes (the gnepines hypothesis) and Ginkgo clustered with cycads. Adding more cupressophyte taxa could not improve the accuracy of chloroplast phylogenomics for the five gymnosperm groups. In contrast, removal of high heterotachous genes from data sets is simple and can increase confidence in evaluating the phylogeny of gymnosperms.

Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae

Molecular Phylogenetics and Evolution, 2005

Noncoding DNA sequences from numerous regions of the chloroplast genome have provided a signiWcant source of characters for phylogenetic studies in seed plants. In lycophytes and monilophytes (leptosporangiate ferns, eusporangiate ferns, Psilotaceae, and Equisetaceae), on the other hand, relatively few noncoding chloroplast DNA regions have been explored. We screened 30 lycophyte and monilophyte species to determine the potential utility of PCR ampliWcation primers for 18 noncoding chloroplast DNA regions that have previously been used in seed plant studies. Of these primer sets eight appear to be nearly universally capable of amplifying lycophyte and monilophyte DNAs, and an additional six are useful in at least some groups. To further explore the application of noncoding chloroplast DNA, we analyzed the relative phylogenetic utility of Wve cpDNA regions for resolving relationships in Botrychium s.l. (Ophioglossaceae). Previous studies have evaluated both the gene rbcL and the trnL UAA -trnF GAA intergenic spacer in this group. To these published data we added sequences of the trnS GCU -trnG UUC intergenic spacer + the trnG UUC intron region, the trnS GGA -rpS4 intergenic spacer + rpS4 gene, and the rpL16 intron. Both the trnS GCU -trnG UUC and rpL16 regions are highly variable in angiosperms and the trnS GGA -rpS4 region has been widely used in monilophyte phylogenetic studies. Phylogenetic resolution was equivalent across regions, but the strength of support for the phylogenies varied among regions. Of the Wve sampled regions the trnS GCU -trnG UUC spacer + trnG UUC intron region provided the strongest support for the inferred phylogeny. 

Towards understanding basal angiosperm diversification: recent insights using rapidly evolving genomic regions

The prevailing view in molecular phylogenetics is that relationships at deeper levels, for example among major angiosperm lineages, should be inferred using rather conserved genes. Rapidly evolving DNA has been deemed unsuitable because of putative high levels of homoplasy caused by multiple substitutions and frequent microstructural mutations resulting in their non-alignability. Recent analyses of rapidly evolving spacers and introns in the chloroplast genome from basal angiosperms show that extreme sequence variability is confined to certain mutational hotspots. These hotspots correlate with structural elements (stem loops), where selective pressure is low. Phylogenetic trees of basal angiosperms inferred from rapidly evolving genomic regions are well resolved and highly supported statistically. Reasons are not only greater amounts of informative sites in rapidly evolving DNA, but also differing levels of homoplasy that can result in better phylogenetic signal per informative site. Based on these findings, perspectives for further utilizing non-coding DNA in angiosperm phylogenetic studies are explored. Zusammenfassung Nach vorherrschenden Konzepten werden zur Phylogenie-Rekonstruktion von Verwandtschaftsverhältnissen auf tieferer Ebene, z. B. zwischen den Hauptgruppen der Angiospermen, vorwiegend konservierte Gene eingesetzt. Schnell evolvierende DNA wurde als ungeeignet angesehen, weil von starken Homoplasie-Effekten durch Saturierung (multiple Nukleotid-Substitutionen) sowie fehlender Alignbarkeit durch häufige mikrostrukturelle Mutationen ausgegangen wurde. Neuere Analysen schnell evolvierender Spacer und Introns des Chloroplastengenoms bei basalen Angiospermen zeigen aber, daß extreme Sequenzvariabilität auf bestimmte Mutations-Hotspots konzentriert ist. Diese korrelieren mit Strukturelementen (z. B. Stem-Loops), die geringen selektiven Zwängen unterliegen. Stammbaumhypothesen basaler Angiospermen, basierend auf schnell evolvierenden Genomabschnitten, sind gut aufgelöst und hoch statistisch gestützt. Gründe dafür liegen nicht nur in der größeren Zahl informativer Positionen in schnell evolvierender DNA, sondern auch in anderen Homoplasieverhältnissen, die ein stärkeres phylogenetisches Signal pro informativer Position bedeuten können. Anhand der vorliegenden Daten werden Perspektiven für die weitergehende Anwendung von nicht-codierender DNA in der Evolutionsforschung bei Angiospermen erörtert.

Relationships in the Caryophyllales as Suggested by Phylogenetic Analyses of Partial Chloroplast DNA ORF2280 Homolog Sequences

American Journal of Botany, 1997

Phylogenetic relationships within the angiosperm order Caryophyllales were investigated by comparative sequencing of two portions of the highly conserved inverted repeat (totaling some 1100 base pairs) coinciding with the region occupied by ORF2280 in Nicotiana, the largest gene in the plastid genomes of most land plants. Data were obtained for 33 species in 11 families within the order and for one species each of Plumbaginaceae, Polygonaceae, and Nepenthaceae. These data, when analyzed along with previously published ORF (open reading frame) sequences from Nicotiana, Spinacia, Epifagus, and Pelargonium using parsimony, neighbor-joining, and maximum likelihood methods, reveal that: (1) Amaranthus, Celosia, and Froelichia (all Amaranthaceae) do not comprise a monophyletic group; (2) Amaranthus may be nested within a paraphyletic Chenopodiaceae; (3) Sarcobatus (Chenopodiaceae) is allied with Nyctaginaceae ϩ Phytolaccaceae (the latter family excluding Stegnosperma but including Petiveria); and (4) Caryophyllaceae (with Corrigiola basal within the clade) are sister group to Chenopodiaceae ϩ Amaranthaceae. Basal relations within the order remain obscure. Sequence divergence values in pairwise comparisons across all Caryophyllales taxa ranged from 0.1 to 5% of nucleotides. However, despite these low values, 23 insertion and deletion events were apparent, of which five were informative phylogenetically and bolstered several of the relationships listed above. A polymerase chain reaction (PCR) survey for ORF homolog length variants in representatives from 70 additional angiosperm families revealed major deletions, of ഠ 100 to 1400 base pairs, in 19 of these families. Although the ORF is located within the mutationally retarded inverted repeat region of most angiosperm chloroplast DNAs, this gene appears particularly prone to length mutation.

Angiosperm Phylogeny Inferred from 18S Ribosomal DNA Sequences

Annals of the Missouri Botanical Garden, 1997

Parsimony analyses were conducted for 223 species representing all major groups of angiosperms using entire 18S ribosomal DNA (rDNA) sequences. Although no search swapped to completion, the topologies recovered are highly concordant with those retrieved via broad analyses based on the chloroplast gene rbcL. The general congruence of 18S rDNA and rbcL topologies further clarifies the broad picture of angiosperm phylogeny. In all analyses, the first-branching angiosperms are Amborellaceae, Austrobaileyaceae, Illiciaceae, and Schisandraceae, all woody magnoliids. These taxa are always followed by the paleoherb family Nymphaeaceae. This same general order of early-branching taxa is preserved with several suites of outgroups. In most searches, the remaining early-branching taxa represent Piperales and other orders of subclass Magnoliidae (sensu Cronquist). With the exception of Acorus, the monocots are supported as monophyletic and typically have as their sister Ceratophyllum. In most analyses, taxa with uniaperturate pollen form a grade at the base of the angiosperms; a large eudicot lade is composed primarily of taxa having triaperturate pollen. Two large subclades are present within the eudicots, one consisting largely of Rosidae and a second corresponding closely to Asteridae sensu lato. Subclasses Dilleniidae and Hamamelidae are highly polyphyletic. These data sets of 18S rDNA sequences also permit an analysis of the patterns of molecular evolution of this gene. Problems deriving from both the prevalence of indels and uncertain alignment of 18S rDNA sequences have been overstated in previous studies. With the exception of a few well-defined regions, insertions and deletions are relatively uncommon in 18S rDNA; sequences are therefore easily aligned by eye across the angiosperms. Indeed, several indels in highly conserved regions appear to be phylogenetically informative. Initial analyses suggest that both stem and loop bases are important sources of phylogenetic information, although stem positions are prone to compensatory substitutions. Of the stem changes analyzed, only 27% destroy a base-pairing couplet; 73% maintain or restore base pairing.

Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant …

Molecular biology and evolution, 2007

Phylogenetic relationships among the 5 groups of extant seed plants are presently unsettled. To reexamine this longstanding debate, we determine the complete chloroplast genome (cpDNA) of Cycas taitungensis and 56 protein-coding genes encoded in the cpDNA of Gnetum parvifolium. The cpDNA of Cycas is a circular molecule of 163,403 bp with 2 typical large inverted repeats (IRs) of 25,074 bp each. We inferred phylogenetic relationships among major seed plant lineages using concatenated 56 protein-coding genes in 37 land plants. Phylogenies, generated by the use of 3 independent methods, provide concordant and robust support for the monophylies of extant seed plants, gymnosperms, and angiosperms. Within the modern gymnosperms are 2 highly supported sister clades: Cycas-Ginkgo and Gnetum-Pinus. This result agrees with both the ''gnetifer'' and ''gnepines'' hypotheses. The sister relationships in Cycas-Ginkgo and Gnetum-Pinus clades are further reinforced by cpDNA structural evidence. Branch lengths of Cycas-Ginkgo and Gnetum were consistently the shortest and the longest, respectively, in all separate analyses. However, the Gnetum relative rate test revealed this tendency only for the 3rd codon positions and the transversional sites of the first 2 codon positions. A WtufA located between psbE and petL genes is here first detected in Anthoceros (a hornwort), cycads, and Ginkgo. We demonstrate that the WtufA is a footprint descended from the chloroplast tufA of green algae. The duplication of ycf2 genes and their shift into IRs should have taken place at least in the common ancestor of seed plants more than 300 MYA, and the tRNAPro-GGG gene was lost from the angiosperm lineage at least 150 MYA. Additionally, from cpDNA structural comparison, we propose an alternative model for the loss of large IR regions in black pine. More cpDNA data from non-Pinaceae conifers are necessary to justify whether the gnetifer or gnepines hypothesis is valid and to generate solid structural evidence for the monophyly of extant gymnosperms.

Molecular evolutionary history of ancient aquatic angiosperms

Proceedings of the National Academy of Sciences, 1991

Aquatic plants are notoriously difficult to study systematically due to convergent evolution and reductionary processes that result in confusing arrays of morphological features. Plant systematists have frequently focused their attention on the "water lilies," putative descendants of the most archaic angiosperms. Classification of these 10 plant genera varies from recognition of one to three orders containing three to six families. We have used DNA sequence analysis as a means of overcoming many problems inherent in morphologically based studies of the group. Phylogenetic analyses of sequence data obtained from a 1.2-kilobase portion of the chloroplast gene rbcL provide compelling evidence for the recognition of three distinct lineages of "water lily" plants. Molecular phylogenies including woody Magnoliidae sequences and sequences of these aquatic plants depict Ceratophyllum as an early diverging genus. Our results support hypotheses that most taxonomic concepts...