Abstract:
:Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all. Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora) have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Zhang Z,Green BR,Cavalier-Smith Tdoi
10.1007/s002390010064keywords:
subject
Has Abstractpub_date
2000-07-01 00:00:00pages
26-40issue
1eissn
0022-2844issn
1432-1432pii
10.1007/s002390010064journal_volume
51pub_type
杂志文章abstract::Photosynthetic eukaryotes can, according to features of their chloroplasts, be divided into two major groups: the red and the green lineage of plastid evolution. To extend the knowledge about the evolution of the red lineage we have sequenced and analyzed the chloroplast genome (cp-genome) of Cyanidium caldarium RK1, ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010101
更新日期:2000-10-01 00:00:00
abstract::Drosophilidae is a large, widely distributed family of Diptera including 61 genera, of which Drosophila is the most representative. Drosophila feeding is part of the saprophytic trophic chain, because of its dependence upon decomposing organic matter. Many species have adapted to fermenting fruit feeding or to artific...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006378
更新日期:1998-08-01 00:00:00
abstract::Ca(2+)/cation antiporter (CaCA) proteins are integral membrane proteins that transport Ca(2+) or other cations using the H(+) or Na(+) gradient generated by primary transporters. The CAX (for CAtion eXchanger) family is one of the five families that make up the CaCA superfamily. CAX genes have been found in bacteria, ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-006-0048-4
更新日期:2006-12-01 00:00:00
abstract::Cytochrome proteins perform a broad spectrum of biological functions ranging from oxidative metabolism to electron transport and are thus essential to all organisms. The b-type cytochrome proteins bind heme noncovalently, are expressed in many different forms and are localized to various cellular compartments. We repo...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00160314
更新日期:1995-10-01 00:00:00
abstract::Analysis of occurrence of simple amino acid repeats in large ensemble of prokaryotic and eukaryotic sequences reveals that nearly all amino acids found in the repeats belong to those which have in their codon repertoires aggressively expanding triplets, all of three known pathologically expanding classes GCU (GCU, CUG...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-010-9425-0
更新日期:2011-02-01 00:00:00
abstract::The slow-evolving mitochondrial DNAs of plants have potentially conserved information on the phylogenetic branching of the earliest land plants. We present the nad2 gene structures in hornworts and liverworts and in the presumptive earliest-branching vascular land plant clade, the Lycopodiopsida. Taken together with t...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-002-2324-2
更新日期:2002-09-01 00:00:00
abstract::Annotated, complete DNA sequences are available for 213 mitochondrial genomes from 132 species. These provide an extensive sample of evolutionary adjustment of codon usage and meaning spanning the history of this organelle. Because most known coding changes are mitochondrial, such data bear on the general mechanism of...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010220
更新日期:2001-10-01 00:00:00
abstract::A 6.0-kb DNA fragment from Gorilla gorilla including the 5' part of the beta-globin gene and about 4.5 kb of its upstream flanking region was cloned and sequenced. The sequence was compared to the human, chimpanzee, and macaque delta-beta intergenic region. This analysis reveals four tandemly repeated sequences (RS), ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00163849
更新日期:1992-01-01 00:00:00
abstract::Nucleotide polymorphisms in two North American balsam poplars (Populus trichocarpa Torr. & Gray and P. balsamifera L.; section Tacamahaca), and one Eurasian aspen (P. tremula L.; section Populus) were compared using nine loci involved in defense, stress response, photoperiodism, freezing tolerance, and housekeeping. N...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-012-9504-5
更新日期:2012-06-01 00:00:00
abstract::The nucleotide sequences of 5S rRNAs from three protozoa, Bresslaua vorax, Euplotes woodruffi and Chlamydomonas sp. have been determined and aligned together with the sequences of 12 protozoa species including unicellular green algae already reported by the authors and others. Using this alignment, a phylogenic tree o...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02102316
更新日期:1983-01-01 00:00:00
abstract::The genome of Glycine max (L.) Merr. cv. "Dare" contains a chlorophyll a/b binding (Cab) protein gene family consisting of 10 genes. The primary structures of two linked Cab genes (Cab 4 and Cab 5) were determined. A comparison of the nucleic acid and predicted amino acid sequences of Cab 4 and Cab 5 revealed a high d...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02100210
更新日期:1989-09-01 00:00:00
abstract::We have identified and completely sequenced a novel plasmid isolated from the aphid Rhopalosiphum padi. Evidence which suggests that the plasmid occurs localized within the bacterial endosymbionts is presented. The plasmid contains the four genes that constitute the entire leucine operon. This fact makes it really uni...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00174042
更新日期:1995-07-01 00:00:00
abstract::Seven new Italian and two new British HTLV-II isolates were obtained from injecting drug users and the entire long terminal repeat (LTR) region was sequenced. Restriction analysis showed that all the Italian isolates are of the IIb subtype, whereas the British isolates are of the IIa subtype. To understand whether the...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006340
更新日期:1998-05-01 00:00:00
abstract::Orphan genes, lacking detectable homologs in outgroup species, typically represent 10-30% of eukaryotic genomes. Efforts to find the source of these young genes indicate that de novo emergence from non-coding DNA may in part explain their prevalence. Here, we investigate the roots of orphan gene emergence in the Droso...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-020-09939-z
更新日期:2020-05-01 00:00:00
abstract::Heterokonts are evolutionarily important as the most nutritionally diverse eukaryote supergroup and the most species-rich branch of the eukaryotic kingdom Chromista. Ancestrally photosynthetic/phagotrophic algae (mixotrophs), they include several ecologically important purely heterotrophic lineages, all grossly unders...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-0353-8
更新日期:2006-04-01 00:00:00
abstract::The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall e...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00173421
更新日期:1994-11-01 00:00:00
abstract::Characterization of sequences homologous to the Drosophila melanogaster gypsy transposable element was carried out in Drosophila subobscura (gypsyDS). They were found to be widely distributed among natural populations of this species. From Southern blot and in situ analyses, these sequences appear to be mobile in this...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00166248
更新日期:1993-02-01 00:00:00
abstract::The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9156-7
更新日期:2008-12-01 00:00:00
abstract::Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic information from mitochondria to the nucleus offer a unique opportunity to compare different regimes of molecular evolution. Analyzing a 1621-nt-long numt of the rRNA specifying mitochondrial DNA residing on human chromosom...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-0293-3
更新日期:2005-07-01 00:00:00
abstract::Sequence comparisons of 14 distinct MHC class I cDNA clones isolated from species representing the three major taxonomic lineages of Felidae (domestic cat lineage, ocelot lineage, and pantherine lineage) revealed that feline MHC class I alleles have highly mosaic structures with short polymorphic sequence motifs that ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00178246
更新日期:1994-07-01 00:00:00
abstract::The evolution rates of mtDNA in early metazoans hold important implications for DNA barcoding. Here, we present a comprehensive analysis of intra- and interspecific COI variabilities in Porifera and Cnidaria (separately as Anthozoa, Hydrozoa, and Scyphozoa) using a data set of 619 sequences from 224 species. We found ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9069-5
更新日期:2008-02-01 00:00:00
abstract::Sequence divergence among orthologous proteins was characterized with 34 amino acid replacement matrices, sequence context analysis, and a phylogenetic tree. The model was trained on very large datasets of aligned protein sequences drawn from 15 organisms including protists, plants, Dictyostelium, fungi, and animals. ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-005-0060-0
更新日期:2005-11-01 00:00:00
abstract::DNA methylation is one of the many hypotheses proposed to explain the observed deficiency in CpG dinucleotides in a variety of genomes covering a wide taxonomic distribution. Recent studies challenged the methylation hypothesis on empirical grounds. First, it cannot explain why the Mycoplasma genitalium genome exhibit...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-003-0003-6
更新日期:2003-01-01 00:00:00
abstract::The sequence of the mitochondrial DNA (mtDNA) molecule of the European hedgehog (Erinaceus europaeus) was determined. The length of the sequence presented is 17,442 nucleotides (nt). The molecule is thus the largest eutherian mtDNA molecule so far reported. The organization of the molecule conforms with that of other ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00173175
更新日期:1995-12-01 00:00:00
abstract::Nuclear DNA contents were estimated by microdensitometry in five species of Akodon rodents: Arodon molinae, A. dolores, A. mollis, A. azarae, Bolomys obscurus) and in three chromosomal varieties of A. molinae (2n = 42; 2n = 43, 2n = 22). The data obtained showed that the species with the highest DNA content was B. obs...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02101640
更新日期:1983-01-01 00:00:00
abstract::The core histone genes of Saccharomyces cerevisiae are arranged as duplicate nonallelic sets of specifically paired genes. The identity of structural organization between the duplicated gene pairs would have its simplest evolutionary origin in the duplication of a complete locus in a single event. In such a case, the ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02111238
更新日期:1987-01-01 00:00:00
abstract::Several studies in Drosophila have shown a paucity of male-biased genes (i.e., genes that express higher in males than in females) on the X chromosome. Dosage compensation (DC) is a regulatory mechanism of gene expression triggered in males that hypertranscribes the X-linked genes to the level of transcription in fema...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-016-9735-y
更新日期:2016-05-01 00:00:00
abstract::The major histocompatibility complex (MHC) consists of polymorphic frozen blocks (PFBs) that are linked to form megabase haplotypes. These blocks consist of polymorphic sequences and define regions where recombination appears to be inhibited. We have been able to show, using a highly polymorphic sequence centromeric o...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006194
更新日期:1997-07-01 00:00:00
abstract::Synonymous codon usage in yeast appears to be influenced by natural selection on gene expression, as well as regional variation in compositional bias. Because of the large number of potential targets of selection (i.e., most of the codons in the genome) and presumed small selection coefficients, codon usage is an exce...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-003-2459-9
更新日期:2003-07-01 00:00:00
abstract::We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus--Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color visio...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-009-9283-9
更新日期:2009-10-01 00:00:00