Molecular phylogeny of the family of apes and humans

Genome ◽  
1989 ◽  
Vol 31 (1) ◽  
pp. 316-335 ◽  
Author(s):  
Morris Goodman ◽  
Ben F. Koop ◽  
John Czelusniak ◽  
David H. A. Fitch ◽  
Danilo A. Tagle ◽  
...  
Keyword(s):  
Globin Gene ◽  
Gene Clusters ◽  
Nucleotide Sequences ◽  
Primate Phylogeny ◽  
Dna Evidence ◽  
Overwhelming Evidence ◽  
The Family ◽  
Rate Of Molecular Evolution ◽  
Morphological Picture ◽  
Molecular Picture

The morphological picture of primate phylogeny has not unambiguously identified the nearest outgroup of Anthropoidea and has not resolved the branching pattern within Hominoidea. The molecular picture provides more resolution and clarifies the systematics of Hominoidea. Protein and DNA evidence divides Hominoidea into Hylobatidae (gibbons) and Hominidae, family Hominidae into Ponginae (orangutan) and Homininae, and subfamily Homininae into two tribes, one for Gorilla, and the other for Pan (chimpanzee) and Homo. Parsimony and maximum likelihood analyses, carried out on orthologous noncoding nucleotide sequences from primate β-globin gene clusters, provide significant evidence for the human-chimpanzee tribe and overwhelming evidence for the human-chimpanzee-gorilla clade. These analyses also indicate that the rate of molecular evolution became slower in hominoids than in other primates and mammals.Key words: primate phylogeny, gene clusters, nucleotide sequences.

scholarly journals A systematic revision of Capparaceae and Cleomaceae in Egypt: an evaluation of the generic delimitations of Capparis and Cleome using ecological and genetic diversity

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Mohamed Abd. S. El zayat ◽  
Mahmoud El Sayd Ali ◽  
Mohamed Hamdy Amar
Keyword(s):  
Genetic Diversity ◽  
Morphological Characteristics ◽  
Systematic Position ◽  
Diversity Analysis ◽  
Polymorphic Markers ◽  
Ecological Distribution ◽  
Specific Group ◽  
Systematic Revision ◽  
Dna Evidence ◽  
The Family

Abstract Background The Capparaceae family is commonly recognized as a caper, while Cleomaceae represents one of small flowering family within the order Brassicales. Earlier, Cleomaceae was included in the family Capparaceae; then, it was moved to a distinct family after DNA evidence. Variation in habits and a bewildering array of floral and fruit forms contributed to making Capparaceae a “trash-basket” family in which many unrelated plants were placed. Indeed, family Capparaceae and Cleomaceae are in clear need of more detailed systematic revision. Results Here, in the present study, the morphological characteristics and the ecological distribution as well as the genetic diversity analysis among the twelve species of both Capparaceae and Cleomaceae have been determined. The genetic analysis has been checked using 15 ISSR, 30 SRAP, and 18 ISTR to assess the systematic knots between the two families. In order to detect the molecular phylogeny, a comparative analysis of the three markers was performed based on the exposure of discriminating capacity, efficiency, and phylogenetic heatmap. Our results indicated that there is a morphological and ecological variation between the two families. Moreover, the molecular analysis confirmed that ISTR followed by SRAP markers has superior discriminating capacity for describing the genetic diversity and is able to simultaneously distinguish many polymorphic markers per reaction. Indeed, both the PCA and HCA data have drawn a successful annotation relationship in Capparaceae and Cleome species to evaluate whether the specific group sort individual or overlap groups. Conclusion The outcomes of the morphological and ecological characterization along with the genetic diversity indicated an insight solution thorny interspecies in Cleome and Gynandropsis genera as a distinct family (Cleomaceae) and the other genera (Capparis, Cadaba, Boscia, and Maerua) as Capparaceae. Finally, we recommended further studies to elucidate the systematic position of Dipterygium glaucum.

Nucleotide sequences from a rabbit alpha globin gene inserted in a chimeric plasmid

Science ◽  
1977 ◽  
Vol 196 (4286) ◽  
pp. 192-195 ◽  
Author(s):  
A. Liu ◽  
G. Paddock ◽  
H. Heindell ◽  
W Salser
Keyword(s):  
Globin Gene ◽  
Nucleotide Sequences ◽  
Alpha Globin

scholarly journals Karyotype Characterization of Nine Periwinkle Species (Gastropoda, Littorinidae)

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 517 ◽  
Author(s):  
Daniel García-Souto ◽  
Sandra Alonso-Rubido ◽  
Diana Costa ◽  
José Eirín-López ◽  
Emilio Rolán-Álvarez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Chromosome Numbers ◽  
Gene Clusters ◽  
Chromosomal Mapping ◽  
Closely Related Species ◽  
Submetacentric Chromosome ◽  
The Family ◽  
Littorina Arcana

Periwinkles of the family Littorinidae (Children, 1834) are common members of seashore littoral communities worldwide. Although the family is composed of more than 200 species belonging to 18 genera, chromosome numbers have been described in only eleven of them. A molecular cytogenetic analysis of nine periwinkle species, the rough periwinkles Littorina arcana, L. saxatilis, and L. compressa, the flat periwinkles L. obtusata and L. fabalis, the common periwinkle L. littorea, the mangrove periwinkle Littoraria angulifera, the beaded periwinkle Cenchritis muricatus, and the small periwinkle Melarhaphe neritoides was performed. All species showed diploid chromosome numbers of 2n = 34, and karyotypes were mostly composed of metacentric and submetacentric chromosome pairs. None of the periwinkle species showed chromosomal differences between male and female specimens. The chromosomal mapping of major and minor rDNA and H3 histone gene clusters by fluorescent in situ hybridization demonstrated that the patterns of distribution of these DNA sequences were conserved among closely related species and differed among less related ones. All signals occupied separated loci on different chromosome pairs without any evidence of co-localization in any of the species.

scholarly journals Uncovering the unexplored diversity of thioamidated ribosomal peptides in Actinobacteria using the RiPPER genome mining tool

2018 ◽  
Author(s):  
Javier Santos-Aberturas ◽  
Govind Chandra ◽  
Luca Frattaruolo ◽  
Rodney Lacret ◽  
Thu H. Pham ◽  
...  
Keyword(s):  
Genome Mining ◽  
Gene Clusters ◽  
Chemical Diversity ◽  
Bioactive Molecules ◽  
Post Translational Modification ◽  
Biosynthetic Gene Clusters ◽  
New Family ◽  
The Family ◽  
Modified Peptides ◽  
Mining Tool

ABSTRACTThe rational discovery of new specialized metabolites by genome mining represents a very promising strategy in the quest for new bioactive molecules. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a major class of natural product that derive from genetically encoded precursor peptides. However, RiPP gene clusters are particularly refractory to reliable bioinformatic predictions due to the absence of a common biosynthetic feature across all pathways. Here, we describe RiPPER, a new tool for the family-independent identification of RiPP precursor peptides and apply this methodology to search for novel thioamidated RiPPs in Actinobacteria. Until now, thioamidation was believed to be a rare post-translational modification, which is catalyzed by a pair of proteins (YcaO and TfuA) in Archaea. In Actinobacteria, the thioviridamide-like molecules are a family of cytotoxic RiPPs that feature multiple thioamides, and it has been proposed that a YcaO-TfuA pair of proteins also catalyzes their formation. Potential biosynthetic gene clusters encoding YcaO and TfuA protein pairs are common in Actinobacteria but the chemical diversity generated by these pathways is almost completely unexplored. A RiPPER analysis reveals a highly diverse landscape of precursor peptides encoded in previously undescribed gene clusters that are predicted to make thioamidated RiPPs. To illustrate this strategy, we describe the first rational discovery of a new family of thioamidated natural products, the thiovarsolins from Streptomyces varsoviensis.

scholarly journals The Draft Genome Sequence of The Endophytic Streptomyces Strain VITGV156

2021 ◽  
Author(s):  
Veilumuthu P ◽  
Nagarajan T ◽  
Sasikumar S ◽  
Siva R ◽  
J Godwin Christopher
Keyword(s):  
Secondary Metabolites ◽  
Draft Genome ◽  
Gc Content ◽  
Gene Clusters ◽  
Dominant Group ◽  
Protein Coding ◽  
Peptide Synthetase ◽  
The Family ◽  
Modified Peptides ◽  
Endophytic Streptomyces

Abstract Streptomyces species is one among the dominant group of bacteria in the family Actinobacteria with a rich repertoire of secondary metabolites. Secondary metabolites with antimicrobial activity and plant growth promotor have been isolated from various Streptomyces sp. Here in this investigation, we present the draft genome of a new species, Streptomyces sp. VITGV156 isolated from healthy tomato plant (Lycopersicon esculentum) which has some rare antimicrobial secondary metabolites, like coelichelin, fluostatins, vicenistatin, nystatin, sipanmycin, and informatipeptin. The genome is 8.18 Mb in size with 6,259 protein coding genes. The average GC content of the genome is 72.61 %. Preliminary analysis with antiSMASH 6.0 revealed the presence of 29 biosynthetic gene clusters for the synthesis of potential secondary metabolites. These includes 4 NRPS (non – ribosomal peptide synthetase), 7 PKS (Polyketide Synthases), 2 RiPP (Ribosomally synthesized and post-translationally modified peptides) clusters. When we look into genes associated with secondary metabolites, 406 genes are present which includes 184 genes for cofactor and vitamins, 72 genes for terpenoids and polyketides, 70 genes for xenobiotics and 80 genes for other metabolites are present. Comparative genome analysis of VITGV156 with its closest neighbor Streptomyces luteus strain TRM45540 revealed ANI 91.22% and dDDH value 44.00%.

Charles Spence Bate: what’s in a name?

Zootaxa ◽  
2018 ◽  
Vol 4497 (3) ◽  
pp. 429 ◽  
Author(s):  
PAUL F. CLARK
Keyword(s):  
Special Reference ◽  
Manual Search ◽  
Overwhelming Evidence ◽  
The Family

The citation of Charles Spence Bate has become a source of uncertainly in the literature. Indeed, for some taxa his authority is given as “Spence Bate”, whilst others “Bate” e.g. Artemesia longinaris Spence Bate, 1888 compared with Ibacus brevipes Bate, 1888. In order to resolve this inconsistency, a lengthy manual search of selected contemporary journals for the period from ca. 1854 to 1889 was undertaken with special reference to the name Charles Spence Bate being listed alphabetically by family/surname either under “Bate”, “Spence Bate” or “Spence-Bate”. Overwhelming evidence indicated that his family/surname is Bate. Furthermore, as there are a number of carcinologists also with the family name Bate, therefore it is recommended that taxa described by Charles Spence Bate should be referred to as C.S. Bate, for example Artemesia longinaris C.S. Bate, 1888 and Ibacus brevipes C.S. Bate, 1888. 

scholarly journals Expression of the chicken beta-globin gene cluster in mice: correct developmental expression and distributed control.

1995 ◽  
Vol 15 (1) ◽  
pp. 407-414 ◽  
Author(s):  
M M Mason ◽  
E Lee ◽  
H Westphal ◽  
M Reitman
Keyword(s):  
Developmental Stage ◽  
Globin Gene ◽  
Stage Iv ◽  
Gene Clusters ◽  
Developmental Expression ◽  
Single Element ◽  
Globin Genes ◽  
Beta Globin ◽  
Variable Expression ◽  
Hypersensitive Sites

To investigate the regulation of gene clusters, we introduced the entire chicken beta-globin cluster into mice. This 35-kb region includes the four globin genes (rho-beta H-beta A-epsilon), the four upstream hypersensitive sites, and the intergenic beta A/epsilon enhancer. The chicken globins are not arranged in order of developmental expression, which is unlike the case for the human beta-globin cluster, in which gene order plays a role in the regulation of globin expression. Mice carrying the chicken cluster expressed the transgenes with the same developmental patterns as seen in the chicken. Therefore, stage-specific erythroid transcriptional milieus existed before the divergence of birds and mammals and have been conserved since then. Mice bearing the complete cluster except for a deletion removing the beta A/epsilon enhancer displayed markedly reduced expression of the beta H, beta A, and epsilon genes with efficient (but variable) rho expression. Mice carrying the four genes and beta A/epsilon enhancer but without the upstream hypersensitive sites showed reduced expression of rho, beta H, and beta A, with variable expression of epsilon. We conclude that (i) all of the genes (except possibly rho) are under the control of both the upstream hypersensitive sites and the enhancer, (ii) the influence of the control elements can extend beyond the nearest active gene, (iii) a single element (the enhancer) can influence more than one gene in a single developmental stage, (iv) the enhancer can work bidirectionally, and (v) neither the upstream sites (as a group) nor the enhancer showed developmental stage specificity. Thus, the regulation of this cluster is achieved by interaction of two distinct control regions with each of the globin genes.

scholarly journals Distribution and Evolution of Nonribosomal Peptide Synthetase Gene Clusters in the Ceratocystidaceae

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 328 ◽  
Author(s):  
Mohammad Sayari ◽  
Magriet A. van der Nest ◽  
Emma T. Steenkamp ◽  
Nicole C. Soal ◽  
P. Markus Wilken ◽  
...  
Keyword(s):  
Gene Clusters ◽  
Nonribosomal Peptide Synthetase ◽  
Main Element ◽  
Biosynthetic Pathways ◽  
Biosynthetic Gene Clusters ◽  
Nrps Gene ◽  
Nonribosomal Peptide ◽  
Peptide Synthetase ◽  
The Family ◽  
Multifunctional Enzymes

In filamentous fungi, genes in secondary metabolite biosynthetic pathways are generally clustered. In the case of those pathways involved in nonribosomal peptide production, a nonribosomal peptide synthetase (NRPS) gene is commonly found as a main element of the cluster. Large multifunctional enzymes are encoded by members of this gene family that produce a broad spectrum of bioactive compounds. In this research, we applied genome-based identification of nonribosomal peptide biosynthetic gene clusters in the family Ceratocystidaceae. For this purpose, we used the whole genome sequences of species from the genera Ceratocystis, Davidsoniella, Thielaviopsis, Endoconidiophora, Bretziella, Huntiella, and Ambrosiella. To identify and characterize the clusters, different bioinformatics and phylogenetic approaches, as well as PCR-based methods were used. In all genomes studied, two highly conserved NRPS genes (one monomodular and one multimodular) were identified and their potential products were predicted to be siderophores. Expression analysis of two Huntiella species (H. moniliformis and H. omanensis) confirmed the accuracy of the annotations and proved that the genes in both clusters are expressed. Furthermore, a phylogenetic analysis showed that both NRPS genes of the Ceratocystidaceae formed distinct and well supported clades in their respective phylograms, where they grouped with other known NRPSs involved in siderophore production. Overall, these findings improve our understanding of the diversity and evolution of NRPS biosynthetic pathways in the family Ceratocystidaceae.

scholarly journals Developmental switch in the relative expression of the alpha 1- and alpha 2-globin genes in humans and in transgenic mice

Blood ◽  
1992 ◽  
Vol 79 (9) ◽  
pp. 2471-2474 ◽  
Author(s):  
M Albitar ◽  
FE Cash ◽  
C Peschle ◽  
SA Liebhaber
Keyword(s):  
Transgenic Mice ◽  
Globin Gene ◽  
Gene Activation ◽  
Experimental System ◽  
Gene Clusters ◽  
Globin Genes ◽  
Beta Globin ◽  
Relative Expression ◽  
Structural Identity ◽  
Alpha Globin

Abstract Human alpha-globin is encoded by two adjacent genes, alpha 2 and alpha 1. Despite their remarkable level of structural identity, the more 5′ (alpha 2) gene is the major alpha-globin locus in the normal adult, expressed at 2.6-fold higher levels than the adjacent and more 3′ (alpha 1) globin gene. In light of the well-characterized pattern of gene activation in the human alpha- and beta-globin gene clusters during development, we considered the possibility that the relative expression of these two alpha-globin loci might be developmentally controlled. Analysis of human embryonic and early fetal erythroid RNA samples confirmed this possibility; levels of mRNA encoded by the two alpha-globin loci are equal in the embryo and subsequently shift to dominant expression of the alpha 2-globin locus at week 8 in utero. In transgenic mice carrying the entire human alpha-globin cluster (except for the theta gene) we show the same shift from equal expression of the alpha 1- and alpha 2-globin loci at the embryonic stage to predominance of the alpha 2-globin locus in the adult. These data demonstrate a switch in the expression of the two adjacent alpha-globin genes during the embryonic-to-fetal switch in erythroid development and provide an experimental system for its further characterization.

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