Speciation and Domestication in Maize and Its Wild Relatives: Evidence From the Globulin-1 Gene

Abstract The grass genus Zea contains the domesticate maize and several wild taxa indigenous to Central and South America. Here we study the genetic consequences of speciation and domestication in this group by sampling DNA sequences from four taxa—maize (Zea mays ssp. mays), its wild progenitor (Z. mays ssp. parviglumis), a more distant species within the genus (Z. luxurians), and a representative of the sister genus (Tripsacum dactyloides). We sampled a total of 26 sequences from the glb1 locus, which encodes a nonessential seed storage protein. Within the Zea taxa sampled, the progenitor to maize contains the most sequence diversity. Maize contains 60% of the level of genetic diversity of its progenitor, and Z. luxurians contains even less diversity (32% of the level of diversity of Z. mays ssp. parviglumis). Sequence variation within the glb1 locus is consistent with neutral evolution in all four taxa. The glb1 data were combined with adh1 data from a previous study to make inferences about the population genetic histories of these taxa. Comparisons of sequence data between the two morphologically similar wild Zea taxa indicate that the species diverged ∼700,000 years ago from a common ancestor of intermediate size to their present populations. Conversely, the domestication of maize was a recent event that could have been based on a very small number of founding individuals. Maize retained a substantial proportion of the genetic variation of its progenitor through this founder event, but diverged rapidly in morphology.

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MODIFICATION OF THE BEAN BETA-PHASEOLIN GENE AND RELATED IMPACT ON EXPRESSION IN TRANSGENIC TOBACCO.

HortScience ◽

10.21273/hortsci.25.9.1072h ◽

1990 ◽

Vol 25 (9) ◽

pp. 1072h-1073

Author(s):

Nancy A. Reichert ◽

John D. Kemp

Keyword(s):

Dna Sequences ◽

Seed Storage Protein ◽

Developmental Regulation ◽

Seed Storage ◽

French Bean ◽

Protein Accumulation ◽

Phaseolus Vulgaris L ◽

Nicotiana Tabacum L ◽

Seed Storage Protein Gene ◽

Agrobacterium Tumefaciens Transformation

Beta-phaseolin, the seed storage protein gene isolated from French bean (Phaseolus vulgaris L.) displays the same developmental pattern of protein accumulation when transferred into tobacco (Nicotiana tabacum L.) The phaseolin gene was modified and then introduced into tobacco via Agrobacterium tumefaciens transformation to look for changes in phaseolin gene expression. Modifications included substitution of the promoter region with that of CaMV 35S, the removal of 3, 4, or all 5 introns, substitution of the 3' untranslated region with that of nopaline synthase, and reversal of internal DNA sequences. All gene constructions (with the exception of those containing reversed sequences) displayed overall correct developmental regulation-phaseolin protein preferentially accumulated to comparable levels at the correct stage of seed maturation.

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A phylogeny of members of the family Taeniidae based on the mitochondrial cox1 and nad1 gene data

Parasitology ◽

10.1017/s003118200800499x ◽

2008 ◽

Vol 135 (12) ◽

pp. 1457-1467 ◽

Cited By ~ 70

Author(s):

A. LAVIKAINEN ◽

V. HAUKISALMI ◽

M. J. LEHTINEN ◽

H. HENTTONEN ◽

A. OKSANEN ◽

...

Keyword(s):

Dna Sequences ◽

Nadh Dehydrogenase ◽

Sequence Variation ◽

Sequence Data ◽

Distinct Species ◽

Epidemiological Studies ◽

Sister Taxon ◽

The Family ◽

Nad1 Gene ◽

Gene Data

SUMMARYThe cestode family Taeniidae consists of 2 genera, Taenia and Echinococcus, which both have been the focus of intensive taxonomic and epidemiological studies because of their zoonotic importance. However, a comprehensive molecular phylogeny of this family has yet to be reconstructed. In this study, 54 isolates representing 9 Taenia species were characterized using DNA sequences in the mitochondrial cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) genes. Phylogenetic relationships within the family Taeniidae were inferred by combining cox1 and nad1 sequence data of the present and previous studies. In the phylogenetic analysis, the genus Echinococcus was shown to be monophyletic, but Taenia proved to be paraphyletic due to the position of T. mustelae as a probable sister taxon of Echinococcus. This indicates that T. mustelae should form a genus of its own. Taenia ovis krabbei was placed distant from T. ovis ovis, as a sister taxon of T. multiceps, supporting its recognition as a distinct species, T. krabbei. High intraspecific sequence variation within both T. polyacantha and T. taeniaeformis suggests the existence of cryptic sister species.

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Phaseolin nucleotide sequence diversity in Phaseolus. I. Intraspecific diversity in Phaseolus vulgaris

Genome ◽

10.1139/g94-107 ◽

1994 ◽

Vol 37 (5) ◽

pp. 751-757 ◽

Cited By ~ 20

Author(s):

James A. Kami ◽

Paul Gepts

Keyword(s):

Phaseolus Vulgaris ◽

Dna Sequences ◽

Storage Protein ◽

Gene Pool ◽

Seed Storage Protein ◽

Seed Storage ◽

Direct Repeat ◽

Intraspecific Diversity ◽

Cdna Clones ◽

Gene Pools

Most information about the molecular biology of phaseolin, the major seed storage protein in Phaseolus vulgaris, has been obtained from the T-type phaseolin, which is characteristic of the Andean gene pool of the species. In the work reported here, two cDNA clones for the S-type phaseolin representing the other major, Middle American gene pool were isolated and sequenced. Analysis of the DNA sequences revealed the presence of two subtypes of S phaseolin, α and β, depending on the presence or absence, respectively, of a 27-bp direct repeat. These are similar to the α- and β-phaseolin subtypes found in the Andean, T phaseolin; however, the additional 15-bp direct repeat also found in the T α-phaseolin gene type was apparently absent from the S α-phaseolin genes. The overall sequence identity was greater between the α or β subtypes of different gene pools than between the a or p subtypes within gene pools. This implies that the gene subtypes were formed prior to the formation of the two major gene pools of P. vulgaris. Analysis of the putative amino acid sequence revealed that both the 'Sanilac' phaseolin subtypes contained an additional methionine, however, not at the same site. This opens the possibility of increasing the nutritionally limiting methionine level in phaseolin either through protein engineering or by screening accessions for recombinant phaseolin sequences that combine both substitutions.Key words: seed storage protein, multigene family, direct repeat.

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Sequence specificity of the post-translational proteolytic cleavage of vicilin, a seed storage protein of pea (Pisum sativum L.)

Biochemical Journal ◽

10.1042/bj2120427 ◽

1983 ◽

Vol 212 (2) ◽

pp. 427-432 ◽

Cited By ~ 54

Author(s):

J A Gatehouse ◽

G W Lycett ◽

A J Delauney ◽

R R D Croy ◽

D Boulter

Keyword(s):

Pisum Sativum ◽

Seed Storage Protein ◽

Sequence Data ◽

Seed Storage ◽

Proteolytic Cleavage ◽

Polar Regions ◽

Sequence Specificity ◽

Basic Residue ◽

Pisum Sativum L ◽

Distinct Sequence

Amino acid sequence data from vicilin of pea (Pisum sativum L.) were compared with predicted sequences from complementary DNA species. The sites of potential post-translational proteolytic cleavage of vicilin precursor polypeptides were located in polar regions of the polypeptide, at acidic or amide residues. Proteolysis did not take place in precursors containing a functionally distinct sequence: neutral residue-hydrophobic residue-basic residue at the cleavage site. Differences between the genomic sequences encoding vicilin thus specify proteolytic cleavage of vicilin precursor polypeptides.

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DNA sequence variation in the fruit tree Inga inicuil (Leguminosae: Mimosoideae) from contrasting altitude distinguishes two different species

Botanical Sciences ◽

10.17129/botsci.638 ◽

2016 ◽

Vol 94 (4) ◽

pp. 686

Author(s):

Ma. Teresa P. Pulido-Salas ◽

Dolores González ◽

Arturo Pérez-Vázquez ◽

Francisco Lorea-Hernández

Keyword(s):

Dna Sequences ◽

Coastal Plain ◽

Sequence Variation ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sugar Content ◽

Fruit Tree ◽

Leguminous Tree ◽

Altitudinal Distribution ◽

Dna Sequence Variation

Inga inicuil is a leguminous tree in Veracruz, Mexico whose fruits are locally commercialized. One taxonomic hypothesis suggests that I. inicuil is a species with a wide altitudinal range, while another segregates I. paterno from I. inicuil by altitude and morphology. DNA sequences from the nuclear ITS1-5.8S-ITS2 and the chloroplast trnL-F regions were used to explore the genetic variation between individuals of I. inicuil compare it with their altitudinal distribution and evaluate the possible relationship between altitude and sugar content in the fruits. Results indicated that sugar content is not related to altitude or with sequence variation. However, sequences from the trnL-F revealed an insertion/deletion of approximately 309 nucleotides present only in trees growing on the low-elevation coastal plain. Phylogenetic analyses with sequence data support the hypothesis that I. inicuil and I. paterno are two different species. The remarkable differences of sequence data from the trnL-F within the species make necessary further research increasing taxon sampling.

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The number of spaced-word matches between two DNA sequences as a function of the underlying pattern weight

10.1101/527515 ◽

2019 ◽

Cited By ~ 5

Author(s):

Sophie Röhling ◽

Burkhard Morgenstern

Keyword(s):

Dna Sequences ◽

Sequence Comparison ◽

Word Length ◽

Common Ancestor ◽

Sequence Data ◽

High Accuracy ◽

Last Common Ancestor ◽

Statistical Stability ◽

Alignment Free ◽

Simulated Sequence

AbstractWe study the number Nk of (spaced) word matches between pairs of evolutionarily related DNA sequences depending on the word length or pattern weight k, respectively. We show that, under the Jukes-Cantor model, the number of substitutions per site that occurred since two sequences evolved from their last common ancestor, can be esti-mated from the slope of a certain function of Nk. Based on these considerations, we implemented a software program for alignment-free sequence comparison called Slope-SpaM. Test runs on simulated sequence data show that Slope-SpaM can estimate phylogenetic dis-tances with high accuracy for up to around 0.5 substitutions per po-sitions. The statistical stability of our results is improved if spaced words are used instead of contiguous k-mers. Unlike previous methods that are based on the number of (spaced) word matches, our approach can deal with sequences that share only local homologies.

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MODIFICATION OF THE BEAN BETA-PHASEOLIN GENE AND RELATED IMPACT ON EXPRESSION IN TRANSGENIC TOBACCO.

HortScience ◽

10.21273/hortsci.25.9.1072 ◽

1990 ◽

Vol 25 (9) ◽

pp. 1072H-1073

Author(s):

Nancy A. Reichert ◽

John D. Kemp

Keyword(s):

Dna Sequences ◽

Seed Storage Protein ◽

Developmental Regulation ◽

Seed Storage ◽

French Bean ◽

Protein Accumulation ◽

Phaseolus Vulgaris L ◽

Nicotiana Tabacum L ◽

Seed Storage Protein Gene ◽

Agrobacterium Tumefaciens Transformation

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Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

Beni-Suef University Journal of Basic and Applied Sciences ◽

10.1186/s43088-020-00094-4 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Kuldeepsingh A. Kalariya ◽

Ram Prasnna Meena ◽

Lipi Poojara ◽

Deepa Shahi ◽

Sandip Patel

Keyword(s):

Dna Sequences ◽

Genomic Dna ◽

Competitive Inhibition ◽

Sequence Data ◽

Homology Model ◽

Squalene Synthase ◽

Gymnema Sylvestre ◽

Gardenia Jasminoides ◽

Ramachandran Plots ◽

Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

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Molecular cytogenetical and biochemical studies on some Lupinus species

Bulletin of the National Research Centre ◽

10.1186/s42269-021-00493-2 ◽

2021 ◽

Vol 45 (1) ◽

Author(s):

Hoda B. M. Ali ◽

Samy A. A. Heiba

Keyword(s):

Related Species ◽

Storage Protein ◽

Seed Storage Protein ◽

Lupinus Albus ◽

Seed Storage ◽

Rrna Genes ◽

Large Chromosome ◽

45S Rdna ◽

Lupinus Polyphyllus ◽

Electrophoretic Patterns

Abstract Background Lupins are cultivated as human consumption grains and forage legumes. The chromosomes of lupins are too small to be karyotyped by conventional techniques, because they reveal a general lack of distinctive cytological features. In the current study, Fluorescence in situ Hybridization (FISH) was used to locate 5S and 45S ribosomal gene sites on the chromosomes of Lupinus albus ssp albus, Lupinus albus ssp graecus, Lupnus termis (all with 2n = 50), and Lupinus polyphyllus lindl var. polyphyllus (2n = 48), FISH together with seed storage protein electrophoretic patterns were used to find out the relationship among these species. Results The double-target FISH on the chromosomes of the studied species with rDNA probes revealed that the two types of rRNA genes are located on different chromosomes. The detected loci of rRNA genes partially reflected the taxonomical similarity among the two Lupinus albus subspecies and L. termis. Lupinus polyphyllus lindl var. polyphyllus was exception by having unique large chromosome mostly is covered by one signal of 45S rDNA, whereas its homologous chromosome seems to be normal-sized and have the other 45S rDNA locus. The similarity matrix among the Lupinus species as computed according to Jaccardʼs Coefficient from the SDS-PAGE, showed that L. albus ssp. Albus and L. albus ssp. Graecus are the most similar species (~ 97%), and then comes L. termis, and L. polyphyllus lindl var. polyphylus has been placed in separate clade and still the most related species to it among the studied species is L. termis (~ 70%). Conclusion It could be postulated from FISH and seed storage protein electrophoretic patterns that the relationships among the studied species is as follows, Lupinus albus ssp albus, is the most related species to Lupinus albus ssp graecus then comes Lupnus termis and Lupinus polyphyllus lindl var. polyphyllus at a distal position.

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A Chromosome-Based Model for Estimating the Number of Conserved Segments Between Pairs of Species From Comparative Genetic Maps

Genetics ◽

10.1093/genetics/154.1.323 ◽

2000 ◽

Vol 154 (1) ◽

pp. 323-332

Author(s):

David Waddington ◽

Anthea J Springbett ◽

David W Burt

Keyword(s):

Maximum Likelihood ◽

Dna Sequences ◽

Common Ancestor ◽

Length Distribution ◽

Genetic Maps ◽

Segment Length ◽

Syntenic Block ◽

Comparative Maps

Abstract Comparative genetic maps of two species allow insights into the rearrangements of their genomes since divergence from a common ancestor. When the map details the positions of genes (or any set of orthologous DNA sequences) on chromosomes, syntenic blocks of one or more genes may be identified and used, with appropriate models, to estimate the number of chromosomal segments with conserved content conserved between species. We propose a model for the distribution of the lengths of unobserved segments on each chromosome that allows for widely differing chromosome lengths. The model uses as data either the counts of genes in a syntenic block or the distance between extreme members of a block, or both. The parameters of the proposed segment length distribution, estimated by maximum likelihood, give predictions of the number of conserved segments per chromosome. The model is applied to data from two comparative maps for the chicken, one with human and one with mouse.

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