Sequence analysis of Maturase K (matK): A chloroplast-encoding gene in some selected pulses

The application and utilization of sequence data has been found very informative in the characterization and phylogenetic relationship of different crops species. This study aimed to use bioinformatics tools to characterize the matK gene in some  selected legumes with special reference to pigeon pea [cajanus cajan (L.)Millsp]  matK sequence as a quarry sequence. Nucleotide and amino acid sequence of matK gene of 10 legumes were retrieved from NCBI database and analysed for homology, physiochemical properties, motifs, GC content as well as phylogenetic relationships. Results showed that the nucleotide and amino acid sequence lengths of this gene among the selected legumes differs. Its nucleotide length varied between  631-1580bp, while the amino acids sequence varied between 21 and 509 residues. P. tetragonolobus matK and C. cajan matK sequences had percentage identity of 88% while V. sativa had the lowest percentage identity of 70%. G.tomentella and P. tetragonolobus matK sequence shared the same percentage similarity of 91% with C.cajan while V. sativa had the least (78%) with C.cajan. The motif predicted were tyrosine kinase phosphorylation site, N-myristoylation site, N-glycosylation site, protein kinase phosphorylation site, casein kinase II phosphorylation site and cAMP- and –cGMP dependent protein kinase phosphorylation site. However,  microbodies C-terminal targeting site was only predicted in the amino acid  sequence of matK gene of P. sativum and C.cajan. Phylogenetically, two major clades were revealed with P.sativum, V.sativa, and C. arientinum matK gene sequence in clade A and matK gene sequence of P.tetragonolobus, C. cajan, G. tomentella,  P.vulgaris, V.unguiculata, V. angularis and V. radiate in clade B. It showed that clade A diverged from the ancestry legume approximately 39MYA while legume  sequences in clade B diverged from the ancestor about 57MYA. GC content of the nucleotide sequence of matK gene of V. sativa was highest (31.37%) with the range in the selected legume varying between 7.29%-31.37%. The secondary structure of amino acids sequence of matK gene in the selected legume revealed the alpha helix (34.14%-41.27%), extended strand (11.56%-20.99%) and random coil (39.48%- 51.76%). The major domain architecture found in the amino acid  sequence were single and double types. Implicitly, though maturase K gene  sequences in the selected legumes differ in lengths physiochemical properties, GC content and motif. The result of this study revealed that C.cajan matK gene sequences is closely related to that of P. tetragonolobus but distant to V.  unguiculata as well as P. vulgaris.Keywords: Maturase K (matK) gene, bioinformatics, phylogenetics, selected legumes, breedin

Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids

<p>Abstract</p> <p>Background</p> <p>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 <it>matR </it>gene from 174 species representing 72 families of putative rosids and examined phylogenetic relationships and phylogenetic utility of <it>matR </it>in rosids. We also inferred phylogenetic relationships within the "rosid clade" based on a combined data set of 91 taxa and four genes including <it>matR</it>, two plastid genes (<it>rbcL</it>, <it>atpB</it>), and one nuclear gene (18S rDNA).</p> <p>Results</p> <p>Comparison of mitochondrial <it>matR </it>and two plastid genes (<it>rbcL </it>and <it>atpB</it>) showed that the synonymous substitution rate in <it>matR </it>was approximately four times slower than those of <it>rbcL </it>and <it>atpB</it>; however, the nonsynonymous substitution rate in <it>matR </it>was relatively high, close to its synonymous substitution rate, indicating that the <it>matR </it>has experienced a relaxed evolutionary history. Analyses of our <it>matR </it>sequences supported the monophyly of malvids and most orders of the rosids. However, fabids did not form a clade; instead, the COM clade of fabids (Celastrales, Oxalidales, Malpighiales, and Huaceae) was sister to malvids. Analyses of the four-gene data set suggested that Geraniales and Myrtales were successively sister to other rosids, and that Crossosomatales were sister to malvids.</p> <p>Conclusion</p> <p>Compared to plastid genes such as <it>rbcL </it>and <it>atpB</it>, slowly evolving <it>matR </it>produced less homoplasious but not less informative substitutions. Thus, <it>matR </it>appears useful in higher-level angiosperm phylogenetics. Analysis of <it>matR </it>alone identified a novel deep relationship within rosids, the grouping of the COM clade of fabids and malvids, which was not resolved by any previous molecular analyses but recently suggested by floral structural features. Our four-gene analysis supported the placements of Geraniales, Myrtales at basal nodes of the rosid clade and placed Crossosomatales as sister to malvids. We also suggest that the core part of rosids should include fabids, malvids and Crossosomatales.</p

Parentage determination of Vanda Miss Joaquim (Orchidaceae) through two chloroplast genes rbcL and matK

This manuscript describes the use of the DNA barcoding regions matK and rbcL to determine the seed parent of the popular orchid hybrid and Singapore's national flower, Vanda Miss Joaquim. The pollen parent was inferred by exclusion to be V. hookeriana and the pod parent V. teres var. andersonii

Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes

Three mitochondrial (atp1, matR, nad5), four chloroplast (atpB, matK, rbcL, rpoC2), and one nuclear (18S) genes from 162 seed plants, representing all major lineages of gymnosperms and angiosperms, were analyzed together in a supermatrix or in various partitions using likelihood and parsimony methods. The results show that Amborella + Nymphaeales together constitute the first diverging lineage of angiosperms, and that the topology of Amborella alone being sister to all other angiosperms likely represents a local long branch attraction artifact. The monophyly of magnoliids, as well as sister relationships between Magnoliales and Laurales, and between Canellales and Piperales, are all strongly supported. The sister relationship to eudicots of Ceratophyllum is not strongly supported by this study; instead a placement of the genus with Chloranthaceae receives moderate support in the mitochondrial gene analyses. Relationships among magnoliids, monocots, and eudicots remain unresolved. Direct comparisons of analytic results from several data partitions with or without RNA editing sites show that in multigene analyses, RNA editing has no effect on well supported relationships, but minor effect on weakly supported ones. Finally, comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloroplast genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147147/1/tax25065680.pd

From milk to diet: feed recognition for milk authenticity.

The presence of plastidial DNA fragments of plant origin in animal milk samples has been confirmed. An experimental plan was arranged with 4 groups of goats, each provided with a different monophytic diet: 3 fresh forages (oats, ryegrass and X-triticosecale) and 1 two week-old silage (X-triticosecale). Feed-derived rubisco (ribulose bisphosphate carboxylase, rbcL) DNA fragments were detected in 100 % of the analyzed goat milk samples and the nucleotide sequence of the PCR amplified fragments was found to be 100 % identical to the corresponding fragments amplified from the plant species consumed in the diet. Two additional chloroplast-based molecular markers were used to set up an assay for distinctiveness, conveniently based on a simple polymerase chain reaction. In one case, differences in single nucleotides occurring within the gene encoding for plant maturase K (matK) were exploited. In the other, plant species recognition was based on the difference in the length of the intron present within the trnL gene. The presence of plastidial plant DNA, ascertained with the PCR-based amplification of the rbcL fragment, was also assessed in raw cow milk samples collected directly from stock farms or taken from milk sold in the commercial market. In this case the nucleotide sequence of the amplified DNA fragments reflected the multiple forages present in the diet fed to the animals

Angiosperm phylogeny inferred from sequences of four mitochondrial genes

An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes, atp1, matR, nad5 , and rps3 , from 380 species that represent 376 genera and 296 families of seed plants. It is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB, matK , and rbcL , and nuclear 18S rDNA. The basalmost lineage consists of Amborella and Nymphaeales (including Hydatellaceae). Austrobaileyales follow this clade and are sister to the mesangiosperms, which include Chloranthaceae, Ceratophyllum , magnoliids, monocots, and eudicots. With the exception of Chloranthaceae being sister to Ceratophyllum , relationships among these five lineages are not well supported. In eudicots, Ranunculales, Sabiales, Proteales, Trochodendrales, Buxales, Gunnerales, Saxifragales, Vitales, Berberidopsidales, and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and asterids. Within rosids, the COM (Celastrales–Oxalidales–Malpighiales) clade is sister to malvids (or rosid II), instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of angiosperms. Santalales and Caryophyllales are members of an expanded asterid clade. This study shows that the mitochondrial genes are informative markers for resolving relationships among genera, families, or higher rank taxa across angiosperms. The low substitution rates and low homoplasy levels of the mitochondrial genes relative to the chloroplast genes, as found in this study, make them particularly useful for reconstructing ancient phylogenetic relationships. A mitochondrial gene-based angiosperm phylogeny provides an independent and essential reference for comparison with hypotheses of angiosperm phylogeny based on chloroplast genes, nuclear genes, and non-molecular data to reconstruct the underlying organismal phylogeny.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79100/1/JSE_97_sm_FigS2-1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/79100/2/JSE_97_sm_FigS2-2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/79100/3/JSE_97_sm_FigS3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/79100/4/j.1759-6831.2010.00097.x.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/79100/5/JSE_97_sm_FigS1.pd

Using Phylogenomic Data to Untangle the Patterns and Timescale of Flowering Plant Evolution

Angiosperms are one of the most dominant groups on Earth, and have fundamentally changed global ecosystem patterns and function. Therefore, unravelling their evolutionary history is key to understanding how the world around us was formed, and how it might change in the future. In this thesis, I use genome-scale data to investigate the evolutionary patterns and timescale of angiosperms at multiple taxonomic levels, ranging from angiosperm-wide to genus-level data sets. I begin by using the largest combination of taxon and gene sampling thus far to provide a novel estimate for the timing of angiosperm origin in the Triassic period. Through a range of sensitivity analyses, I demonstrate that this estimate is robust to many important components of Bayesian molecular dating. I then explore tactics for phylogenomic dating using multiple molecular clocks. I evaluate methods for estimating the number and assignment of molecular clock models, and strategies for partitioning molecular clock models in analyses of multigene data sets. I also demonstrate the importance of critically evaluating the precision in age estimates from molecular dating analyses. Finally, I assess the utility of plastid data sets for resolving challenging phylogenetic relationships, focusing on Pimelea Banks & Sol. ex Gaertn. Through analysis of a multigene data set, sampled from many taxa, I provide an improved phylogeny for Pimelea and its close relatives. I then generate a plastome-scale data set for a representative sample of species to further refine the Pimelea phylogeny, and characterise discordant phylogenetic signals within their chloroplast genomes. The work in this thesis demonstrates the power of genome- scale data to address challenging phylogenetic questions, and the importance of critical evaluation of both methods and results. Future progress in our understanding of angiosperm evolution will depend on broader and denser taxon sampling, and the development of improved phylogenetic methods

Assessing the evolutionary patterns of plastid genome reduction in a group of non-photosynthetic parasitic Angiosperms (Orobanchaceae)

Der Plastid, der als Schlüsselfunktion der autotrophen Lebensweise die Photosynthese ausführt, besitzt ein semi-autonomes genetisches System mit eigenem Genom (Plastom), welches für Proteine des Photosyntheseapparates sowie wenige Enzyme anderer metabolischer Prozesse und Untereinheiten grundlegender genetischer Prozesse kodiert. Aufgrund des Überganges zu einer unterschiedlich stark ausgeprägten heterotrophen Lebensweise weisen parasitische Pflanze enorm modifizierte Plastome auf. Diese sind durch eine extreme funktionelle und strukturelle Reduktion sowie stark erhöhte DNS-Substitutionsraten charakterisiert. Gegenstand dieser Dissertation ist es, evolutive Trends der Plastomreduktion bei verminderten Selektionsdrücken zu rekonstruieren. Zu diesem Zweck wurden die Plastome verschiedener zur Photosynthese fähiger und unfähiger Vertreter der Sommerwurzgewächse (Orobanchaceae) vollständig sequenziert und mittels moderner Methoden der vergleichenden Genomanalyse hinsichtlich folgender Aspekte analysiert: (i) strukturelle Änderungen, (ii) potentielle Funktionalität von Photosynthese-assoziierten Plastidengenen, (iii) Pseudogenisierung und Gendeletion, und (iv) Evolution und Auswirkung erhöhter plastidärer DNS-Substitutionsraten. Darüber hinaus behandelt ein Kapitel methodologische Aspekte der Sequenzierung von Plastidengenomen mittels Pyrosequenzierung gesamt-genomischer DNS-Extrakte. Die Analyse plastidärer DNS nah-verwandter Orobanchaceae erlaubt es erstmals, komplexe Muster der Genomreduktion in parasitischen Pflanzen aufzudecken. Unter anderem kann gezeigt werden, dass bereits der Übergang zu einer heterotrophen Lebensweise für strukturelle Änderungen des Plastoms ausschlaggebend ist und zu einem Verlust der Funktionalität bestimmter Gene und einer Erhöhung der Substitutionsraten führt. Innerhalb der Orobanchaceae schreitet die Plastomreduktion mit zunehmender Heterotrophie mit linienspezifischer Geschwindigkeit voran. Das Ausmaß von Pseudogenisierung und Deletion nicht-essentieller Genomabschnitte wird dabei maßgeblich durch die Distanz zu essentiellen genischen Elementen und von der plastidären Operonstruktur beeinflusst. Darüber hinaus weisen die zusammengetragenen Ergebnisse darauf hin, dass parasitische Pflanzen die Funktion einzelner Photosynthese-assoziierter Proteinkomplexe möglicherweise aufrechterhalten und eine erhöhte Rate an intrazellulärem DNS-Transfer aufweisen. Veränderungen der DNS-Substitutionsmuster bei zur Photosynthese fähigen heterotrophen Orobanchaceae implizieren eine Korrelation des Übertritts zur parasitischen Lebensweise mit der Verminderung der Selektion bestimmter plastidärer Genen. Im Vergleich zu photosynthetisch aktiven Pflanzen, weisen Vollparasiten differenzierte Muster bezüglich DNS-Substitutionen auf, einschließlich linienspezifischer Ratenerhöhung und –reduktion. In der vorliegenden Arbeit wird anhand der Analyse von simulierten und experimentell generierten 454-Datensätzen erstmals gezeigt, dass die erfolgreiche Plastomrekonstruktion signifikant von der verwendeten Sequenzdatenmenge bestimmt wird. Darüber hinaus wird eine Methode zur a priori Schätzung der optimalen Datenmenge unter Verwendung weniger Parameter erarbeitet.The prime function of the plastid organelle is to carry out photosynthesis thereby providing autotrophy to the plant kingdom. Plastids retain a semi-autonomous genetic system including a genome (plastome) encoding subunits for photosynthesis-related and unrelated processes as well as proteins for basic functions of the genetic apparatus. Due to the transition from an autotrophic to a semi- or holo-heterotrophic lifestyle, parasitic plants show major plastomic reconfigurations with extreme reductions of plastome size and coding capacity as well as extraordinarily elevated nucleotide substitution rates. Using the broomrape family (Orobanchaceae) as a model group, this dissertation thesis reconstructs molecular evolutionary patterns of reductive plastome evolution of the plastid chromosome under relaxed evolutionary constraints. Employing comparative-evolutionary analyses of completely sequenced plastid genomes from several hemi- and holoparasitic members of Orobanchaceae this work examines aspects concerning the (i) co-linearity and structural rearrangements of plastomes, (ii) potential functionality of genes involved in photosynthesis, (iii) pseudogenization and gene loss, and (iv) accelerated substitution rates in plastid genomes. In addition, one chapter evaluates methodological aspects of plastid genome sequencing employing whole-genome shotgun pyrosequencing. This work reveals that genetic and genomic changes concerning plastome structure, nucleotide substitution rates and selectional constraints occur in a complex and highly lineage specific manner, and it provides novel insights into factors influencing reductive evolution of plastome. Increasing host-dependency notably seeds excessive non-functionalization of plastid genes due to pseudogenization or deletion, and severely relaxes the structural maintenance of the plastid chromosome. Pseudogenization and segmental deletions of newly dispensable regions depend significantly on the operon-structure of the plastid chromosomes as well as on the distribution of essential genes in Orobanchaceae. There is evidence for maintained or alternative function of a photosynthesis-related complex as well as for putatively increased rates of intracellular gene transfer in parasitic plants. Analyses of nucleotide substitutions reveal significantly elevated rates in both housekeeping and photosynthesis genes already in photosynthetic heterotrophs indicating that relaxation of selective constraints relates to the transition to a parasitic lifestyle. Compared to hemiparasites and autotrophs, distinctive trends of rate and selectional changes exist among holoparasite lineages including both local accelerations and rate reductions. Above that, this thesis shows for the first time that the successful reconstruction of plastid chromosomes from whole-genome shotgun pyrosequencing strongly depends on the size of the assembled read pool. Using the results of simulated and empirical 454 datasets in combination with a resampling scheme for automated quality assessment, a method for a parameter-less a priori assessment of the optimal read pool size is established that should ease assembly efforts