scholarly journals Diploid Genomic Architecture of Nitzschia Hildebrandi, An Elite Biomass Production Diatom

2021 ◽  
Author(s):  
Aaron Oliver ◽  
Sheila Podell ◽  
Agnieszka Pinowska ◽  
Jesse C. Traller ◽  
Sarah R. Smith ◽  
...  
Keyword(s):  
Nuclear Genome ◽  
Acid Synthesis ◽  
Repeat Sequence ◽  
Gliding Motility ◽  
Specific Marker ◽  
Carbonic Anhydrases ◽  
Algae Biomass ◽  
Chloroplast Genomes ◽  
Competitive Success ◽  
Species Specific

Abstract A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia hildebrandi. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. hildebrandi genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.

scholarly journals Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aaron Oliver ◽  
Sheila Podell ◽  
Agnieszka Pinowska ◽  
Jesse C. Traller ◽  
Sarah R. Smith ◽  
...  
Keyword(s):  
Nuclear Genome ◽  
Acid Synthesis ◽  
Repeat Sequence ◽  
Gliding Motility ◽  
Specific Marker ◽  
Carbonic Anhydrases ◽  
Algae Biomass ◽  
Chloroplast Genomes ◽  
Competitive Success ◽  
Species Specific

AbstractA near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.

scholarly journals Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shizhuo Xiao ◽  
Pan Xu ◽  
Yitong Deng ◽  
Xibin Dai ◽  
Lukuan Zhao ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genetic Structure ◽  
Chloroplast Genome ◽  
Wild Species ◽  
Ipomoea Batatas ◽  
Nuclear Genome ◽  
Ipomoea Trifida ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
Chloroplast Dna Markers

Abstract Background Sweetpotato (Ipomoea batatas [L.] Lam.) is an important food crop. However, the genetic information of the nuclear genome of this species is difficult to determine accurately because of its large genome and complex genetic background. This drawback has limited studies on the origin, evolution, genetic diversity and other relevant studies on sweetpotato. Results The chloroplast genomes of 107 sweetpotato cultivars were sequenced, assembled and annotated. The resulting chloroplast genomes were comparatively analysed with the published chloroplast genomes of wild species of sweetpotato. High similarity and certain specificity were found among the chloroplast genomes of Ipomoea spp. Phylogenetic analysis could clearly distinguish wild species from cultivars. Ipomoea trifida and Ipomoea tabascana showed the closest relationship with the cultivars, and different haplotypes of ycf1 could be used to distinguish the cultivars from their wild relatives. The genetic structure was analyzed using variations in the chloroplast genome. Compared with traditional nuclear markers, the chloroplast markers designed based on the InDels on the chloroplast genome showed significant advantages. Conclusions Comparative analysis of chloroplast genomes of 107 cultivars and several wild species of sweetpotato was performed to help analyze the evolution, genetic structure and the development of chloroplast DNA markers of sweetpotato.

Evolution of the chloroplast genome and polymorphic ITS regions in Allium subg. Melanocrommyum

Genome ◽  
1999 ◽  
Vol 42 (2) ◽  
pp. 237-247 ◽  
Author(s):  
Ted HM Mes ◽  
Reinhard M Fritsch ◽  
Sven Pollner ◽  
Konrad Bachmann
Keyword(s):  
Concerted Evolution ◽  
Morphological Evolution ◽  
Restriction Analysis ◽  
Nuclear Genome ◽  
Restriction Enzymes ◽  
Border Region ◽  
Chloroplast Genomes ◽  
Central Asian ◽  
Its Regions ◽  
Chloroplast Haplotypes

Relationships based on PCR-RFLPs of non-coding regions of cpDNA indicate that some of the largest subgenera of the genus Allium and five of the largest sections of the Central Asian subg. Melanocrommyum are artificial. Internested synapomorphic mutations without homoplasy were found only in the chloroplast genomes of plants of subg. Melanocrommyum that occur in the border region of Tajikistan, Uzbekistan, Afghanistan, and Kyrgyzstan. Eighteen of 49 plants surveyed were polymorphic for their ITS regions. Even plants that had identical chloroplast genomes were polymorphic for nuclear ribosomal regions. These individuals had markedly different frequencies of ITS variants that were detected with various restriction enzymes. The geographic partitioning of chloroplast haplotypes and the fact that the ITS variants could not be ordered hierarchically can readily be envisioned to result from gene flow. Processes such as concerted evolution and parallel morphological evolution may also be partly responsible for the disconcordance of mutations in the chloroplast and nuclear genome. However, the chimeric nature of the nuclear ribosomal regions indicates that concerted evolution is not the dominating process in Allium subg. Melanocrommyum.Key words: polymorphic, phylogeny, restriction analysis.

scholarly journals Development of specific markers for the detection of Tolypella canadensis eDNA in water samples

2021 ◽  
Vol 4 ◽  
Author(s):  
Christina Wiebe ◽  
Petra Nowak ◽  
Hendrik Schubert
Keyword(s):  
Rare Species ◽  
Environmental Samples ◽  
Large Scale ◽  
Morphological Characters ◽  
Its2 Region ◽  
Specific Marker ◽  
Specific Primers ◽  
Species Specific ◽  
Taxonomic Groups ◽  
Scale Integration

Assessing the biodiversity of an ecosystem plays a major role in ecosystem management. However, proper determination on species-level is often tricky when morphological features are scarce and especially rare species require huge sampling efforts to be detected in the aquatic realm. As an alternative to conventional methods, environmental samples can be examined via the eDNA method, allowing for large-scale integration as well as taxa resolution independent from expression of morphological characters. However, to apply this technique genetic markers that are specific to a species or at least a genus are required. Such markers until now have been successfully developed only for a few well studied taxonomic groups like, e.g., fishes and amphibians, but are still missing for others, especially plants and algae (e.g. Bista et al. 2017). This project focusses on the development of species-specific markers for the macrophytic green algae Tolypella canadensis (Characeae, Charophyta), a rare alga preferring deep water and known so far mainly from remote places. Tolypella canadensis is a circumpolar species and prefers oligotrophic lakes, where it grows in depths up to 13 m (Langangen 2002; Romanov and Kopyrina 2016). In addition, proper determination of Tolypella-species is a field of a few specialists, further complicating monitoring or even detection of this rare species. The design of the species-specific primers was based on reference nucleotide sequences of the chloroplast genes rbcL, psbC and atpB and of the ribosomal internal transcribed spacer regions ITS1 and ITS2, obtained from GenBank (Perez et al. 2017). To determine the specificity of the newly designed primers, DNA isolates obtained from T. canadensis specimens collected from the Torneträsk (Sweden, 2018) and other charophyte species were prepared in different proportions. The sensitivity of the primers was experimentally assayed by using serial dilutions of T. canadensis DNA. Additionally, a mock test comprised of a sample with the DNA of several charophyte species was conducted and finally, the markers were tested on environmental samples from the Torneträsk. Tolypella canadensis-specific primers of the ITS2 region yielded positive PCR amplifications of one single band when T. canadensis was present in a sample. Cross-amplification was not found during the mock test; other charophyte species did not yield positive amplification. The eDNA samples from the Torneträsk validated the performance of the ITS2 marker. The T. canadensis-specific marker designed in this project was proven to be sensitive and accurate. It could be recommended as a useful tool to detect the presence of T. canadensis DNA, even at low concentration and in complex samples containing other charophyte species.

Novel authentication approach for coffee beans and the brewed beverage using a nuclear-based species-specific marker coupled with high resolution melting analysis

LWT ◽  
2021 ◽  
Vol 137 ◽  
pp. 110336
Author(s):  
Irini Bosmali ◽  
Georgios Lagiotis ◽  
Evangelia Stavridou ◽  
Nadia Haider ◽  
Maslin Osathanunkul ◽  
...  
Keyword(s):  
High Resolution ◽  
High Resolution Melting ◽  
High Resolution Melting Analysis ◽  
Specific Marker ◽  
Coffee Beans ◽  
Melting Analysis ◽  
Species Specific

scholarly journals Species-Specific Marker Discovery in Tilapia

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mochamad Syaifudin ◽  
Michaël Bekaert ◽  
John B. Taggart ◽  
Kerry L. Bartie ◽  
Stefanie Wehner ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Restriction Site ◽  
De Novo ◽  
Snp Markers ◽  
Specific Marker ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Species Analysis ◽  
Species Specific ◽  
Marker Discovery

Abstract Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.

scholarly journals Cytogenetics of two Farlowella species (Loricariidae: Loricariinae): implications on the taxonomic status of the species

2018 ◽  
Vol 16 (4) ◽  
Author(s):  
Leandro Marajó ◽  
Patrik F. Viana ◽  
Milena Ferreira ◽  
Lúcia H. Rapp Py-Daniel ◽  
Eliana Feldberg
Keyword(s):  
Chromosome Number ◽  
Species Complex ◽  
Chromosomal Rearrangements ◽  
5S Rdna ◽  
Taxonomic Status ◽  
Specific Marker ◽  
Genetic Studies ◽  
Molecular Cytogenetic ◽  
Metacentric Pair ◽  
Species Specific

ABSTRACT Farlowella is one of the most diverse genera of the Loricariinae, restricted to South America rivers. The taxonomic and phylogenetic relationships among its species are contentious and, while genetic studies would contribute to the understanding of their relationships, the only available datum refer to the karyotype description of only one species. In the present study two Amazonian species, Farlowella cf. amazonum and F. schreitmuelleri, were analyzed using conventional and molecular cytogenetic procedures. Both species had diploid chromosome number 58, but different fundamental numbers (NF) 116 and 112, respectively, indicative of chromosomal rearrangements. C-banding is almost poor, especially in F. cf. amazonum, and occurs predominantly in the centromeric and in some telomeric regions, although genome of F. schreitmuelleri possessed a much larger heterochromatin amount then those of F. cf. amazonum. The chromosomes bearing the NOR sites were likely the same for both species, corresponding to the 1st metacentric pair in F. cf. amazonum and to the 28th acrocentric in F. schreitmuelleri. The location of the 5S rDNA was species-specific marker. This study expanded the available cytogenetic data for Farlowella species and pointed the remarkable karyotype diversity among species/populations, indicating a possible species complex within genus.

DNA barcode based species-specific marker for Ocimum tenuiflorum and its applicability in quantification of adulteration in herbal formulations using qPCR

2020 ◽  
Vol 23 ◽  
pp. 100376
Author(s):  
Amit Kumar ◽  
Vereena Rodrigues ◽  
Kuppusamy Baskaran ◽  
Ashutosh K. Shukla ◽  
Velusamy Sundaresan
Keyword(s):  
Dna Barcode ◽  
Specific Marker ◽  
Ocimum Tenuiflorum ◽  
Species Specific ◽  
Herbal Formulations

scholarly journals Asymmetrical natural hybridization between Populus deltoides and P. balsamifera (Salicaceae)This note is one of a selection of papers published in the Special Issue on Poplar Research in Canada.

2007 ◽  
Vol 85 (12) ◽  
pp. 1227-1232 ◽  
Author(s):  
Mona Hamzeh ◽  
Christina Sawchyn ◽  
Pierre Périnet ◽  
Selvadurai Dayanandan
Keyword(s):  
Populus Deltoides ◽  
Female Parent ◽  
Forest Tree ◽  
Snp Markers ◽  
Natural Hybridization ◽  
Populus Balsamifera ◽  
Chloroplast Genomes ◽  
Species Specific ◽  
Evolutionary Consequences ◽  
Species Being

Natural hybridization has long been recognized as a means for gene flow between species and has important evolutionary consequences. Although hybridization is generally considered to be symmetrical, with both hybridizing species being equally likely to be the male or female parent, several studies have demonstrated the presence of asymmetrical hybridization and introgression from one species to the other. We investigated the direction of natural hybridization between two sympatric forest tree species in North America ( Populus deltoides Bartr. ex Marsh. and Populus balsamifera L.) using species-specific single nucleotide polymorphism (SNP) markers in both the nuclear and chloroplast genomes. All natural hybrid individuals, identified from morphological traits, had nuclear alleles corresponding to both parental species, while the chloroplast genotypes showed similarity to P. deltoides, indicating asymmetrical hybridization with P. deltoides as the maternal and P. balsamifera as the paternal donor species. This observed asymmetrical hybridization may be attributable to cytonuclear interactions.

scholarly journals Species diversity and geographic distribution of Gymnotus (Pisces: Gymnotiformes) by nuclear (GGAC)n microsatellite analysis

2000 ◽  
Vol 23 (4) ◽  
pp. 803-807 ◽  
Author(s):  
F.M.C. Fernandes-Matioli ◽  
S.R. Matioli ◽  
L.F. Almeida-Toledo
Keyword(s):  
Species Diversity ◽  
Geographic Distribution ◽  
Nuclear Genome ◽  
Dna Amplification ◽  
River Basins ◽  
Microsatellite Analysis ◽  
Species Specific ◽  
Single Primer ◽  
Amplification Reaction ◽  
Simple Sequence

Patterns of amplified DNA fragments flanked by (GGAC)n microsatellites, obtained by single primer amplification reaction (SPAR), from 198 Gymnotus specimens (Pisces: Gymnotiformes) sampled from 8 southeastern Brazilian river basins were analyzed. The species studied were Gymnotus carapo, G. pantherinus, G. inaequilabiatus, and G. sylvius. The indirectly obtained patterns reflected the distribution of simple sequence repeats in the nuclear genome of the specimens. Species-specific patterns of DNA amplification were found and were useful for the analysis of the geographic distribution of Gymnotus species. Monomorphic patterns were found in G. carapo, G. pantherinus, and G. inaequilabiatus. Three polymorphic patterns were found in G. sylvius populations. The SPAR technique could be a useful molecular tool in conservation programs involving communities of neotropical freshwater fish.

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