Journal: Journal of Fungi

Article Title: DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems

doi: 10.3390/jof8040330

Figure Lengend Snippet: Read abundance of Phytophthora taxa identified in the three surveyed areas obtained by DNA metabarcoding. ALE/CAC = P. aleatoria / P. cactorum ; ASP = P. asparagi ; CAS/QUE = P. castanetorum / P. quercina ; CIP = P. citrophthora ; IRA = P. iranica -like; MUL = P. multivora ; NIC = P. nicotianae ; OCC = P. occultans ; PLU = P. plurivora ; PSY = P. psychrophila ; SYR = P. syringae ; UNK 1 = Phytophthora unknown sp. 1 ; UNK 2 = Phytophthora unknown sp. 2; UNK 3 = Phytophthora unknown sp. 3; UNK 4 = Phytophthora unknown sp. 4; UNK 5 = Phytophthora unknown sp. 5.

Article Snippet: In order to test the above hypotheses and to compare the efficacy and limits of traditional soil baiting and Illumina metabarcoding to understand the diversity of soil-borne Phytophthora communities in different ecosystems, both methods were used to analyze rhizosphere samples, including both soil and fine roots, collected from different ecosystems.

Techniques:

Journal: Journal of Fungi

Article Title: DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems

doi: 10.3390/jof8040330

Figure Lengend Snippet: Comparison of diversity indices of the Phytophthora community in DNA metabarcoding rhizosphere soil-positive samples from the three surveyed areas. Data were analyzed with the Kruskal–Wallis test.

Article Snippet: In order to test the above hypotheses and to compare the efficacy and limits of traditional soil baiting and Illumina metabarcoding to understand the diversity of soil-borne Phytophthora communities in different ecosystems, both methods were used to analyze rhizosphere samples, including both soil and fine roots, collected from different ecosystems.

Techniques: Comparison

Journal: Journal of Fungi

Article Title: DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems

doi: 10.3390/jof8040330

Figure Lengend Snippet: Values of the diversity indices, Shannon diversity, Pielou’s evenness and Simpson dominance, calculated basing on DNA metabarcoding Phytophthora -positive rhizosphere soil samples from the three surveyed areas. Data were analyzed with the Kruskal–Wallis test. Different letters indicate significant differences according to Dunn’s multiple comparison tests ( p ≤ 0.01).

Article Snippet: In order to test the above hypotheses and to compare the efficacy and limits of traditional soil baiting and Illumina metabarcoding to understand the diversity of soil-borne Phytophthora communities in different ecosystems, both methods were used to analyze rhizosphere samples, including both soil and fine roots, collected from different ecosystems.

Techniques: Comparison

Journal: Journal of Fungi

Article Title: DNA Metabarcoding and Isolation by Baiting Complement Each Other in Revealing Phytophthora Diversity in Anthropized and Natural Ecosystems

doi: 10.3390/jof8040330

Figure Lengend Snippet: Comparison between: (i) number of Phytophthora -positive rhizosphere soil samples by ( a ) baiting and DNA metabarcoding; ( b ) DNA metabarcoding-processing of roots and soil; (ii) Phytophthora taxa recorded by ( c ) baiting and DNA metabarcoding; ( d ) DNA metabarcoding-processing of roots and soil. ALE/CAC = P. aleatoria / P. cactorum ; ASP = P. asparagi ; BIL = P. bilorbang ; CAS/QUE = P. castanetorum / P. quercina ; CIP = P. citrophthora ; CRY = P. cryptogea ; GON = P. gonapodyides ; IRA-like = P. iranica -like; MUL = P. multivora ; NIC = P. nicotianae ; OCC = P. occultans ; PAR = P. parvispora ; PLU = P. plurivora ; PSC = P. pseudocryptogea ; PSY = P. psychrophila ; SYR = P. syringae ; UNK 1 = Phytophthora unknown sp. 1; UNK 2 = Phytophthora unknown sp. 2; UNK 3 = Phytophthora unknown sp. 3; UNK 4 = Phytophthora unknown sp. 4; UNK 5 = Phytophthora unknown sp. 5.

Article Snippet: In order to test the above hypotheses and to compare the efficacy and limits of traditional soil baiting and Illumina metabarcoding to understand the diversity of soil-borne Phytophthora communities in different ecosystems, both methods were used to analyze rhizosphere samples, including both soil and fine roots, collected from different ecosystems.

Techniques: Comparison

Journal: Current Research in Parasitology & Vector-borne Diseases

Article Title: Haemoprotozoan surveillance in peri-urban native and introduced wildlife from Australia

doi: 10.1016/j.crpvbd.2021.100052

Figure Lengend Snippet: List of primers used for the amplification of haemoprotozoans from Australian wildlife samples

Article Snippet: Summary of sequences obtained from trypanosome 18S rRNA metabatcoding (Illumina MiSeq). (A) Library size (i.e. number of sequences) obtained from samples. (B) Distribution of the number of reads in sample categories blood, tick and tissue.

Techniques: Amplification, Sequencing

Journal: Current Research in Parasitology & Vector-borne Diseases

Article Title: Haemoprotozoan surveillance in peri-urban native and introduced wildlife from Australia

doi: 10.1016/j.crpvbd.2021.100052

Figure Lengend Snippet: Maximum likelihood (ML) phylogenetic reconstruction of trypanosome zOTUs based on a 426 bp alignment of the 18S rRNA locus. Substitution model TIM3e + I + G4 with 10,000 replicates. Node values correspond to bootstrap support where values > 0.7 are indicated by solid circles. Number of substitutions per nucleotide position is represented by the scale-bar. Sequences generated in the present study are in bold.

Article Snippet: Summary of sequences obtained from trypanosome 18S rRNA metabatcoding (Illumina MiSeq). (A) Library size (i.e. number of sequences) obtained from samples. (B) Distribution of the number of reads in sample categories blood, tick and tissue.

Techniques: Generated

Journal: Current Research in Parasitology & Vector-borne Diseases

Article Title: Haemoprotozoan surveillance in peri-urban native and introduced wildlife from Australia

doi: 10.1016/j.crpvbd.2021.100052

Figure Lengend Snippet: Maximum likelihood (ML) phylogenetic reconstruction of piroplasm species based on an 852 bp alignment of the 18S rRNA locus. Substitution model TIM3 + F + I + G4 with 10,000 replicates. Node values correspond to bootstrap support where values > 0.7 are indicated by solid circles. Number of substitutions per nucleotide position is represented by the scale-bar. Sequences generated in the present study are in bold.

Article Snippet: Summary of sequences obtained from trypanosome 18S rRNA metabatcoding (Illumina MiSeq). (A) Library size (i.e. number of sequences) obtained from samples. (B) Distribution of the number of reads in sample categories blood, tick and tissue.

Techniques: Generated

Journal: Current Research in Parasitology & Vector-borne Diseases

Article Title: Haemoprotozoan surveillance in peri-urban native and introduced wildlife from Australia

doi: 10.1016/j.crpvbd.2021.100052

Figure Lengend Snippet: Maximum likelihood (ML) phylogenetic reconstruction of Hepatozoon based on an 829 bp alignment of the 18S rRNA locus. Substitution model HKY + F + I + G4 with 10,000 replicates. Node values correspond to bootstrap support where values > 0.7 are indicated by solid circles. Number of substitutions per nucleotide position is represented by the scale-bar. Sequences generated in the present study are in bold.

Article Snippet: Summary of sequences obtained from trypanosome 18S rRNA metabatcoding (Illumina MiSeq). (A) Library size (i.e. number of sequences) obtained from samples. (B) Distribution of the number of reads in sample categories blood, tick and tissue.

Techniques: Generated

Journal: The ISME Journal

Article Title: Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters

doi: 10.1038/ismej.2016.120

Figure Lengend Snippet: Origins and culture conditions of prasinophytes clade VII strains used in this study

Article Snippet: V9 rRNA metabarcodes (129 bp on average) were sequenced with Illumina HiSeq (Illumina, San Diego, CA, USA) sequencing at a typical depth of 2 M sequences per sample ( Supplementary Table 3 ).

Techniques: Isolation

Journal: The ISME Journal

Article Title: Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters

doi: 10.1038/ismej.2016.120

Figure Lengend Snippet: ML tree inferred from nuclear 18S rRNA sequences belonging to prasinophytes clade VII. Nodes supported by NJ, ML and Bayesian methods are shown by a solid dot (▪). Nodes supported by ML and Bayes only are indicated by a gray dot (). Empty dot (○) represents a node supported by only one method, either ML or Bayes.

Article Snippet: V9 rRNA metabarcodes (129 bp on average) were sequenced with Illumina HiSeq (Illumina, San Diego, CA, USA) sequencing at a typical depth of 2 M sequences per sample ( Supplementary Table 3 ).

Techniques:

Journal: The ISME Journal

Article Title: Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters

doi: 10.1038/ismej.2016.120

Figure Lengend Snippet: ML tree inferred from nuclear 16S rRNA sequences belonging to prasinophytes clade VII. Nodes supported by NJ, ML and Bayesian methods are shown by a solid dot (▪).

Article Snippet: V9 rRNA metabarcodes (129 bp on average) were sequenced with Illumina HiSeq (Illumina, San Diego, CA, USA) sequencing at a typical depth of 2 M sequences per sample ( Supplementary Table 3 ).

Techniques: