scholarly journals Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

2021 ◽  
Author(s):  
Bin-Bin Liu ◽  
Zhi-Yao Ma ◽  
Chen Ren ◽  
Richard G.J. Hodel ◽  
Miao Sun ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Sequencing Depth ◽  
Nuclear Genes ◽  
Nuclear Ribosomal Dna ◽  
Plant Systematics ◽  
Genome Skimming ◽  
Enrichment Experiments ◽  
And Performance

With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coverage in silico. We tested the performance of the four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of the Vitis clade at the genus-level and Vitaceae at the family-level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10x coverage. Without the steps of synthesizing baits and enrichment experiments, we showcase that deep genome skimming (DGS) is effective for capturing large datasets of SCNs, in addition to plastomes, mtDNA, and entire nrDNA repeats, and may serve as an economical alternative to the widely used target enrichment Hyb-Seq approach.

Additions to Ochroconis from India

Phytotaxa ◽  
2019 ◽  
Vol 427 (3) ◽  
pp. 186-199
Author(s):  
ARCHANA SINGH ◽  
NIKHIL KUMAR SINGH ◽  
PARAS NATH SINGH ◽  
RAGHVENDRA SINGH ◽  
NAWAL KISHORE DUBEY
Keyword(s):  
New Species ◽  
Medicinal Plant ◽  
Ribosomal Dna ◽  
Leaf Surface ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Nuclear Ribosomal Dna ◽  
Monophyletic Clade ◽  
Protein Coding

Ochroconis helicteris, a novel species of the oligotrophic genus Ochroconis (Sympoventuriaceae, Venturiales), has been described and illustrated. Morphologically, this species has characters similar to allied species in the genus Ochroconis, but differs in conidial dimensions and shape. Phylogenetic analyses using nuclear ribosomal DNA gene ITS and protein coding gene BT2 revealed it clustering as monophyletic clade which was separated from known Ochroconis species. New species was isolated from leaf surface of medicinal plant Helicteris isora L.

Phylogenetic analyses of Nematoctonus and Hohenbuehelia (Pleurotaceae)

2007 ◽  
Vol 85 (8) ◽  
pp. 762-773 ◽  
Author(s):  
Alexandra T.E. Koziak ◽  
Kei Chin Cheng ◽  
R. Greg Thorn
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Nuclear Ribosomal Dna ◽  
Monophyletic Clade ◽  
Parasitoid Species ◽  
Internal Transcribed Spacer Region ◽  
Species Limits ◽  
Additional Gene

Hohenbuehelia (Agaricales, Pleurotaceae) and Nematoctonus (Hyphomycetes) are the names for the sexual and asexual stages of a genus of nematode-destroying fungi (Basidiomycota). We obtained partial sequences of nuclear ribosomal DNA, including the internal transcribed spacer region and the 5′ end of the large subunit, of 37 isolates of Hohenbuehelia and Nematoctonus representing 13 of the 16 described species in Nematoctonus. Phylogenetic analyses support Hohenbuehelia–Nematoctonus as a monophyletic clade of the Pleurotaceae, within which the species were placed in five main subclades. Exclusively predatory species ( Nematoctonus brevisporus Thorn & G.L. Barron, Nematoctonus campylosporus Drechsler, Nematoctonus robustus F.R. Jones, and Nematoctonus sp. UAMH 5317) appear to be basal. In these species, adhesive knobs to capture prey are produced on their hyphae but not on their conidia. A single mycelial individual may feed on many nematodes. From these have arisen both exclusively parasitoid species ( Nematoctonus cylindrosporus Thorn & G.L. Barron, Nematoctonus leiosporus Drechsler, Nematoctonus leptosporus Drechsler, Nematoctonus pachysporus Drechsler, Nematoctonus tylosporus Drechsler), and species that we call intermediate predators ( Nematoctonus angustatus Thorn & G.L. Barron, Nematoctonus concurrens Drechsler, Nematoctonus geogenius Thorn & GL. Barron, Nematoctonus hamatus Thorn & G.L. Barron, and Nematoctonus subreniformis Thorn & G.L. Barron). Exclusively parasitoid species have conidia that germinate to form sticky knobs that attach to passing nematodes but lack adhesive knobs on the hyphae. Each mycelial individual feeds on only one nematode. Intermediate predators have adhesive knobs both on hyphae and on germinated conidia and can act in both predatory and parasitoid modes. Most morphospecies are resolved as monophyletic, but sequences of additional gene regions are required to clarify species limits within the N. angustatus – N. geogenius group.

Phylogenetic Analyses of Septoria Species Based on the ITS and LSU-D2 Regions of Nuclear Ribosomal DNA

Mycologia ◽  
2004 ◽  
Vol 96 (3) ◽  
pp. 558 ◽  
Author(s):  
Gerard J. M. Verkley ◽  
Mieke Starink-Willemse ◽  
Arien van Iperen ◽  
Edwin C. A. Abeln
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Analyses ◽  
Nuclear Ribosomal Dna

Russula darjeelingensis, a new species from Eastern Himalaya, India

Phytotaxa ◽  
2018 ◽  
Vol 358 (1) ◽  
pp. 83 ◽  
Author(s):  
SOUMITRA PALOI ◽  
KANAD DAS ◽  
KRISHNENDU ACHARYA
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Nuclear Ribosomal Dna ◽  
Eastern Himalaya ◽  
Morphological Description ◽  
Molecular Phylogenetic ◽  
Internal Transcribed Spacer Sequences ◽  
A New Species

Russula darjeelingensis is characterized by its small sized white pileus with a tall and narrow stipe, white spore print, basidiospores with amyloid suprahilar spot and a pileipellis containing encrusted pileocystidia and absence of primordial hyphae. The combination of all these characters and molecular phylogenetic analyses of internal transcribed spacer sequences of nuclear ribosomal DNA confirmed it as a new species in genus Russula Pers., subg. Russula Romagn. emend. sect. Polychromae (Maire) Sarnari subsect. Paraintegrinae Sarnari. A comprehensive morphological description, illustrations, and comparisons with morphologically similar and phylogenetically related species are provided in the present study.

scholarly journals Plastid phylogenomics of Pleurothallidinae (Orchidaceae): Conservative plastomes, new variable markers, and comparative analyses of plastid, nuclear, and mitochondrial data

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256126
Author(s):  
Anna Victoria Silvério R. Mauad ◽  
Leila do Nascimento Vieira ◽  
Valter Antônio de Baura ◽  
Eduardo Balsanelli ◽  
Emanuel Maltempi de Souza ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Single Copy ◽  
Nuclear Ribosomal Dna ◽  
Molecular Characteristics ◽  
Lineage Sorting ◽  
Variable Regions ◽  
Mutational Hotspots ◽  
Phylogenomic Analyses

We present the first comparative plastome study of Pleurothallidinae with analyses of structural and molecular characteristics and identification of the ten most-variable regions to be incorporated in future phylogenetic studies. We sequenced complete plastomes of eight species in the subtribe and compared phylogenetic results of these to parallel analyses of their nuclear ribosomal DNA operon (26S, 18S, and 5.8S plus associated spacers) and partial mitochondrial genome sequences (29–38 genes and partial introns). These plastomes have the typical quadripartite structure for which gene content is similar to those of other orchids, with variation only in the composition of the ndh genes. The independent loss of ndh genes had an impact on which genes border the inverted repeats and thus the size of the small single-copy region, leading to variation in overall plastome length. Analyses of 68 coding sequences indicated the same pattern of codon usage as in other orchids, and 13 protein-coding genes under positive selection were detected. Also, we identified 62 polymorphic microsatellite loci and ten highly variable regions, for which we designed primers. Phylogenomic analyses showed that the top ten mutational hotspots represent well the phylogenetic relationships found with whole plastome sequences. However, strongly supported incongruence was observed among plastid, nuclear ribosomal DNA operon, and mitochondrial DNA trees, indicating possible occurrence of incomplete lineage sorting and/or introgressive hybridization. Despite the incongruence, the mtDNA tree retrieved some clades found in other analyses. These results, together with performance in recent studies, support a future role for mitochondrial markers in Pleurothallidinae phylogenetics.

Sign in / Sign up

Export Citation Format

Share Document