scholarly journals Phylogenetic placement of Hanseniaspora–Kloeckera species using multigene sequence analysis with taxonomic implications: descriptions of Hanseniaspora pseudoguilliermondii sp. nov. and Hanseniaspora occidentalis var. citrica var. nov.

2006 ◽  
Vol 56 (5) ◽  
pp. 1157-1165 ◽  
Author(s):  
Neza Cadez ◽  
Peter Raspor ◽  
Maudy Th. Smith
Keyword(s):  
Type Strain ◽  
Large Subunit ◽  
Elongation Factor ◽  
Sequence Divergence ◽  
Species Group ◽  
Ribosomal Gene ◽  
Internal Transcribed Spacers ◽  
Polymorphism Analysis ◽  
Protein Coding ◽  
Protein Coding Genes

Two protein-coding genes, actin and translation elongation factor-1α (EF-1α), as well as two ribosomal gene regions, D1/D2 domains of the large subunit and both internal transcribed spacers including the 5.8S gene region, were evaluated regarding their usefulness for reconstruction of phylogenetic relationships in the Hanseniaspora–Kloeckera species group. This included analyses of sequence divergence values, heterogeneity of evolutionary rates and the reliability of the inferred trees. Both protein-coding genes showed greater capacities to resolve at the strain level and between the closely related species of Hanseniaspora–Kloeckera, compared with the ribosomal gene regions. However, to obtain a fully resolved and reliable phylogenetic tree that reflected the biological relationships it was necessary to combine three congruent sequence datasets. The novel species Hanseniaspora pseudoguilliermondii sp. nov. (type strain CBS 8772T) is described as a result of the application of various molecular approaches to delimit species. Furthermore, incongruent gene genealogies of genetically divergent strains of Hanseniaspora occidentalis, as determined by amplified fragment length polymorphism analysis and DNA–DNA reassociation measurements, indicated the presence of two novel varieties, H. occidentalis var. occidentalis (type strain CBS 2592T) and H. occidentalis var. citrica var. nov. (type strain CBS 6783T), which could be distinguished by habitat preference.

scholarly journals Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

2019 ◽  
Author(s):  
Ryan Bracewell ◽  
Anita Tran ◽  
Kamalakar Chatla ◽  
Doris Bachtrog
Keyword(s):  
X Chromosome ◽  
Genome Assembly ◽  
De Novo ◽  
Pericentromeric Region ◽  
Species Group ◽  
Chromosome 15 ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Chromosome Level

ABSTRACTThe Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromere, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome ∼15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

Spegazzinia camelliae sp. nov. (Didymosphaeriaceae, Pleosprales), a new endophytic fungus from northern Thailand

Phytotaxa ◽  
2021 ◽  
Vol 483 (2) ◽  
pp. 117-128
Author(s):  
NAKARIN SUWANNARACH ◽  
JATURONG KUMLA ◽  
SAISAMORN LUMYONG
Keyword(s):  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Small Subunit ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Full Description ◽  
Translation Elongation ◽  
Spine Length ◽  
Elongation Factor 1 Alpha

A new endophytic ascomycete, described herein as Spegazzinia camelliae, was isolated from leaves of Camellia sinensis var. assamica collected from Nan Province, Thailand. This species is characterized by basauxic conidiophores and dark brown to blackish brown α and β conidia. It can be distinguished from previously described Spegazzinia species by the spine length of the α conidia and the size of the β conidia. Multi-gene phylogenetic analyses of the small subunit (SSU), large subunit (LSU) and internal transcribed spacers (ITS) of the nuclear ribosomal DNA (rDNA) and the translation elongation factor 1-alpha (tef1) genes also support S. camelliae is a distinct new species within Spegazzinia. A full description, color photographs, illustrations and a phylogenetic tree showing the position of S. camelliae are provided.

scholarly journals Fusarium incarnatum-equiseti complex from China

2019 ◽  
Vol 43 (1) ◽  
pp. 70-89 ◽  
Author(s):  
M.M. Wang ◽  
Q. Chen ◽  
Y.Z. Diao ◽  
W.J. Duan ◽  
L. Cai
Keyword(s):  
Rna Polymerase ◽  
Elongation Factor ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Ribosomal Gene ◽  
Internal Transcribed Spacers ◽  
Translation Elongation ◽  
Cultural Methods ◽  
Wide Range

The Fusarium incarnatum-equiseti species complex (FIESC) is shown to encompass 33 phylogenetic species, across a wide range of habitats/hosts around the world. Here, 77 pathogenic and endophytic FIESC strains collected from China were studied to investigate the phylogenetic relationships within FIESC, based on a polyphasic approach combining morphological characters, multi-locus phylogeny and distribution patterns. The importance of standardised cultural methods to the identification and classification of taxa in the FIESC is highlighted. Morphological features of macroconidia, including the shape, size and septum number, were considered as diagnostic characters within the FIESC. A multi-locus dataset encompassing the 5.8S nuclear ribosomal gene with the two flanking internal transcribed spacers (ITS), translation elongation factor (EF-1α), calmodulin (CAM), partial RNA polymerase largest subunit (RPB1) and partial RNA polymerase second largest subunit (RPB2), was generated to distinguish species within the FIESC. Nine novel species were identified and described. The RPB2 locus is demonstrated to be a primary barcode with high success rate in amplification, and to have the best species delimitation compared to the other four tested loci.

scholarly journals Complete Genome Sequence of Acinetobacter indicus Type Strain SGAir0564 Isolated from Tropical Air Collected in Singapore

2018 ◽  
Vol 6 (18) ◽  
pp. e00230-18 ◽  
Author(s):  
Vineeth Kodengil Vettath ◽  
Ana Carolina M. Junqueira ◽  
Akira Uchida ◽  
Rikky W. Purbojati ◽  
James N. I. Houghton ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Protein Coding ◽  
Content Type ◽  
Air Samples ◽  
Protein Coding Genes ◽  
Long Reads

ABSTRACT Acinetobacter indicus (Gammaproteobacteria) is a strict aerobic nonmotile bacterium. The strain SGAir0564 was isolated from air samples collected in Singapore. The complete genome is 3.1 Mb and was assembled using a combination of short and long reads. The genome contains 2,808 protein-coding genes, 80 tRNAs, and 21 rRNA subunits.

scholarly journals Complete Genome Sequence of Brachyspira hyodysenteriae Type Strain B-78 (ATCC 27164)

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Nandita S. Mirajkar ◽  
Timothy J. Johnson ◽  
Connie J. Gebhart
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Etiological Agent ◽  
Swine Dysentery ◽  
Protein Coding ◽  
Brachyspira Hyodysenteriae ◽  
Protein Coding Genes ◽  
Rna Genes

Reported herein is the complete genome sequence of the type strain B-78 (ATCC 27164) of Brachyspira hyodysenteriae , the etiological agent of swine dysentery. The 3.1-Mb genome consists of a 3.056-Mb chromosome and a 45-kb plasmid, with 2,617 protein-coding genes, 39 RNA genes, and 40 pseudogenes.

scholarly journals Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

2018 ◽  
Vol 19 (8) ◽  
pp. 2383 ◽  
Author(s):  
Qixiang Lu ◽  
Wenqing Ye ◽  
Ruisen Lu ◽  
Wuqin Xu ◽  
Yingxiong Qiu
Keyword(s):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Early Pleistocene ◽  
Disjunct Distribution ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Protein Coding Genes

The monocot genus Croomia (Stemonaceae) comprises three herbaceous perennial species that exhibit EA (Eastern Asian)–ENA (Eastern North American) disjunct distribution. However, due to the lack of effective genomic resources, its evolutionary history is still weakly resolved. In the present study, we conducted comparative analysis of the complete chloroplast (cp) genomes of three Croomia species and two Stemona species. These five cp genomes proved highly similar in overall size (154,407–155,261 bp), structure, gene order and content. All five cp genomes contained the same 114 unique genes consisting of 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene content, gene order, AT content and IR/SC boundary structures were almost the same among the five Stemonaceae cp genomes, except that the Stemona cp genome was found to contain an inversion in cemA and petA. The lengths of five genomes varied due to contraction/expansion of the IR/SC borders. A/T mononucleotides were the richest Simple Sequence Repeats (SSRs). A total of 46, 48, 47, 61 and 60 repeats were identified in C. japonica, C. heterosepala, C. pauciflora, S. japonica and S. mairei, respectively. A comparison of pairwise sequence divergence values across all introns and intergenic spacers revealed that the ndhF–rpl32, psbM–trnD and trnS–trnG regions are the fastest-evolving regions. These regions are therefore likely to be the best choices for molecular evolutionary and systematic studies at low taxonomic levels in Stemonaceae. Phylogenetic analyses of the complete cp genomes and 78 protein-coding genes strongly supported the monophyly of Croomia. Two Asian species were identified as sisters that likely diverged in the Early Pleistocene (1.62 Mya, 95% HPD: 1.125–2.251 Mya), whereas the divergence of C. pauciflora dated back to the Late Miocene (4.77 Mya, 95% HPD: 3.626–6.162 Mya). The availability of these cp genomes will provide valuable genetic resources for further population genetics and phylogeographic studies on Croomia.

scholarly journals Chromosome-Level Assembly of Drosophila bifasciata Reveals Important Karyotypic Transition of the X Chromosome

2020 ◽  
Vol 10 (3) ◽  
pp. 891-897 ◽  
Author(s):  
Ryan Bracewell ◽  
Anita Tran ◽  
Kamalakar Chatla ◽  
Doris Bachtrog
Keyword(s):  
X Chromosome ◽  
Genome Assembly ◽  
De Novo ◽  
Pericentromeric Region ◽  
Species Group ◽  
Chromosome 15 ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Chromosome Level

The Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes. Here we present a de novo genome assembly and annotation of D. bifasciata, a species which represents an important subgroup for which no high-quality chromosome-level genome assembly currently exists. We combined long-read sequencing (Nanopore) and Hi-C scaffolding to achieve a highly contiguous genome assembly approximately 193 Mb in size, with repetitive elements constituting 30.1% of the total length. Drosophila bifasciata harbors four large metacentric chromosomes and the small dot, and our assembly contains each chromosome in a single scaffold, including the highly repetitive pericentromeres, which were largely composed of Jockey and Gypsy transposable elements. We annotated a total of 12,821 protein-coding genes and comparisons of synteny with D. athabasca orthologs show that the large metacentric pericentromeric regions of multiple chromosomes are conserved between these species. Importantly, Muller A (X chromosome) was found to be metacentric in D. bifasciata and the pericentromeric region appears homologous to the pericentromeric region of the fused Muller A-AD (XL and XR) of pseudoobscura/affinis subgroup species. Our finding suggests a metacentric ancestral X fused to a telocentric Muller D and created the large neo-X (Muller A-AD) chromosome ∼15 MYA. We also confirm the fusion of Muller C and D in D. bifasciata and show that it likely involved a centromere-centromere fusion.

The reassignment of three ‘lost’ Taphrina species (Taphrina bullata, Taphrina insititiae and Taphrina rhizophora) supported by the divergence of nuclear and mitochondrial DNA

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 3091-3098 ◽  
Author(s):  
Jana Petrýdesová ◽  
Kamila Bacigálová ◽  
Pavol Sulo
Keyword(s):  
Vascular Plants ◽  
Type Strain ◽  
Gene Sequence ◽  
Ribosomal Subunit ◽  
Sequence Divergence ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
As Species ◽  
Morphological And Physiological Traits ◽  
26S Rrna

The ascomycetous genus Taphrina Fries originally contained more than 90 phytopathogenic microscopic dimorphic ascomycetes causing specific infections in different vascular plants. Although species have mainly been identified historically according to their host and morphological and physiological traits, they can be studied and preserved in the form of yeasts arising from germinating ascospores. Due to low DNA sequence divergence and the lack of available strains, the number of accepted Taphrina species has currently been reduced to 28. The aim of this study is the description of three previously accepted species. Taphrina bullata (type strain CCY 58-4-1 = CBS 12783), Taphrina insititiae (type strain CCY 58-5-1 = CBS 12782) and Taphrina rhizophora (type strain CCY 58-6-1 = CBS 12781), which have been omitted from a recent key. The host range, the divergence of the 26S rRNA gene sequence, internal transcribed spacers (ITS) and the mitochondrial small ribosomal subunit (rns) sequence strongly support their reassignment as species.

Candida ficus sp. nov., a novel yeast species from the gut of Apriona germari larvae

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2805-2809 ◽  
Author(s):  
Feng-Li Hui ◽  
Qiu-Hong Niu ◽  
Tao Ke ◽  
Zheng Liu
Keyword(s):  
Type Strain ◽  
Yeast Species ◽  
Large Subunit ◽  
Sequence Divergence ◽  
Central China ◽  
Rrna Gene ◽  
The Novel ◽  
Ascomycetous Yeasts ◽  
Large Subunit Rrna ◽  
Wood Boring

A novel yeast species is described based on three strains from the gut of wood-boring larvae collected in a tree trunk of Ficus carica cultivated in parks near Nanyang, central China. Phylogenetic analysis based on sequences of the D1/D2 domains of the large subunit rRNA gene showed that these strains occurred in a separate clade that was genetically distinct from all known ascomycetous yeasts. In terms of pairwise sequence divergence, the novel strains differed by 15.3 % divergence from the type strain of Pichia terricola, and by 15.8 % divergence from the type strains of Pichia exigua and Candida rugopelliculosa in the D1/D2 domains. All three are ascomycetous yeasts in the Pichia clade. Unlike P. terricola, P. exigua and C. rugopelliculosa, the novel isolates did not ferment glucose. The name Candida ficus sp. nov. is proposed to accommodate these highly divergent organisms, with STN-8T ( = CICC 1980T = CBS 12638T) as the type strain.

scholarly journals Naganishia floricola sp. nov., a novel basidiomycetous yeast species isolated from flowers of Sorbaria sorbifolia

2020 ◽  
Vol 70 (8) ◽  
pp. 4496-4501 ◽  
Author(s):  
Yu Zhou ◽  
Bi-Si Jia ◽  
Yu-Guang Zhou ◽  
Ai-Hua Li ◽  
Lu Xue
Keyword(s):  
Phylogenetic Analysis ◽  
Rna Polymerase Ii ◽  
Novel Species ◽  
Large Subunit ◽  
Elongation Factor ◽  
Sequence Divergence ◽  
Its Region ◽  
Small Subunit ◽  
Basidiomycetous Yeast ◽  
D2 Domain

Two yeast strains representing a novel species in the basidiomycetous yeast genus Naganishia were isolated from flowers of Sorbaria sorbifolia collected in Beijing Olympic Forest Park, PR China. Results of multi-gene phylogenetic analysis indicated that the two strains were closely related to the type strains of Naganishia bhutanensis (CBS 6294T) and Naganishia antarctica (CBS 7687T). However, the new isolates differed from N. bhutanensis CBS 6294T by 1.79 % sequence divergence in the D1/D2 domain (11 nt substitutions and three indels), and 2.42 % (15 nt differences and one indel) to N. antarctica CBS 7687T. In the ITS region, the new isolates showed 1.15 % divergence (7 nt substitutions and one indel) to N. bhutanensis CBS 6294T and 0.92 % divergence (5 nt substitutions and no indels) to N. antarctica CBS 7687T. A phylogenetic analysis employing the sequences of six genes (D1/D2 domain of large subunit rDNA, ITS, small subunit rDNA, two subunits of the RNA polymerase II and elongation factor-1α) indicated that the novel species belonged to the genus Naganishia and formed a well-supported clade with N. bhutanensis, N. antarctica and N. indica. Moreover, the two strains differed from their closest relatives by the ability to grow on distinct carbon and nitrogen sources and ability to grow at 30 °C. On the basis of these findings, we propose a novel species in the genus Naganishia (Filobasidiales), Naganishia floricola sp. nov. (holotype CGMCC 2.5856).

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