Subgenus Classification Research Articles

An alternative subgeneric classification of Kalanchoe (Crassulaceae subfam. Cotyledonoideae) globally: a nomenclatural and taxonomic review, with a new status for K. subg. Pubescentes

In the most recently presented global synopsis of Kalanchoe (Crassulaceae subfam. Cotyledonoideae), which was published in 2003 by Bernard Marie Descoings (1931–2018), only two sections, K. sect. Kalanchoe [geographically widespread] and K. sect. Bryophyllum [geographically naturally limited to Madagascar, but with some species and nothospecies naturalised elsewhere], were recognised in the genus. Three years later, Descoings changed his views on the infrageneric classification of Kalanchoe when, in 2006, he published the subgenus name K. subg. Calophygia for a rather disparate group of species from virtually across the entire natural geographical distribution range of the genus. In this regard, Descoings built on and expanded the kalanchooid infrageneric concept that Sijfert Hendrik Koorders (1863–1919) put forward for Kalanchoe almost 90 years earlier. Apart from recognising K. subg. Calophygia in 2006, Descoings additionally upheld the autonymic K. subg. Kalanchoe and K. subg. Bryophyllum, both of which he recognised at the rank of section in 2003. The infrageneric classification of Kalanchoe that recognises primary diversity in the genus at the rank of subgenus, rather than at that of section, is now firmly entrenched. Following on from Descoings recognising three subgenera in 2006, the subgenus classification of Kalanchoe has recently been expanded with the publication of a further four subgenus names, in 2018 (K. subg. Kitchingia), in 2020 (K. subg. Fernandesiae), in 2023 (K. subg. Alatae), and in 2024 (K. subg. Pubescentes). The most up-to-date subgenus classification of Kalanchoe is presented here, with five subgenera recognised. With the exception of the geographically widespread K. subg. Kalanchoe, the four other subgenera are naturally endemic to Madagascar.

Description of the female, nymph and larva and mitochondrial genome, and redescription of the male of Ixodes barkeri Barker, 2019 (Acari: Ixodidae), from the short-beaked echidna, Tachyglossus aculeatus, with a consideration of the most suitable subgenus for this tick

BackgroundIxodes barkeri, a tick with a distinctive ventrolateral horn-like projection on palpal segment 1, was described in 2019 from two male ticks from the Wet Tropics of Far North Queensland, Australia. However, females lie at the core of the taxonomy and subgenus classification of Ixodes; hence, we sought specimens of female ticks, successfully recovering females, plus nymphs and larvae. Mitochondrial genomes are also desirable additions to the descriptions of species of ticks particularly regarding subgenus systematics. So, we sequenced the mt genomes of I. barkeri Barker, 2019, and the possible relatives of I. barkeri that were available to us (I. australiensis Neumann, 1904, I. fecialis Warburton & Nuttall, 1909, and I. woyliei Ash et al. 2017) with a view to discovering which if any of the subgenera of Ixodes would be most suitable for I. barkeri Barker, 2019.ResultsThe female, nymph, larva and mitochondrial genome of Ixodes barkeri Barker, 2019, are described for the first time and the male of I. barkeri is redescribed in greater detail than previously. So far, I. barkeri is known only from a monotreme, the short-beaked echidna, Tachyglossus aculeatus (Shaw, 1792), from the highland rainforests of the Wet Tropics of Far North Queensland, Australia.ConclusionsOur phylogeny from entire mitochondrial genomes indicated that I. barkeri and indeed I. woyliei Ash et al., 2017, another tick that was described recently, are best placed in the subgenus Endopalpiger Schulze, 1935.Graphical

Analysis of partial sequences of the RNA-dependent RNA polymerase gene as a tool for genus and subgenus classification of coronaviruses.

The recent reclassification of the Riboviria, and the introduction of multiple new taxonomic categories including both subfamilies and subgenera for coronaviruses (family Coronaviridae, subfamily Orthocoronavirinae), represents a major shift in how official classifications are used to designate specific viral lineages. While the newly defined subgenera provide much-needed standardization for commonly cited viruses of public health importance, no method has been proposed for the assignment of subgenus based on partial sequence data, or for sequences that are divergent from the designated holotype reference genomes. Here, we describe the genetic variation of a 387 nt region of the coronavirus RNA-dependent RNA polymerase (RdRp), which is one of the most used partial sequence loci for both detection and classification of coronaviruses in molecular epidemiology. We infer Bayesian phylogenies from more than 7000 publicly available coronavirus sequences and examine clade groupings relative to all subgenus holotype sequences. Our phylogenetic analyses are largely coherent with whole-genome analyses based on designated holotype members for each subgenus. Distance measures between sequences form discrete clusters between taxa, offering logical threshold boundaries that can attribute subgenus or indicate sequences that are likely to belong to unclassified subgenera both accurately and robustly. We thus propose that partial RdRp sequence data of coronaviruses are sufficient for the attribution of subgenus-level taxonomic classifications and we supply the R package, MyCoV, which provides a method for attributing subgenus and assessing the reliability of the attribution.

Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles

ABSTRACT The prevalence of nontuberculous mycobacteria (NTM) pulmonary diseases has been increasing worldwide. NTM consist of approximately 200 species and distinguishing between them at the subspecies level is critical to treatment. In this study, we sequenced 63 NTM genomes, 27 of which were newly determined, by hybrid assembly using sequencers from Illumina and Oxford Nanopore Technologies (ONT). This analysis expanded the available genomic data to 175 NTM species and redefined their subgenus classification. We also developed a novel multi-locus sequence typing (MLST) database based on 184 genes from 7547 assemblies and an identification software, mlstverse, which can also be used for detecting other bacteria given a suitable MLST database. This method showed the highest sensitivity and specificity amongst conventional methods and demonstrated the capacity for rapid detection of NTM, 10 min of sequencing of the ONT MinION being sufficient. Application of this methodology could improve disease epidemiology and increase the cure rates of NTM diseases.

Microspore morphology of Selaginellaceae in China and its systematic significance

In this paper, we report the microspore morphology of 18 species in genus Selaginella P.Beauv. of family Selaginellaceae Willk. from China observed using scanning electron microscopy. Among these species, the morphological characteristics of 17 species have not been reported previously. The results show that the surface ornamentation of microspores of Selaginellaceae can be differentiated into nine major types including granulate, tuberculate, verrucate, verrucate-rugulate, spinate, baculate, reticulate, lamellate and cerebroid. These characteristics as taxonomic basis for subgenus classification support the view of Hieronymus (Die naturlichen pflanzenfamilien. Verlag von Wilhelm Engelmann, Leipzig, 1901) that genus Selaginella should be classified as two sub-genera Homoeophyllum and Heterophyllum.

Novel Acanthamoeba 18S rRNA gene sequence type from an environmental isolate.

The free-living amoebae, Acanthamoeba, can act as opportunistic parasites on a wide range of vertebrates and are becoming a serious threat to human health due to the resistance of their cysts to harsh environmental conditions, disinfectants, some water treatment practices, and their ubiquitous distribution. Subgenus classification based on morphology is being replaced by a classification based on the sequences of the 18S rRNA gene with a total of 18 different genotypes (T1-T18). A new environmental strain of Acanthamoeba isolated from a waste water treatment plant is presented in this study as a candidate for the description of the novel genotype T19 after phylogenetic analysis.

Cluster analysis of citrus genotypes using near-infrared spectroscopy

There are many genotypes and varieties in the citrus family. Currently, citrus classification systems have significant divergences in varieties of species, and subgenus classification as well. In this study, near-infrared spectroscopy technique was used to acquire spectral information on the surface of citrus fruits. Cluster analysis was consequently conducted to identify citrus genotypes. Results indicated that the combination of 9-point moving average smoothing and multiplicative scattering correction was optimal for preprocessing spectral data. In the spectral range of 1,180–1,220 nm, the cumulative reliability of the first two principal components were greater than 99.4%, and sweet oranges were clustered into an independent class. In 1,280–1,320 nm, systematic clustering performed better than principal component clustering, and all other sour oranges, except Goutoucheng, were clustered into a single clade. With dimensions reduction, the cumulative reliability of first five principle components in full...

A new insight into Serjania Mill. (Sapindaceae, Paullinieae) infrageneric classification: a cytogenetic approach

Serjania (Sapindaceae, Paullinieae) comprises about 230 species, and currently two infrageneric classifications have been proposed but both are difficult to apply. This work tested which infrageneric classification fitted better in relation to cytogenetic traits added to the main morphological features used by the authors of the subgenus arrangements to gain an insight into the evolutionary karyotype relationships. In order to test the relationship between karyotypes and the systematics of this genus, the karyotypes of five species of Serjania belonging to five different sections (sensu Radlkofer) were described. Known karyological information on 26 species was used to complement the results. With these data, a cluster analysis was set up to test which infrageneric classification fitted better. In addition, a principal component analysis (PCA) was performed to examine the relevance of the traits in the subgenus classification. All the karyotypes analyzed (including new as well as previous records) had 2n = 24 chromosomes, and the karyotypes were asymmetrical: submetacentric and metacentric chromosomes were common, whereas telocentric chromosomes were rare. The PCA revealed seven principal components, the first two explained 52 % of the total variation, and the last ones were related to all the karyotypic features studied. The phenogram obtained reflected a scarce fitting into both infrageneric classifications, with only 3 sections of the 12 proposed by Radlkofer and two of the six sections proposed by Acevedo-Rodriguez being represented. Finally, regarding karyotype evolution, the constancy of chromosome number and the variation in the length of the complement suggest that structural chromosome changes would have played a leading role.

Phylogenetic evidence for a new genotype of Acanthamoeba (Amoebozoa, Acanthamoebida)

Acanthamoeba are widespread free-living amoebae, able to cause infection in animals, with keratitis and granulomatous encephalitis as major diseases in humans. Recent developments in the subgenus classification are based on the determination of the nucleotide sequence of the 18S rDNA. By this mean, Acanthamoeba have been clustered into 15 sequence types or genotypes, called T1 to T15. In this study, we analysed near full 18S rDNA of an Acanthamoeba recovered from an environmental sample and various unidentified Acanthamoeba sequences retrieved from GenBank. We provided phylogenetic evidence for a new genotype, which we proposed to name T16.

ITS1 sequence variabilities correlate with 18S rDNA sequence types in the genus Acanthamoeba (Protozoa: Amoebozoa)

The subgenus classification of the ubiquitously spread and potentially pathogenic acanthamoebae still poses a great challenge. Fifteen 18S rDNA sequence types (T1-T15) have been established, but the vast majority of isolates fall into sequence type T4, and so far, there is no means to reliably differentiate within T4. In this study, the first internal transcribed spacer (ITS1), a more variable region than the 18S rRNA gene, was sequenced, and the sequences of 15 different Acanthamoeba isolates were compared to reveal if ITS1 sequence variability correlates with 18S rDNA sequence typing and if the ITS1 sequencing allows a differentiation within T4. It was shown that the variability in ITS1 is tenfold higher than in the 18S rDNA, and that ITS1 clusters correlate with the 18S rDNA clusters and thus corroborate the Acanthamoeba sequence type system. Moreover, high sequence dissimilarities and distinctive microsatellite patterns could enable a more detailed differentiation within T4.

Two new Cryptoxilos species (Hymenoptera:Braconidae:Euphorinae) from New Zealand and Fiji parasitising adult Scolytinae (Coleoptera)

Two new species of Cryptoxilos are described from the South Pacific region. A new species from Auckland, New Zealand, Cryptoxilos thorpei Shaw & Berry, is described and illustrated. This is the first described species of the genus Cryptoxilos from New Zealand. The species is associated with a scolytine bark beetle, Chaetoptelius mundulus (Broun) (Coleoptera : Scolytinae), on a dead Pittosporum tree. A second new species, Cryptoxilos beaveri Shaw & Berry, is described from Fiji, also a new locality record for the genus. The species is associated with cryphaline ambrosia beetles, Hypothenemus curtipennis and Hypothenemus dorsosignatus, in the tree Commersonia bartramia. The existing subgenus classification system is discussed in relation to character states expressed in these two new species. Neither new species can be easily assigned to a subgenus based on the existing system. Given serious problems in the consistent application of the previous subgenus system, we recommend that subgenera be abandoned and we treat subgenus Cryptoxiloides simply as a junior synonym of Cryptoxilos.

Fluorescent oligonucleotide probes for clinical and environmental detection of Acanthamoeba and the T4 18S rRNA gene sequence type.

The first genus- and subgenus-specific fluorescent oligonucleotide probes for in situ staining of Acanthamoeba are described. Sequences of these phylogeny-based probes complement the 18S rRNA and the gene encoding it (18S rDNA). The genus-specific probe (GSP) is a fluorescein-labeled 22-mer specific for Acanthamoeba as shown here by its hybridization to growing trophozoites of all 12 known Acanthamoeba 18S rDNA sequence types and by its failure to hybridize with amoebae of two other genera (Hartmannella vermiformis and Balamuthia mandrillaris), two human cell lines, and two bacteria (Pseudomonas aeruginosa and Escherichia coli). The sequence type T4-specific probe (ST4P) is a rhodamine-labeled 30-mer specific for Acanthamoeba 18S rDNA sequence type T4, as shown here in hybridization tests with trophozoites of all 12 sequence types. T4 is the subgenus group associated most closely with Acanthamoeba keratitis (AK). GSP also was tested with corneal scrapings from 17 patients with a high index of clinical suspicion of AK plus 5 patient controls. GSP stained both trophozoites and cysts, although nonspecific cyst wall autofluorescence also was observed. Results could be obtained with GSP in 1 to 2 days, and based on results from cell culture tests, the probe correctly detected the presence or absence of Acanthamoeba in 21 of 24 specimens from the 22 patients. The use of GSP with cultured trophozoites and cysts from corneal scrapings has illustrated the suitability of using fluorescent oligonucleotide probes for identification of the genus Acanthamoeba in both environmental and clinical samples. In addition, the use of ST4P with cultured amoebae has indicated the potential of oligonucleotide probes for use in subgenus classification.

Subgenus classification of Acanthamoeba by riboprinting.

Subgenus classification of Acanthamoeba remains uncertain. Twenty-three reference strains of Acanthamoeba including 18 (neo)type-strains were subjected for classification at the subgenus level by riboprinting. PCR/RFLP analysis of 18S rRNA gene (rDNA). On the dendrogram reconstructed on the basis of riboprint analyses, two type-strains (A. astronyxis and A. tubiashi) of morphological group 1 diverged early from the other strains and were quite distinct from each other. Four type-strains of morphological group 3, A. culbertsoni, A. palestinensis, A. healyi were considered taxonomically valid, but A. pustulosa was regarded as an invalid synonym of A. palestinensis. Strains of morphological group 2 were classified into 6 subgroups. Among them, A. griffini which has an intron in its 18S rDNA was the most divergent from the remaining strains. Acanthamoeba castellanii Castellani, A. quina Vil3, A. lugdunensis L3a, A. polyphaga Jones, A. triangularis SH621, and A. castellanii Ma strains belonged to a subgroup, A. castellanii complex. However, A. quina and A. lugdunensis were regarded as synonyms of A. castellanii. The Chang strain could be regarded as A. hatchetti. Acanthamoeba mauritaniensis, A. divionensis, A. paradivionensis could be considered as synonyms of A. rhysodes. Neff strain was regarded as A. polyphaga rather than as A. castellanii. It is likely that riboprinting can be applied for rapid identification of Acanthamoeba isolated from the clinical specimens and environments.