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Abstract Background Colocasia gigantea, Caladium bicolor and Xanthosoma sagittifolium are three worldwide famous ornamental and/or vegetable plants in the Araceae family, these species in the subfamily Aroideae are phylogenetically perplexing due to shared interspecific morphological traits and variation. Result This study, for the first time ever, assembled and analyzed complete chloroplast genomes of C. gigantea, C. bicolor and X. sagittifolium with genome sizes of 165,906 bp, 153,149 bp and 165,169 bp in length, respectively. The genomes were composed of conserved quadripartite circular structures with a total of 131 annotated genes, including 8 rRNA, 37 tRNA and 86 protein-coding genes. A comparison within Aroideae showed seven protein-coding genes (accD, ndhF, ndhK, rbcL, rpoC1, rpoC2 and matK) linked to environmental adaptation. Phylogenetic analysis confirmed a close relationship of C. gigantea with C. esculenta and S. colocasiifolia, and the C. bicolor with X. sagittifolium. Furthermore, three DNA barcodes (atpH-atpI + psaC-ndhE, atpH-atpI + trnS-trnG, atpH-atpI + psaC-ndhE + trnS-trnG) harbored highly variable regions to distinguish species in Aroideae subfamily. Conclusion These results would be beneficial for species identification, phylogenetic relationship, genetic diversity, and potential of germplasm resources in Aroideae.

Simple Summary: Toxocara vitulorum is a common parasitic nematode of cattle and buffalos, and represents a severe health threat and economic burden on both populations. Poor understanding the epidemiology, population genetics, and molecular ecology of this nematode negative affects the prevention and control of T. vitulorum, and the mitogenome can yield a foundation for studying these areas. Herein, the first whole mitogenome of T. vitulorum was sequenced and characterized with bioinformatic pipeline analyses. Comparative mitogenomics and phylogenies defined a novel sister-species relationship of T. vitulorum with the congeneric species in the Toxocaridae, and supported nad4 and nad6 genes as new genetic markers for phylogenetic and evolutionary studies of the Ascaridida species. These results should contribute to a better understanding of phylogenetic relationships of Toxocaridae species, and also provide the resource of markers for population genetics, systematics, and epidemiology of this bovine nematode. Toxocara vitulorum (Ascaridida: Nematoda) is one of the most common intestinal nematodes of cattle and buffalos and, therefore, represents a serious threat to their populations worldwide. Despite its significance in veterinary health the epidemiology, population genetics, and molecular ecology of this nematode remain poorly understood. The mitogenome can yield a foundation for studying these areas and assist in the surveillance and control of T. vitulorum. Herein, the first whole mitogenome of T. vitulorum was sequenced utilizing Illumina technology and characterized with bioinformatic pipeline analyses. The entire genome of T. vitulorum was 15,045 bp in length and contained 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). The gene arrangement (GA) of T. vitulorum was similar to those of other Toxocara species under GA3. The whole genome showed significant levels of AT and GC skew. Comparative mitogenomics including sequence identities, Ka/Ks, and sliding window analysis, indicated a purifying selection of 12 PCGs with cox1 and nad6 having the lowest and highest evolutionary rate, respectively. Whole amino acid sequence-based phylogenetic analysis supported a novel sister-species relationship of T. vitulorum with the congeneric species Toxocara canis, Toxocara cati, and Toxocara malaysiensis in the family Toxocaridae. Further, 12 (PCGs) single gene-based phylogenies suggested that nad4 and nad6 genes shared same topological trees with that of the whole genome, suggesting that these genes were suitable as novel genetic markers for phylogenetic and evolutionary studies of Ascaridida species. This complete mitogenome of T. vitulorum refined phylogenetic relationships in Toxocaridae and provided the resource of markers for population genetics, systematics, and epidemiology of this bovine nematode. [ABSTRACT FROM AUTHOR]

Darwin's finches are the most classic case of evolution. Early studies on the evolution of this species were mainly based on morphology. Until now, the mitochondrial genome of Geospiza magnirostris has been sequenced and the study explored the characteristics of the complete genome of G. magnirostris and verified the evolutionary position of it. The 13 PCGs initiated by ATN codons. The stop codons of three PCGs (ND2, COX3 and ND4) were incomplete, with only T- or TA- replacing complete form TAA or TAG. All the tRNA genes expressed a typical cloverleaf secondary structure, except for tRNASer1(AGY), whose dihydrouridine (DHU) arm was lack and instead with a simple loop. In the sequence of the control region of G. magnirostris, we found six simple repeat tandem sequences with a total length of 42 bp. Two characteristic conserved overlapping junction (ATGCTAA) and (CAAGAAAG) were observed as reported for eight selected Passeriformes birds. A special conserved overlapping junction (ATCTTACC) involved in mitochondrial transcription termination was found between tRNATyr and COX1 in G. magnirostris's control region. Four most frequently used amino acids in G. magnirostris's PCGs were Leu1 (CUN), Ile, Thr, Ala. The codon usage of G. magnirostris was relatively average, and there was no particular bias. The ratio Ka/Ks results showed that G. magnirostris receives less natural selection pressure. The phylogenetic relationships and cluster analysis of relative codon usage showed that G. magnirostris and Thraupis episcopus clustered in one branch. The phylogenetic position of G. magnirostris was consistent with the traditional taxonomic of Thraupis. The results supported the conclusion that G. magnirostris belongs to the morphological classification of the family Thraupidae. [ABSTRACT FROM AUTHOR]

Understanding how the interactions of related plant species with pollinators vary on a spatial scale provides the opportunity to establish links between macroevolutionary patterns and microevolutionary processes, as well as to approach the mechanisms underlying plant diversification. In this work, we explore the variation in pollinator assemblages of 15 species and varieties of Nierembergia (Solanaceae) across the distribution range of the genus in Argentina, in relation to variation in floral phenotype and geographic location. By field observations, morphometric measurements of flowers and comparative phylogenetic methods, pollinator assemblages and flowers of Nierembergia taxa were characterized and compared, and the association between pollinator assemblage composition, geographic location, floral morphology and phylogenetic relationships was evaluated. 13 species of oil-collecting bees were recorded as pollinators. The assemblage composition was strongly associated with geographic location, that is, Nierembergia taxa in nearby areas had greater similarity in their pollinator assemblages than geographically distant taxa. This pattern was not associated with phylogenetic relationships among taxa, except for a group of high mountain species in northwestern Argentina. On the other hand, interspecific variation was found in the floral phenotype, mainly in the corolla and the oil-producing gland size. However, Nierembergia taxa with similar floral phenotypes did not share the composition of the pollinator assemblage, as expected. In conclusion, we found a mixed macroevolutionary pattern in which some phylogenetically distant Nierembergia taxa converge geographically in the composition of pollinator assemblages, while this attribute is conserved in a phylogenetic clade. This pattern suggests that the role of pollinators in Nierembergia diversification is more complex than previously thought. [ABSTRACT FROM AUTHOR]

Lipaphis erysimi (Lipaphis erysimi erysimi and Lipaphis erysimi pseudobrassicae) group, often known as the mustard or turnip aphid, is one of the most devastating specialist aphid of Rapeseed-mustard, causing yield losses of 9 to 96%. This study was carried out with a goal of precisely identifying the dominant specialist aphid of Rapeseed-mustard and to address the issues such as genetic differentiation from different Rapeseed-mustard growing regions covering all the six zones of India. The dendrogram, Principal component analysis (PCA) and phylogenetic relationships revealed that populations of Jorhat (North Eastern India) were highly diverged. Phylogenetic relationship produced by Tamura 3-parameter with Gamma distribution (T92 + G) model using mtCOI demonstrated the presence of L. e. pseudobrassicae in all of the surveyed locations in India including Chintapalli (Andhra Pradesh) a Southern India, where it was reported for the first time. Neutrality tests viz. Tajima and Fisher test supported neutral theory of evolution. Furthermore, our findings in mapping the distribution of L. e. pseudobrassicae in various locations will pave the way for future research and the development of area-wide management tactics for L. e. pseudobrassicae in India. [ABSTRACT FROM AUTHOR]

Background: CesA and Csl gene families, which belong to the cellulose synthase gene superfamily, plays an important role in the biosynthesis of the plant cell wall. Although researchers have investigated this gene superfamily in several model plants, to date, no comprehensive analysis has been conducted in the common bean. Results: In this study, we identified 39 putative cellulose synthase genes from the common bean genome sequence. Then, we performed a bioinformatics analysis of this gene family involving sequence alignment, phylogenetic analysis, gene structure, collinearity analysis and chromosome location. We found all members possess a cellulose_synt domain. Phylogenetic analysis revealed that these cellulose synthase genes may be classified into five subfamilies, and that members in the same subfamily share conserved exon-intron distribution and motif compositions. Abundant and distinct cis-acting elements in the 2 k basepairs upstream regulatory regions indicate that the cellulose synthase gene family may plays a vital role in the growth and development of common bean. Moreover, the 39 cellulose synthase genes are distributed on 10 of the 11 chromosomes. Additionally expression analysis shows that all CesA/Csl genes selected are constitutively expressed in the pod development. Conclusions: This research reveals both the putative biochemical and physiological functions of cellulose synthase genes in common bean and implies the importance of studying non-model plants to understand the breadth and diversity of cellulose synthase genes. [ABSTRACT FROM AUTHOR]

Paeonia lactiflora Pall. is widely used in medicine, garden applications, and as a potted ornamental. Cultivated varieties of paeonifloras suitable for cut flowers are urgently needed. In this study, the pollen morphology of P. lactiflora was studied and the characters of different varieties were compared, so as to provide reference for selecting suitable parents for new hybrid varieties. We examined the pollen morphology of 15 herbaceous peony varieties using scanning electron microscopy and analyzed the external pollen morphology and genetic relationship of the varieties. The pollen grains of the studied varieties were spheroidal or subspheroidal, bilaterally symmetrical monads, circular in polar view, and circular or elliptical in equatorial view. The exine of the pollen grains was observed as being relatively smooth under the light microscope, with the area around the equatorial axis having more lumina under the scanning electron microscope. The pollen grain exine sculpture was either reticular or pit type. The pollen apertures were tricolporate, arranged longitudinally, and equally spaced. The pollen grains were of two sizes: medium and small. The differences between the varieties were mainly reflected in the exine sculpture of the pollen. The closer the genetic relationship between the 15 peony varieties, the more subtle the differences in the exine sculpture. In the same cluster group, the morphological characteristics of herbaceous peony pollen were correlated with the shapes of flower and scale buds and the texture of the petals. However, the study identified no direct correlation with the cultivar type and flower color. [ABSTRACT FROM AUTHOR]

Firmiana is a small genus within the subfamily Sterculioideae of the Malvaceae. There are nine Firmiana species distributed in South and South-west China, most of which are endangered. Due to the shortage of plastid genomes data, the phylogenetic relationships and the evolutionary history of this genus remain unclear. Therefore, the complete chloroplast genomes of F. calcarean and F. hainanensis were sequenced using high-throughput sequencing and then compared with the chloroplast genomes of other reported Firmiana species. The genome size of F. calcarean and F. hainanensis is 161,263 and 160,031 bp long, respectively, containing a total of 131 genes (including 85 protein coding genes, 37 tRNAs, 8 rRNAs, and one pseudogene). Comparative analysis revealed that the genome structure, GC content, gene content and order, as well as the RNA editing sites within the chloroplast genomes of F. calcarean and F. hainanensis were similar to previously reported Firmiana species. ML phylogenetic analysis revealed that F. danxiaensis, F. hainanensis, F. calcarean, F. simplex, and F. major form a sister group to F. colorata, F. pulcherrima, and F. kwangsiensis. The SSRs, long repeats, and 21 highly divergent regions (Pi > 0.01) identified in this study might provide potential DNA markers for further population genetics and phylogenetic studies of Firmiana. Our findings can help design new species-specific molecular markers and the general framework to further explore the evolutionary history of Firmiana and to address their conservation challenges. [ABSTRACT FROM AUTHOR]

The objective of this study was to characterize mitochondrial genome and investigate phylogenetic evolution in Tibetan chicken. In this study, four haplotypes were identified based on D-loop sequencing in Tibetan chicken (n = 40), and each representative of four haplotypes was selected for total mitochondrial genome sequencing and analyzed together with published mitochondrial genome data of red jungle fowl. Four haplotypes belonged to three previously published clades, i.e., Clade A, clade B and clade E. Based on D-loop sequencing data, the average haplotype diversity and nucleotide diversity were 0.658 ± 0.065 and 0.00442 ± 0.00094, respectively. The mitochondrial genome of Tibetan chicken is 16,785 bp in size, consisting of 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, 13 protein-coding genes and one non-coding control region (CR). Compared with the mitochondrial genome, a phylogenetic tree based on the D-loop sequence had a messy distribution, and no breed cluster pattern was observed in Tibetan chicken. The results indicate that Tibetan chicken populations in our study have relatively low nucleotide and haplotype diversity and likely share multiple maternal lineages. The D-loop sequence has limited power for the resolution of phylogenetic relationships in comparison with the complete mitochondrial genome. [ABSTRACT FROM AUTHOR]

"Saccharum complex" is a hypothetical group of species, which is supposed to be involved in the origin of modern sugarcane, and displays large genomes and complex chromosomal alterations. The utilization of restricted parents in breeding programs of modern cultivated sugarcane has resulted in a genetic blockage, which controlled its improvement because of the limited genetic diversity. The use of wild relatives is an effective way to broaden the genetic composition of cultivated sugarcane. Due to the infrequent characterization of genomes, the potential of wild relatives is diffused in improving the cultivated sugarcane. To characterize the genomes of the wild relatives, the genome size and phylogenetic relationships among eight species, including Saccharum spontaneum, Erianthus arundinaceus, E. fulvus, E. rockii, Narenga porphyrocoma, Miscanthus floridulus, Eulalia quadrinervis, and M. sinensis were evaluated based on flow cytometry, genome surveys, K-mer analysis, chloroplast genome sequencing, and whole-genome SNPs analysis. We observed highly heterozygous genomes of S. spontaneum, E. rockii, and E. arundinaceus and the highly repetitive genome of E. fulvus. The genomes of Eulalia quadrinervis, N. porphyrocoma, M. sinensis, and M. floridulus were highly complex. Phylogenetic results of the two approaches were dissimilar, however, both indicate E. fulvus displayed closer relationships to Miscanthus and Saccharum than other species of Saccharum complex. Eulalia quadrinervis was more closely related to M. floridulus than M. sinensis; E. arundinaceus differ significantly from Miscanthus, Narenga, and Saccharum, but was relatively close to Erianthus. We proved the point of E. rockii and E. fulvus should not be classified as one genus, and E. fulvus should be classified as the Saccharum genus. [ABSTRACT FROM AUTHOR]

Chili pepper is an important economic vegetable worldwide. MYB family gene members play an important role in the metabolic processes in plant growth and development. In this study, 103 pepper MYB-related members were identified and grouped into nine subfamilies according to phylogenetic relationships. Additionally, a total of 80, 20, and 37 collinear gene pairs were identified between pepper and tomato, pepper and Arabidopsis, and tomato and Arabidopsis, respectively. We performed promoter cis-element analysis and showed that CaMYB-related members may be involved in multiple biological processes such as growth and development, secondary metabolism, and circadian rhythm regulation. Expression pattern analysis indicated that CaMYB37 is significantly more enriched in fruit placenta, suggesting that this gene may be involved in capsaicin biosynthesis. Through VIGS, we confirmed that CaMYB37 is critical for the biosynthesis of capsaicin in placenta. Our subcellular localization studies revealed that CaMYB37 localized in the nucleus. On the basis of yeast one-hybrid and dual-luciferase reporter assays, we found that CaMYB37 directly binds to the promoter of capsaicin biosynthesis gene AT3 and activates its transcription, thereby regulating capsaicin biosynthesis. In summary, we systematically identified members of the CaMYB-related family, predicted their possible biological functions, and revealed that CaMYB37 is critical for the transcriptional regulation of capsaicin biosynthesis. This work provides a foundation for further studies of the CaMYB-related family in pepper growth and development. [ABSTRACT FROM AUTHOR]

The Glyptothorax species from the Middle East are taxonomically revised based on extensive geographic range and taxon sampling, tree topologies from mitochondrial COI and Cyt b and nuclear RAG2 markers (2532 bps), molecular species delimitation and genetic distance analyses of DNA sequences against morphometric and morphological characters. A majority-rule consensus based on conceptually different molecular species delimitation analyses combined with the Bayesian and maximum likelihood tree topologies considered all the name-bearing Iranian endemic clades of Glyptothorax, except for G. pallens (i.e., G. alidaeii, G. galaxias, G. hosseinpanahii, G. shapuri and G. silviae) as a single molecular entity. We also lent our years of experience to the morphology of Iranian Glyptothorax populations and tried to perceive consistent morphological differences, but without success. Therefore, based on this integrated molecular and morphological study, we treat G. alidaeii, G. galaxias, G. hosseinpanahii and G. shapuri as conspecific with G. silviae. Furthermore, our molecular and morphological results confirmed the first record of G. cous in Iranian waters. The species G. armeniacus, G. cous, G. daemon, G. kurdistanicus, G. pallens, G. silviae and G. steindachneri are considered as valid species. [ABSTRACT FROM AUTHOR]

In plants, a large multigene family encodes 14-3-3 proteins, which are commonly found in eukaryotes. They are involved in plant development and environmental stress regulation. The current study aims to identify and characterize the 14-3-3 gene family in four important legumes, viz. Cicer arietinum, Cajanus cajan, Vigna radiata and Arachis hypogaea. The 14-3-3 proteins were clustered into ε and non-ε groups based on phylogenetic analysis, which was further confirmed by gene structure analysis, and motif composition analysis. Our study suggests that segmental duplication events played a pivotal role in the evolution and expansion of this gene family. Evidence of both stress-responsive, and hormone-responsive cis-regulatory elements in the promoter region of the 14-3-3 genes points to the possibility that they might be involved in the interplay between hormone and stress signalling pathways. The expression profiling using RNA-seq data sets showed a variation in expression level in most 14-3-3 genes under multiple stress conditions, and in different developmental stages. Hence, this study affirms the participation of the 14-3-3 genes in multiple stress regulation, and in growth and development of the legumes. The results obtained from this study provide crucial information for improved understanding, and stress response analysis of the 14-3-3 gene family in C. arietinum, C. cajan, V. radiata and A. hypogaea. [ABSTRACT FROM AUTHOR]

Mitochondrial genomes (mitogenomes) are valuable resources in molecular and evolutionary studies, such as phylogeny and population genetics. The complete mitogenomes of two crocodile newts, Tylototriton broadoridgus and Tylototriton gaowangjienensis, were sequenced, assembled, and annotated for the first time using next-generation sequencing. The complete mitogenomes of T. broadoridgus and T. gaowangjienensis were 16,265 bp and 16,259 bp in lengths, which both composed of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and 1 control region. The two mitogenomes had high A + T content with positive AT-skew and negative GC-skew patterns. The ratio of non-synonymous and synonymous substitutions showed that, relatively, the ATP8 gene evolved the fastest and COI evolved the slowest among the 13 PCGs. Phylogenetic trees from BI and ML analyses resulted in identical topologies, where the Tylototriton split into two groups corresponding to two subgenera. Both T. broadoridgus and T. gaowangjienensis sequenced here belonged to the subgenus Yaotriton, and these two species shared a tentative sister group relationship. The two mitogenomes reported in this study provided valuable data for future molecular and evolutionary studies of the genus Tylotoriton and other salamanders. [ABSTRACT FROM AUTHOR]

In order to authenticate the genomic information of Barleriacristata L., B. lupulina Lindl., B. repens Nees, B. siamensis Craib, and B. strigosa Willd, cp genomes were investigated. They revealed a general structure with a total size of 151,997–152,324 bp. The genomes encoded a total of 131 genes, including 86 CDS, 37 tRNA, and 8 rRNA genes. Other details found were as follows: different numbers and types of SSRs; identical gene content, which is adjacent to the border regions, except for B. strigosa, that revealed a shorter ndhF gene sequence and lacked the ycf1 gene; slightly different genetic distance values, which can be used for species identification; three distinct gaps of nucleotide variations between the species located at the intergenic spacer regions of the LSC and CDS of the SSC; three effective molecular markers derived from divergent hotspot regions, including the ccsA-ndhD, ndhA-ndhH-rps15, and ycf1. The genetic relationships derived from the cp genome and the CDS phylogenetic trees of Barleria and the 13 genera in Acanthaceae and different families, Scrophulariaceae and Phrymaceae, showed similar results. The six Barleria species as monophyletic groups with inner and outer outgroups were found to have perfect discrimination. These results have helped to authenticate the five Barleria species and the six genera in Acanthaceae. [ABSTRACT FROM AUTHOR]

Recent molecular research has revealed the significance of hybridization and reticulate evolution in the evolution of temperate woody bamboos at both intergeneric and intrageneric levels. Although the monophyly of Fargesia s.l. is debated, species of Fargesia s.l. with the spathe-like leaf sheath syndrome form a clade as the Fargesia spathacea complex. A previous study showed varying degrees of genetic diversity and an excess of heterozygotes across the F. spathacea complex, but phylogenetic relationships within this complex remain unclear. Here, we sampled 24 populations and 72 individuals of the F. spathacea complex and three outgroups: Yushania confusa, Fargesia setosa, and Bashania fargesii. Using phylogenomic data, we generated a robust phylogeny and explored the implications of the phylogeny for previous hybridization and introgression hypotheses. The phylogenetic analyses suggested that the 72 individuals were clustered into four major clades consistent with the genetic structure but different from the statistical results of vegetative traits. Our phylogenetic and biographical evidence demonstrate that the species in the F. spathacea complex originated outside the Hengduan Mountains region and spread to heterogeneous mountain habitats in the Daba and Qinling Mountains. In addition, adaptive radiation to cold climates and reticulate evolution may have driven species diversification within the F. spathacea complex, making it difficult to classify at the population level. [ABSTRACT FROM AUTHOR]

The taxonomy of an ancient gymnosperm genus Taxus, with high value in horticulture and medicine, is perplexing because of few reliable morphological characters for diagnosing species. Here, we performed a comprehensive investigation of the evolutionary dynamics of Taxus chloroplast genomes and estimated phylogenetic relationships, divergence times, and ancestral distributions of Taxus species by comparing 18 complete chloroplast genomes. The variations across the chloroplast genome of different Taxus species indicated that remarkably varied genome variations across lineages have reshaped the genome architecture. Our well-resolved phylogeny supported that T. brevifolia Nutt. was basal lineages followed by the other North America lineages. Divergence time estimation and ancestral range reconstruction suggested that the Taxus species originated in North America in the Late Cretaceous and revealed that extant Taxus species shared a common ancestor whose ancestral distribution area was probably in North America and afterwards the earliest members expanded to Southeast Asia from where Chinese Taxus species originated. The predominant European species have more closer relationship with the Eastern Asian species and the speciation of Eurasia species arose from several dispersal and vicariance events in the Miocene. Genome-wide scanning revealed 18 positively selected genes that were involved in translation and photosynthesis system in Taxus, which might be related to the adaptive evolution of Taxus species. The availability of these complete chloroplast genomes not only enhances our understanding of the elusive phylogenetic relationships and chloroplast genome evolution such as conservation, diversity, and gene selection within Taxus genus but also provides excellent templates and genetic bases for further exploration of evolution of related lineages as well as for plant breeding and improvement. [ABSTRACT FROM AUTHOR]

Facilitates chromatin transcription (FACT) is a histone chaperone composed of SSRP1 and SPT16, which regulates both vegetative and reproductive development in plants. However, its evolutionary history and specific role in anther development remain unexplored. We conducted a comprehensive molecular evolutionary analysis of the SSRP1 and SPT16 genes across eukaryotes, revealing their redundant functions in anther development. SSRP1 and SPT16 have similar evolutionary patterns that originated before plants, animals, and fungi split. Both SSRP1 and SPT16 genes maintained single-copy numbers in animals and fungi, while in plants they were expanded. One gene duplication has occurred in poaceae for SPT16, and one gene duplication has occurred in both monocot and eudicot for SSRP1, respectively. Segmental duplication was the main mechanism for amplifying of SSRP1 and SPT16 in plants. SSRP1 and SPT16 showed similar spatial-temporal expression patterns in anthers. Both the single mutants of ssrp1 and spt16 reduced the numbers of stamens and anther lobes, and the double mutant exhibited more severe anther phenotypes, indicating their redundant functions in male fertility. Our studies provide a deeper understanding of the phylogenetic relationships of SSRP1 and SPT16 genes in eukaryotes and indicate that SSRP1 and SPT16 function in the same pathway to regulate anther lobe formation and anther cell differentiation., Competing Interests: Declaration of competing interest The authors have no conflicts of interest to declare., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The family Clausiliidae was proposed as a model for studying the diversity of breeding biology in land snails. This study assembled a nearly complete mitogenome (15,417 bp) for the clausiliid snail Euphaedusa aculus . The mitogenome includes 13 protein-coding genes (PCGs), two ribosomal RNAs, and 22 transfer RNAs, with a gene order consistent with other clausiliids. Most PCGs use ATN start codons and complete stop codons, except for atp6, nad4 , and nad5 , which start with TTG, and atp6, cox3 , and nad3 , which have incomplete stop codons. Phylogenetic analyses revealed that E. aculus is closely related to E. planostriata . This mitogenome provides a valuable molecular resource for future evolutionary research on land snails., Competing Interests: The authors report there are no competing interests to declare., (© 2024 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Haemoproteus bobricklefsi sp. nov. (Haemosporida, Haemoproteidae) was found in the dunnock Prunella modularis and represents the first blood parasite described in accentor birds of the Prunellidae. The description is based on the morphology of blood stages and includes information about a barcoding segment of the mitochondrial cytochrome b gene (lineage hDUNNO01) and the full mitochondrial genome, which can be used for identification and diagnosis of this infection. The new parasite can be readily distinguished from described species of haemoproteids parasitizing passeriform birds due to markedly variable position of nuclei in advanced and fully grown macrogametocytes. Illustrations of blood stages of the new species are given, and phylogenetic analyses based on partial mitochondrial cytochrome b gene sequences and the full mitochondrial genome identified the closely related lineages. DNA haplotype networks showed that transmission occurs in Europe and North America. This parasite was found in the dunnock in Europe and several species of the Passerellidae in North America. It is probably of Holarctic distribution, with the highest reported prevalence in the UK. The parasite distribution seems to be geographically patchy, with preference for areas of relatively cool climates. Phylogenetic analysis suggests that H. bobricklefsi sp. nov. belongs to the Parahaemoproteus subgenus and is probably transmitted by biting midges belonging to Culicoides (Ceratopogonidae). The available data on molecular occurrence indicate that this pathogen is prone to abortive development, so worth attention in regard of consequences for bird health.

Background: Orchidaceae are one of the two largest families of angiosperms; they exhibit a host of changes -- morphological, ecological and molecular -- that make them excellent candidates for evolutionary study. Such studies are most effectively performed in a phylogenetic context, which provides direction to character change. Understanding of orchid relationships began in the pre-evolutionary classification systems of the 1800's that were based solely on morphology, and now is largely based on genomic analysis. The resulting patterns have been used to update family classification and to test many evolutionary hypotheses in the family., Scope: Recent analyses with dense sampling and large numbers of nuclear loci have yielded well-supported trees that have confirmed many longstanding hypotheses and overturned others. They are being used to understand evolutionary change and diversification in the family. These include dating the origination of the family, analysis of change in ecological habit (from terrestrial to epiphytic and back again in some cases), revealing significant plastid genome change in leafless holomycotrophs, studying biogeographic patterns in various parts of the world, and interpreting patterns of fungal associations with orchids., Conclusion: Understanding of orchid relationships has progressed significantly in recent decades, especially since DNA sequence data have been available. These data have contributed to an increasingly refined classification of orchids and the pattern has facilitated many studies on character evolution and diversification in the family. Whole genome studies of the family are just beginning and promise to reveal fine-level details underlying structure and function in these plants, and, when set in a phylogenetic context, provide a much richer understanding of how the family has been so successful in diversification., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Onchocerca is an important genus of vector-borne filarial nematodes that infect both humans and animals worldwide. Many Onchocerca spp., most of medical and veterinary health relevance, are the focus of a variety of diagnostic and molecular research. However, despite the importance of these parasites, there is growing evidence of previously unexplored genetic diversity of these nematodes, particularly among wild ungulate hosts in North America. These understudied parasites prevent us from comprehending the evolutionary history of the genus Onchocerca, monitoring potential One Health threats, and improving our filarioid diagnostic capabilities. In order to fill these knowledge gaps, we identified five uncharacterized Onchocerca lineages and compared them with other well-known filarioid species using single and concatenated gene regions (i.e., nd5, cox1, 12S, 18S, 28S, hsp70, MyoHC, rbp1). Phylogenetic analyses revealed that the novel Onchocerca lineages of wild North American ungulates segregate into two clades. One clade comprised Onchocerca lineages II, IV, and V and other species found mainly in domestic animals and humans, and the second comprised Onchocerca lineages I and III and other species from a variety of hosts including cervids, bovids, and equids. The formation of two clearly separate clades supports the idea of at least two independent expansion events of ancestral Onchocerca spp. into the North American continent via the Bering land bridge. Cophylogenetic analysis shows evidence of ancestral Onchocerca spp. of Bovidae host-switching to wild Cervidae and giving rise to the novel Onchocerca spp. Lastly, pairwise analysis confirms informative molecular markers of diagnostic relevance in both mitochondrial and nuclear gene regions of filarioid nematodes. The overall information provides greater context to the genus Onchocerca and emphasizes the need to discover, characterize, and monitor neglected parasites, especially those of wildlife origin., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The Mediterranean recluse spider, Loxosceles rufescens, has been discovered for the first time inhabiting human dwellings in Bangkok, Thailand. Expeditions across 39 localities revealed five establishments with L. rufescens populations. The highest density was recorded in a storage house on Yaowarat Road, located in the heart of Bangkok's Chinatown, where 315 individuals were found, including adults, juveniles, and spiderlings. This medically significant spider's presence in such a densely populated urban area raises concerns about potential envenomation risks. Thirteen specimens of L. rufescens were extracted for DNA and sequenced for molecular phylogenetic analyses. COI and ITS2 markers were used to investigate relationships within L. rufescens and across available Loxosceles species sequences. Results indicate COI is superior for resolving species-level genetic clusters compared to ITS2. Surprisingly, L. rufescens individuals from the same house were found in significantly distant COI lineages, suggesting mtDNA may not be suitable for studying intra-specific phylogeography in this case. Species delimitation methods ABGD and ASAP demonstrated promising results for both COI and ITS2, while bPTP and GMYC tended to overestimate species numbers. ITS2 exhibited high sequence similarity in L. rufescens, suggesting potential utility as a barcoding marker for identification of this globally distributed species. Genetic distance analyses revealed a potential barcoding gap (K2P) of 8-9 % for COI and <2 % for ITS2 in Loxosceles. This study contributes valuable sequence data for the medically important genus Loxosceles and highlights the need for integrative approaches in understanding its evolution and spread. The findings have important implications for pest management strategies and public health in urban environments., Competing Interests: Declaration of competing interest The authors declare that they have no conflicts of interest related to this work., (Copyright © 2024. Published by Elsevier B.V.)

Abstract Background BBX transcription factors are a kind of zinc finger transcription factors with one or two B-box domains, which partilant in plant growth, development and response to abiotic or biotic stress. The BBX family has been identified in Arabidopsis, rice, tomato and some other model plant genomes. Results Here, 24 CaBBX genes were identified in pepper (Capsicum annuum L.), and the phylogenic analysis, structures, chromosomal location, gene expression patterns and subcellular localizations were also carried out to understand the evolution and function of CaBBX genes. All these CaBBXs were divided into five classes, and 20 of them distributed in 11 of 12 pepper chromosomes unevenly. Most duplication events occurred in subgroup I. Quantitative RT-PCR indicated that several CaBBX genes were induced by abiotic stress and hormones, some had tissue-specific expression profiles or differentially expressed at developmental stages. Most of CaBBX members were predicated to be nucleus-localized in consistent with the transient expression assay by onion inner epidermis of the three tested CaBBX members (CaBBX5, 6 and 20). Conclusion Several CaBBX genes were induced by abiotic stress and exogenous phytohormones, some expressed tissue-specific and variously at different developmental stage. The detected CaBBXs act as nucleus-localized transcription factors. Our data might be a foundation in the identification of CaBBX genes, and a further understanding of their biological function in future studies.

Serine carboxypeptidase-like (SCPL) proteins are a group of acyltransferase enzymes that have important roles in plant growth, development, and stress responses. Although SCPL proteins have been studied in many plants, the biological functions of SCPL genes in grape are still unknown. In this study, 59 putative SCPL proteins were identified from the grape genome. A bioinformatics analysis, including chromosomal locations, exon/intron structures, phylogeny, cis-elements, and conserved motifs, was performed for the gene family. The phylogenetic analysis revealed that VvSCPL proteins could be classified into three groups, with the gene motifs in each group showing high similarity levels. The number of exons in the VvSCPL genes ranged from 1 to 19, suggesting significant variations among grape SCPL genes. The expression of the VvSCPL genes, as assessed by RNA sequencing (RNA-seq) and quantitative real-time PCR, showed that most VvSCPL genes responded to drought- and waterlogging-stress treatments, which indicated their roles in abiotic stress responses. The results provide useful information for further study of SCPL genes in grape.

Zinc finger–homeodomain (ZF-HD) proteins, a family of plant-specific transcription factors, play an important role in regulating plant growth and development, as well as responses to stress. Although ZF-HDs have been investigated in several model plants, no systematic studies have been reported in apple (Malus ×domestica). In this study, 14 putative ZF-HD genes were identified in the apple genome and characterized using bioinformatics tools. All members harbored complete canonical structures of the ZF-HD motif. Phylogenetic analysis demonstrated that ZF-HD genes in the genome of apple could be classified into four subfamilies, with high intragroup similarities. Gene-structure analysis revealed that although 11 MdZHDs had only one exon, MdZHD6 and MdZHD13 had two exons and MdZHD8 had six exons, suggesting limited variation among the apple ZHD genes. The expression profiles of MdZHD genes revealed their involvement in the growth and development of different tissues. Numerous binding sites for transcription factors, such as MYB, bZIP, and AP2, were found in the promoter region of the putative MdZHD genes. Nearly all putative MdZHDs were predicted to localize in the nucleus. Finally, the expression levels of the MdZHD genes under abiotic stress were examined in apple rootstock Malus hupehensis and the results showed that the expression of 10 MdZHD genes was induced in response to three abiotic stress factors. Exceptionally, the expression of MdZHD11 was not induced in response to any of the abiotic stress treatments, MdZHD12 was only induced in response to salt stress, and MdZHD7 and MdZHD9 were induced in response to both drought and salt stress. The present results provide valuable insights into the putative physiological and biochemical functions of MdZHDs in apple.

The complete mitogenome of Polyozellus multiplex (Underw.) Murrill , was first sequenced, assembled, and annotated in the present study. The mitogenome length was 47,054 bp with a GC content of 23.35%, including 14 conserved protein-coding genes, one ribosomal protein (RPS3), two DNA polymerases (DPO), two rRNA genes (RNS and RNL), and 24 transfer RNA (tRNA) genes. Phylogenetic analysis, based on a combined mitochondrial gene dataset from 17 taxa of four orders within the class Agaricomycetes, was conducted using maximum-likelihood (ML) and Bayesian inference (BI) methods. It is revealed that P. multiplex is closely related to Thelephora aurantiotincta Corner 1968, both of them have been clustered into Thelephorales.

Machilus salicina Hance, 1885 is a species of flowering plant in the family Lauraceae and is mainly found at low altitudes in southern China. In this study, we assembled and annotated the complete chloroplast genome of M. salicina for the first time. We analyzed the general features of M. salicina and constructed a phylogenetic tree based on 15 Lauraceae species. The chloroplast genome of M. salicina had a total length of 153,943 bp. The length of a large single copy region, a small single copy region, and two inverted repeat regions were 93,689 bp, 20,070 bp, and 20,092bp, respectively. A total of 128 genes were detected, which included 84 protein-coding genes, 36 tRNAs and 8 rRNAs. The GC content of M. salicina complete chloroplast genome was 39.1%. The phylogenetic tree indicated that M. salicina was closely related to M. yunnanensis.

This study examines the gut bacterial communities of four necrophagous fly species: Lucilia illustris, L. caesar, Chrysomya megacephala, and C. pinguis. The gut bacterial communities exhibited significant variation across species, showcasing a diverse range of bacterial phyla, classes, and genera. Each species harbored a unique set of bacteria, yet there was considerable overlap in taxa among species. Species richness was comparable across all species. However, measures that account for both richness and evenness, such as the Shannon diversity index and the inverse Simpson’s diversity index, indicated significant differences between species, especially between L. illustris and C. pinguis. The functional profiles of the gut bacterial communities mainly centered on metabolic and environmental information processing functions, with no marked differences between species. While this study had limitations in data collection, it still revealed a significant correlation between the phylogenetic distances of some fly species and the distances of their gut bacterial communities. This supports the hypothesis that the gut microbiota is not random but is influenced by the host’s evolutionary history or seasons. We confirmed that an association between phylogeny and gut bacterial community structure, as determined through entanglement analysis, exists. The study focused on only five individuals from the four fly species sampled during spring and summer, which might affect the generalizability of the results. Future research would benefit from replicating this study with a larger sample size across various seasons to ensure the more widespread applicability of the findings.

Floristic regions, conventionally established using species distribution patterns, have often overlooked the phylogenetic relationships among taxa. However, how phylogenetic relationships influence the historical interconnections within and among biogeographic regions remains inadequately understood. In this research, we compiled distribution data for seed plants in Gansu, a region of significant biogeographic diversity located in northwestern China.We proposed a novel framework for floristic regions within Gansu, integrating distribution data and phylogenetic relationships of genera-level native seed plants, aiming to explore the relationship between phylogenetic relatedness, taxonomic composition, and regional phylogenetic delineation. We found that (1) phylogenetic relatedness was strongly correlated with the taxonomic composition among floras in Gansu. (2) The southeastern Gansu region showed the lowest level of spatial turnover in both phylogenetic relationships and the taxonomic composition of floristic assemblages across the Gansu region. (3) Null model analyses indicated nonrandom phylogenetic structure across the region, where most areas showed higher phylogenetic turnover than expected given the underlying taxonomic composition between sites. (4) Our results demonstrated a consistent pattern across various regionalization schemes and highlighted the preference for employing the phylogenetic dissimilarity approach in biogeographical regionalization investigations. (5) Employing the phylogenetic dissimilarity approach, we identified nine distinct floristic regions in Gansu that are categorized into two broader geographical units, namely the northwest and southeast. (6) Based on the phylogenetic graphic regions of China across this area.

A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th–19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.

With more than 2000 species, Piper is regarded as having high medicinal, cosmetic, and edible value. There also remain some taxonomic and evolutionary uncertainties about the genus. This study performed chloroplast genome sequencing of eight poorly studied Piper species and a comparative analysis with black pepper (Piper nigrum). All examined species were highly similar in gene content, with 79 protein-coding genes, 24 tRNAs, and four rRNAs. They also harbored significant structural differences: The number of SSRs ranged from 63 to 87, over 10,000 SNPs were detected, and over 1,000 indels were found. The spatial distribution of structural differences was uneven, with the IR and LSC being relatively more conserved and the SSC region highly variable. Such structural variations of the chloroplast genome can help in evaluating the phylogenetic relationships between species, deciding some hard-to-distinguish evolutionary relationships, or eliminating improper markers. The SSC region may be evolving at high speed, and some species showed a high degree of sequence variation in the SSC region, which seriously affected marker sequence detection. Conversely, CDS sequences tended to lack variation, and some CDSs can serve as ideal markers for phylogenetic reconstruction. All told, this study provides an effective strategy for selecting chloroplast markers, analyzing difficult-to-distinguish phylogenetic relationships and avoiding the taxonomic errors caused by high degree of sequence variations. [ABSTRACT FROM AUTHOR]

Background: Ferula L. is one of the largest and most taxonomically complicated genera as well as being an important medicinal plant resource in the family Apiaceae. To investigate the plastome features and phylogenetic relationships of Ferula and its neighboring genera Soranthus Ledeb., Schumannia Kuntze., and Talassia Korovin, we sequenced 14 complete plastomes of 12 species. Results: The size of the 14 complete chloroplast genomes ranged from 165,607 to 167,013 base pairs (bp) encoding 132 distinct genes (87 protein-coding, 37 tRNA, and 8 rRNA genes), and showed a typical quadripartite structure with a pair of inverted repeats (IR) regions. Based on comparative analysis, we found that the 14 plastomes were similar in codon usage, repeat sequence, simple sequence repeats (SSRs), and IR borders, and had significant collinearity. Based on our phylogenetic analyses, Soranthus, Schumannia, and Talassia should be considered synonymous with Ferula. Six highly divergent regions (rps16/trnQ-UUG, trnS-UGA/psbZ, psbH/petB, ycf1/ndhF, rpl32, and ycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection gene ccsA may be a discriminating DNA barcode for Ferula species. Conclusion: Plastids contain abundant informative sites for resolving phylogenetic relationships. Combined with previous studies, we suggest that there is still much room for improvement in the classification of Ferula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus. [ABSTRACT FROM AUTHOR]

Caucasia is a global biodiversity hotspot, rich in amphibians, including several endemic species. We sequenced samples from Parsley frogs (genus Pelodytes) across their Anatolian range to generate a barcode reference database and to assess patterns of genetic diversity in the species. Different species delimitation methods (ABGD, ASAP, GMYC and PTP) were applied to assess species diversity in the genus Pelodytes based on published and newly obtained mtDNA sequences. A majority of the species delimitation tests (ABGD, GMYC and ASAP) recovered four taxonomic units corresponding to currently accepted taxonomy (P. atlanticus, P. caucasicus, P. ibericus and P. punctatus). PTP, on the other hand, recovered only two taxonomic units, one combining the three Iberian taxa (P. atlanticus, P. ibericus, and P. punctatus), and the other, P. caucasicus. In Anatolia, individuals from Giresun and Trabzon were found to be genetically closer to each other compared to those from Rize and Artvin, based on genetic distances and phylogenetic and haplotype network analyses. [ABSTRACT FROM AUTHOR]

Background: Tetrastigma hemsleyanum is a valuable traditional Chinese medicinal plant widely distributed in the subtropical areas of China. It belongs to the Cayratieae tribe, family Vitaceae, and exhibited significant anti-tumor and anti-inflammatory activities. However, obvious differences were observed on the quality of T. hemsleyanum root from different regions, requiring the discrimination strategy for the geographical origins. Result: This study characterized five complete chloroplast (cp) genomes of T. hemsleynum samples from different regions, and conducted a comparative analysis with other representing species from family Vitaceae to reveal the structural variations, informative markers and phylogenetic relationships. The sequenced cp genomes of T. hemsleyanum exhibited a conserved quadripartite structure with full length ranging from 160,124 bp of Jiangxi Province to 160,618 bp of Zhejiang Province. We identified 112 unique genes (80 protein-coding, 28 tRNA and 4 rRNA genes) in the cp genomes of T. hemsleyanum with highly similar gene order, content and structure. The IR contraction/expansion events occurred on the junctions of ycf1, rps19 and rpl2 genes with different degrees, causing the differences of genome sizes in T. hemsleyanum and Vitaceae plants. The number of SSR markers discovered in T. hemsleyanum was 56–57, exhibiting multiple differences among the five geographic groups. Phylogenetic analysis based on conserved cp genome proteins strongly grouped the five T. hemsleyanum species into one clade, showing a sister relationship with T. planicaule. Comparative analysis of the cp genomes from T. hemsleyanum and Vitaceae revealed five highly variable spacers, including 4 intergenic regions and one protein-coding gene (ycf1). Furthermore, five mutational hotspots were observed among T. hemsleyanum cp genomes from different regions, providing data for designing DNA barcodes trnL and trnN. The combination of molecular markers of trnL and trnN clustered the T. hemsleyanum samples from different regions into four groups, thus successfully separating specimens of Sichuan and Zhejiang from other areas. Conclusion: Our study obtained the chloroplast genomes of T. hemsleyanum from different regions, and provided a potential molecular tracing tool for determining the geographical origins of T. hemsleyanum, as well as important insights into the molecular identification approach and and phylogeny in Tetrastigma genus and Vitaceae family. [ABSTRACT FROM AUTHOR]

Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen, which can cause diseases such as diarrhea, hemorrhagic enteritis, and hemolytic uremic syndrome in humans. Twelve STEC isolates were collected from beeves and feces of commercial animals in China between 2019 and 2020 for this study. In addition to the determination of serotype and Shiga toxin subtype, whole-genome sequencing (WGS) was used for determining phylogenetic relationships, antimicrobial resistance (AMR), virulence genes, and sequence type (ST) of isolates. A total of 27 AMR genes were detected, and each STEC isolate carried more than 10 AMR genes. Eight STEC isolates from ground beef and four STEC isolated from feces were screened. A total of seven serotypes were identified, and one isolate ONT:H10 was undetermined by SeroTypeFinder. Three O157:H7 strains were confirmed and the remaining five serogroups were confirmed as O26:H11, O81:H31, O105:H8, O178:H19, and O136:H12. The phylogenetic analysis showed that STEC isolates of the same serotype or ST were clustered together based on cgMLST. The comparison of the genomes of 157 STEC reference isolates worldwide with our local STEC isolates showed that STEC isolates screened in China represented various collections and could not form a separate cluster but were interspersed among the STEC reference collection, which suggested that several STEC isolates shared a common ancestor irrespective of STEC serotype isolates. cgMLST revealed that isolates of the same O serotype clustered irrespective of their H type. Further investigation is required to determine the pathogenic potential of other serotypes of STEC, particularly in regard to these rare serotypes. [ABSTRACT FROM AUTHOR]

In the present study, on the basis of the analysis of 17 microsatellite loci, 866 horses from nine breeds, including Altai, Tuvan, Kushum, Pechora, Mezen, Transbaikal, Buryat, Russian Riding, and Mongolian breeds, were examined. The studied breeds were characterized by the high level of observed heterozygosity (from 0.699 to 0.798), which did not cause concern. A total of 183 alleles were identified, including 15 private ones. In Mongolian horses of the Tes breed, rare allele D of the AHT4 locus and a previously undescribed allele were identified. Phylogenetic relationships, structure, and interaction of the gene pools of Mongolian and Russian horses were demonstrated. The polymorphism analysis of the mtDNA control region (D‑loop) in 142 horses provided identification of 16 haplotypes, of which four, found in the Mongolian, Buryat, Transbaikal, and Tuvan breeds, were previously found only in ancient horse samples from Europe and Asia. Haplotypes X2 and D3 turned out to be the most common among the studied breeds. The hypothesis that the majority of mtDNA haplotypes were not associated with the particular breed or geographic region was confirmed. Horse populations were different only in the haplotype sets and frequencies. High polymorphism of horse mtDNA is thought to be associated with multiple domestication events, as well as active horse movements across the world and their breeding history. [ABSTRACT FROM AUTHOR]

Dictyocaulus is a globally distributed genus of lungworms of domestic and wild ungulates. Dictyocaulus adults inhabit the bronchi, frequently causing subclinical and clinical disease, and that impacts animal health and production. North American bison (Bison bison) and cattle (Bos taurus) share various parasitic nematode species, particularly in areas where co-grazing occurs. The current assumption is that North American bison share the lungworm D. viviparus with cattle, but this has not been confirmed on a molecular basis. The aim of this study was to molecularly characterize Dictyocaulus lungworm isolates from North American plains bison (Bison bison bison). Fecal samples were collected from 5 wild conservation bison herds located in Iowa, North Dakota, Oklahoma, Colorado, and Montana in 2019 and 2020, and from ranched and feedlot bison from 2 herds in Oklahoma and Texas. First-stage lungworm larvae (L1) were isolated via Baermann technique. Genomic DNA was extracted from L1s of up to 3 samples per herd and followed by PCR and sequencing targeting the internal transcribed spacer 2 (ITS2) region of the nuclear ribosomal DNA and the partial cytochrome oxidase c subunit 1 (cox1) of mitochondrial DNA. Phylogenetic analyses were performed in MEGA X 10.1. Sequences of North American plains bison Dictyocaulus belong to a single, uncharacterized species, clustering in well-supported clades (100% and 100% bootstrap support for ITS2 and cox1 , respectively), differing from D. viviparus of cattle in North America and Europe, and European bison (Bison bonasus). Our results contradict previous assumptions regarding parasite identity, highlighting the need for characterization of this species through morphological and molecular methods, elucidating its biology and host range, and potential impact on host health. Further investigation into the biodiversity of Dictyocaulus species infecting bovids and cervids in North America is warranted. [Display omitted] • We molecularly characterized Dictyocalus of North American plains bison in the USA. • Dictyocaulus sp. in USA plains bison differs significantly from D. viviparus of cattle. • Dictyocaulus sp. of USA plains bison may belong to an uncharacterized species. • Future studies should integrate classical and molecular methods on adult specimens. [ABSTRACT FROM AUTHOR]

Easy and proficient identification of species or organisms is important for various users, such as conservationists, physiologists and ecologists, etc. Taxonomy is a significant branch of biological sciences to classify the different species and understand their relationships. Currently, taxonomy's existence is under crisis and its future protection is required in coming times. Majority of taxonomists are using phylogenetic approach for classifying different species. However, scientists believe that taxonomy should be integrative based on a comprehensive framework for delimiting and describing taxa through integrated information using various data and methodologies. This novel approach does not aim to replace the traditional taxonomy but stresses upon the delineation of species over naming new species. Integrative taxonomy defines the units of species diversity employing multiple approaches; like population genetics, phylogeography, ecology, comparative morphology, development and behaviour, etc. Disagreements among disciplines over the number and demarcation of species can be resolved by using molecular data explaining the evolutionary relationships among species. We present a comprehensive review to explore and identify various non-Apis bees and their relationships using integrated taxonomical approaches. We believe that the phylogenies and supportive data can collectively provide a comparative framework for understanding the evolutionary relationships among bee families. [ABSTRACT FROM AUTHOR]

Climacia McLachlan is a New World genus, and with 21 valid species is currently the second richest genus of Sisyridae. The taxonomic knowledge of this freshwater insect is controversial, with non-standardized terminologies of genitalia and wings venation, additionally, nothing was known about the phylogenetic relationships of its species. Thus, Climacia was reviewed in a phylogenetic context. Description and illustrations are provided to previously described species, and two new species are herein described, C. flinti sp. nov. and C. payaya sp. nov. Moreover, C. desordenata Monserrat, 2005 is re-validated and a neotype for C. californica Chandler, 1953 is designated. We provide standardized terminologies of genitalia and wings venation. The parsimony analysis using morphological characters recovered Climacia as a monophyletic group, and sister group to all the other genera of Sisyridae. A relationship hypothesis is proposed, suggesting a tendency of reduction in RP branches number in the forewing. Identification keys for Sisyridae genera and for all known species of Climacia are also presented. [ABSTRACT FROM AUTHOR]

Wheat streak mosaic virus (WSMV) is a serious and widespread pathogen in the wheat-producing areas in the USA while, in Europe, it has been considered a minor threat to cereal crops. In the past, WSMV was detected in wheat, triticale and maize plants in Poland by DAS-ELISA. Here, we present the biological and molecular characterisation of WSMV-Sze and WSMV-Sosn isolates collected from western and southern Poland and report their transmissibility by the widespread wheat curl mite (WCM) lineage MT-8. The performed bioassays revealed that the analysed WSMV isolates infect wheat, barley, triticale, rye, oat and maize, but they differ in the symptoms induced on the infected plants. Moreover, they infect Bromus hordeaceus Linnaeus, which is increasingly recognised as a virus reservoir. The full-length genome sequence of both isolates was obtained and compared with the others described to date. The phylogenetic analysis revealed that the Polish isolates are clustered with the earlier described type B isolates of WSMV from Europe and Iran. The recombination analysis revealed the presence of recombinant variants in WSMV population and indicated that the WSMV-Sosn might originated from the intra-species recombination of the WSMV-Sze and WSMV-Cz isolates.

Cylicocyclus spp. (Nematoda: Strongylida: Cyathostominae) are the common and important parasitic nematodes found in horses and donkeys worldwide. In this study, the complete mitochondrial genome of Cylicocyclus auriculatus Looss 1900, a representative member of this genus from the donkey in Southwest China was determined using the next-generation DNA sequencing technology. The genome was 13,851 bp in size and consisted of 36 genes including 12 protein-coding genes (atp6, cox1-3, cytb, nad1-6 and nad4L), 22 transfer RNA genes and two ribosomal RNA genes (rrnL and rrnS), as well as two non-coding regions. Phylogenetic analysis showed that C. auriculatus and Cylicocyclus insigne Boulenger 1917 were closely related, and then both grouped with other congeneric species and formed a monophyletic relationship with either species of Cyathostomum, Coronocyclus, Cyathostomum, Cylicostephanus or Cylicodontophorus, demonstrating their phylogenetic stability within Cyathostominae. These cumulative mitochondrial DNA data provide novel and useful genetic markers for molecular diagnostic, systematic and evolutionary biological studies of Cyathostominae nematodes.

The complete chloroplast and mitochondrial genome sequences of Scopelophila cataractae (Pottiaceae, Bryophyta) are determined. The chloroplast genome is 122,290 bp with 118 genes and the mitochondrial genome is 105,607 bp with 67 genes, both genomes are circular. This study showed the S. cataractae plastome contains the smallest genome size, and a functional trnPGGG gene, relative to other pottiaceous species. Phylogenetic inferences support the sister relationship of S. cataractae to all other pottiaceous accessions.

Gymnocypris dobula, classified into the highly specialized Schizothoracine fish, is endemic to Tibet, China. The complete mitochondrial DNA sequence of G. dobula was 16,728 base pairs in length and comprised 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes as well as one control region as in a typical vertebrate mitochondrial DNA gene. The ML and BI trees showed that G. dobula was most closely related to Gymnocypris scleracanthus within the highly specialized group. This mitogenome provides new molecular data for further taxonomic and phylogenetic studies of Schizothoracine fish.

Introducción. El achiote (Bixa orellana L.) es una especie valiosa debido al contenido de bixina presente en el arilo de sus semillas, pigmento que es utilizado en la industria alimentaria, cosmética y medicinal. La caracterización de germoplasma es el punto de partida para iniciar programas de fitomejoramiento y para identificar la variabilidad genética de un banco de germoplasma. Objetivo. Evaluación de las diferencias fenotípicas y genotípicas de 18 accesiones de achiote del Banco de Germoplasma de la Universidad EARTH. Materiales y métodos. El fenotipo se caracterizó por medio de descriptores generales y botánicos que detallan características morfológicas y productivas de los cultivares. El genotipo se caracterizó a partir del análisis de la región ITS2 del ADN ribosómico para establecer relaciones filogenéticas entre las accesiones y determinar las relaciones entre características fenotípicas y moleculares. También se realizaron ensayos de autopolinización para evaluar la respuesta de las accesiones a este método que condujera a la obtención de líneas puras. Resultados. Los resultados a partir del dendrograma Maximum Parsimony permitieron diferenciar 5 grupos filogenéticos, los cuales poseen una estrecha relación con el grado de espinosidad de las cápsulas. Al condensar el dendrograma a un 50% se obtuvieron 2 grupos diferenciados por la presencia o ausencia de espinas en las cápsulas, esto posiciona a esta característica como la determinante para el agrupamiento de los materiales. Las accesiones con espinas presentan mayor número de semillas por cápsula, mientras que las accesiones sin espinas poseen mayor contenido de bixina y mayor peso de semilla. Los ensayos de autopolinización revelaron una aparente autoincompatibilidad de acción tardía en algunas accesiones. Conclusión. Esta investigación generó información sobre la identificación de las accesiones, como una primera fase encaminada a la obtención de líneas homocigotas para conservar la identidad genética de las accesiones del Banco de Germoplasma de la Universidad EARTH.

The family Simuliidae belongs to Diptera whose systematic position is still strongly debated. A few mitochondrial genomes (mitogenomes) of Simuliidae and none of the subgenus Montisimulium in the genus Simulium have previously been available. Therefore, the mitogenome of Simulium jisigouense Chen, Zhang and Liu, 2008 was sequenced to better understand the diversity of mitogenomes within this family. The complete mitogenome of S. jisigouense was 16,384 bp long. It contained 37 genes including 22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs, and an A + T-rich region, which was the same as the arrangement of mitogenomes of ancestral insects. Almost all PCGs used the typical ATN as start codons, except COI used TTG. Almost all tRNAs could be folded into cloverleaf structures except the dihydrouridine (DHU) arm of tRNASer(AGN), which formed a loop. The phylogenetic analysis revealed that Simuliidae was monophyletic and was the sister group to Thaumaleidae. Subgenus Simulium was recovered as paraphyletic and needs more comprehensive sampling in future studies. Divergence time estimation showed that Simuliidae diverged from Thaumaleidae at 239.24 Ma and the subgenera of Simulium diverged from each other from 162.46 to 75.08 Ma.

The genus Cottus contains more than 60 species that are common in freshwater bodies of northern Eurasia and North America. Despite the abundance of species, this genus has been insufficiently studied in Eastern European rivers and lakes. The new taxon Cottus cyclophthalmus sp. nov. was found in the Neman/Nemunas and Venta river systems (Baltic Sea Basin). Cottus cyclophthalmus is sister and most morphologically similar to Cottus gobio. The new species has the following diagnostic characters: round, protruding (tubular) eyes near front of head; dermal papillae on top and sides of head, naked body, absence of bony prickles, full trunk canal with 32–36 pores. The description of Cottus cyclophthalmus and a new finding of Cottus microstomus improved understanding of the Eastern European biodiversity.

The trihelix genes encode plant-specific transcription factors, which play a vital role in plant morphological and developmental processes. However, information about the presence of trihelix genes in sunflower (Helianthus annuus L.) is scarce. Sunflower belongs to composite family and possesses strong drought and salt-alkali tolerance. In this study based on H. annuus genome data, we have identified and analyzed the trihelix genes with a complete description of their physical and chemical properties, phylogenetic relationships, motif composition, chromosome distribution, exon-intron structure, cis-acting elements, and chromosome collinearity. In H. annuus, 31 full-length trihelix genes were identified and categorized into six subgroups (SIP, GT1, SH4, Gδ, GT-γ, and GT2). Multiple Em for motif elicitation (MEME), used for conservative motif analysis, identified 10 distinct motifs unevenly distributed on 31 trihelix genes. In addition to that, chromosome localization analysis showed the number and distribution of these trihelix genes on 17 chromosomes of H. annuus. Transcriptional structure analysis revealed the structure of introns and exons of different gene members. Furthermore, cis-element analysis identified 19 different types of cis-elements mainly related to abiotic stress, hormones, and growth and development of plant. Results of this study manifested novel insights into phylogenetic relationships and possible functions of H. annuus trihelix genes. Moreover, these findings can assist in future studies regarding specific physiological effects of H. annuus trihelix transcription factors.