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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.

Exbucklandia longipetala and Exbucklandia populnea are two evergreen trees of the genus Exbucklandia in the family Hamamelidaceae. In this study, the complete chloroplast genomes of E. longipetala and E. populnea were sequenced, assembled, and annotated. The total lengths of the chloroplast genomes were 160,723 bp and 160,744 bp, respectively, and both had a GC content of 38.1%. The complete chloroplast genomes of these two species had typical quadripartite structures: LSC region (88,972 bp and 88,989 bp), SSC region (18,907 bp and 18,911 bp) and a pair of inverted repeats both of 26,422 bp. Both species contained 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis indicated that E. longipetala and E. populnea are sister species to each other. Our results provide useful genetic resources for further studies on the origin and evolution of Hamamelidaceae.

Vernonia volkameriifolia DC. 1836, is a woody shrub of the subfamily Vernonioideae within the family Asteraceae. The complete chloroplast genome of V. volkameriifolia spans 152,934 bp, comprising four subregions: a large single-copy region (84,035 bp), a small single-copy region (18,543 bp), and a pair of inverted repeats (25,178 bp). Within the chloroplast genome of V. volkameriifolia, 114 unique genes were identified, including 80 unique protein-encoding genes, four ribosomal RNA (rRNA) genes, and 30 transfer RNA (tRNA) genes. Phylogenetic analysis based on the complete chloroplast genome of six related taxa in the Vernonieae tribe indicates that V. volkameriifolia show closer relationships with Vernonia parishii and Strobocalyx arborea. The first chloroplast genome of V. volkameriifolia was reported in this work, contributing to the enrichment of genomic data for the genus Vernonia.

Hypecoum erectum L., a widespread species in northern Eurasia, is a valuable medicinal plant, but its chloroplast genome has not previously been reported. We determined its complete chloroplast genome using a high-throughput sequencing technique. Its total length was 169,241 bp, consisting of a large single-copy region of 93,301 bp and a small single-copy region of 17,316 bp, separated by a pair of inverted repeat regions of 29,312 bp. A total of 140 genes were annotated, including 91 protein coding genes, 41 tRNA genes, and eight rRNA genes. The phylogenetic analysis shows that H. erectum and H. zhukanum of the subfamily Hypecoideae are monophyletic with the highest support.

Abstract Background Engelhardia (Juglandaceae) is a genus of significant ecological and economic importance, prevalent in the tropics and subtropics of East Asia. Although previous efforts based on multiple molecular markers providing profound insights into species delimitation and phylogeography of Engelhardia, the maternal genome evolution and phylogeny of Engelhardia in Juglandaceae still need to be comprehensively evaluated. In this study, we sequenced plastomes from 14 samples of eight Engelhardia species and the outgroup Rhoiptelea chiliantha, and incorporated published data from 36 Juglandaceae and six outgroup species to test phylogenetic resolution. Moreover, comparative analyses of the plastomes were conducted to investigate the plastomes evolution of Engelhardia and the whole Juglandaceae family. Results The 13 Engelhardia plastomes were highly similar in genome size, gene content, and order. They exhibited a typical quadripartite structure, with lengths from 161,069 bp to 162,336 bp. Three mutation hotspot regions (TrnK-rps16, ndhF-rpl32, and ycf1) could be used as effective molecular markers for further phylogenetic analyses and species identification. Insertion and deletion (InDels) may be an important driving factor for the evolution of plastomes in Juglandoideae and Engelhardioideae. A total of ten codons were identified as the optimal codons in Juglandaceae. The mutation pressure mostly contributed to shaping codon usage. Seventy-eight protein-coding genes in Juglandaceae experienced relaxed purifying selection, only rpl22 and psaI genes showed positive selection (Ka/Ks > 1). Phylogenetic results fully supported Engelhardia as a monophyletic group including two sects and the division of Juglandaceae into three subfamilies. The Engelhardia originated in the Late Cretaceous and diversified in the Late Eocene, and Juglandaceae originated in the Early Cretaceous and differentiated in Middle Cretaceous. The phylogeny and divergence times didn’t support rapid radiation occurred in the evolution history of Engelhardia. Conclusion Our study fully supported the taxonomic treatment of at the section for Engelhardia species and three subfamilies for Juglandaceae and confirmed the power of phylogenetic resolution using plastome sequences. Moreover, our results also laid the foundation for further studying the course, tempo and mode of plastome evolution of Engelhardia and the whole Juglandaceae family.

IntroductionGelidocalamus Wen is a small yet taxonomically challenging genus within the Arundinarieae tribe. Recent molecular studies have suggested it may not be monophyletic. However, limited species sampling and insufficient molecular marker information have resulted in poorly resolved phylogenetic relationships within this genus.MethodsThe complete chloroplast genomes covering all 16 species and one variant of Gelidocalamus were sequenced, and comparative analyses were conducted. Phylogenetic analyses were performed using different molecular markers, including chloroplast data, the nuclear ribosomal DNA (nrDNA) repeats region, and 29 mitochondrial protein-coding genes. Additionally, the divergence times of Gelidocalamus were estimated to reveal their evolutionary history.ResultsThe plastomes of Gelidocalamus ranged in size from 139,500 bp to 139,801 bp, with a total of 137 identified genes, including 90 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. The size of the nrDNA repeats ranged from 5,802 bp to 5,804 bp. Phylogenetic analysis based on chloroplast data revealed that Gelidocalamus is polyphyletic, with different subclades distributed within the IV and V clades. However, phylogenetic analysis based on nrDNA and mitochondrial genes did not effectively resolve the relationships within the genus.DiscussionComparative analysis of chloroplast genomes indicated that Gelidocalamus shares a high degree of similarity with closely related genera in terms of chloroplast genome collinearity, codon usage bias, and repetitive sequences. Divergence time estimation suggests that it is a relatively young group, with all members appearing successively over the past four million years. The complex phylogenetic patterns may arise from the rapid radiation of Arundinarieae. This study provides a preliminary foundation for further in-depth research on the phylogeny, genomic structural features, and divergence times of this genus.

Abstract Aglaonema commutatum is a famous species in the Aglaonema genus, which has important ornamental and economic value. However, its chloroplast genome information and phylogenetic relationships among popular green cultivars of Aglaonema in southern China have not been reported. Herein, chloroplast genomes of one variety of A. commutatum and seven green cultivars of Aglaonema, namely, A. commutatum ‘San Remo’, ‘Kai Sa’, ‘Pattaya Beauty’, ‘Sapphire’, ‘Silver Queen’, ‘Snow White’, ‘White Gem’, and ‘White Horse Prince’, were sequenced and assembled for comparative analysis and phylogeny. These eight genomes possessed a typical quadripartite structure that consisted of a LSC region (90,799–91,486 bp), an SSC region (20,508–21,137 bp) and a pair of IR regions (26,661–26,750 bp). Each genome contained 112 different genes, comprising 79 protein-coding genes, 29 tRNA genes and 4 rRNA genes. The gene orders, GC contents, codon usage frequency, and IR/SC boundaries were highly conserved among these eight genomes. Long repeats, SSRs, SNPs and indels were analyzed among these eight genomes. Comparative analysis of 15 Aglaonema chloroplast genomes identified 7 highly variable regions, including trnH-GUG-exon1-psbA, trnS-GCU-trnG-UCC-exon1, trnY-GUA-trnE-UUC, psbC-trnS-UGA, trnF-GAA-ndhJ, ccsA-ndhD, and rps15-ycf1-D2. Reconstruction of the phylogenetic trees based on chloroplast genomes, strongly supported that Aglaonema was a sister to Anchomanes, and that the Aglaonema genus was classified into two sister clades including clade I and clade II, which corresponded to two sections, Aglaonema and Chamaecaulon, respectively. One variety and five cultivars, including A. commutatum ‘San Remo’, ‘Kai Sa’, ‘Pattaya Beauty’, ‘Silver Queen’, ‘Snow White’, and ‘White Horse Prince’, were classified into clade I; and the rest of the two cultivars, including ‘Sapphire’ and ‘White Gem’, were classified into clade II. Positive selection was observed in 34 protein-coding genes at the level of the amino acid sites among 77 chloroplast genomes of the Araceae family. Based on the highly variable regions and SSRs, 4 DNA markers were developed to differentiate the clade I and clade II in Aglaonema. In conclusion, this study provided chloroplast genomic resources for Aglaonema, which were useful for its classification and phylogeny.

Cornus hongkongensis Hemsl. 1888, native to Hong Kong, belongs to the subgenus Syncarpea within the Cornus genus of the Cornaceae family. The complete chloroplast genome of C. hongkongensis spans 156,954 bp, comprising four subregions: a large single-copy region (86,290 bp), a small single-copy region (18,394 bp), and a pair of inverted repeats (26,135 bp). Within the chloroplast genome of C. hongkongensis, we identified 113 unique genes, including 80 protein-encoding genes, four ribosomal RNA (rRNA) genes, and 30 transfer RNA (tRNA) genes. Phylogenetic analysis based on the complete chloroplast genome of 30 related taxa of the Cornus genus indicates that C. hongkongensis has not formed a monophyletic lineage. Analyses of sequence divergence found three intergenic regions including rps19-rpl22, ccsA-ndhD, and atpH-atpI, exhibiting a high degree of variations. The first chloroplast genome of C. hongkongensis was reported in this work contributes to the enrichment of genomic data for the genus Cornus.

Asplenium antiquum Makino 1929 is one of the Endangered endemic species on the Korean Peninsula. The complete chloroplast of A. antiquum is 150,690 bp in length with typical quadripartite structure comprised of large single-copy region of (83,166 bp), a small single copy region (21,932 bp), and two inverted repeat regions, each 22,796 bp in length. 114 genes were detected in the chloroplast genome of A. antiquum, comprising 84 protein-encoding genes, 26 tRNA genes, and 4 rRNA genes. The phylogenetic analysis revealed a monophyletic relationship, placing A. antiquum as a sister to voth A. Prolongatum and A. nidus, forming a subclade of Asplenium species within the Aspleniaceae family. The genomic data obtained from this study will serve as valuable information for the species’ genetic classification of Asplenium.

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

Abstract Pentatomidae includes many species of significant economic value as plant pests and biological control agents. The feeding habits of Pentatomidae are closely related to their energy metabolism and ecological adaptations. In this study, we sequenced the mitochondrial genomes of 12 Asopinae species using the next‐generation sequencing to explore the effect of dietary changes on mitochondrial genome evolution. Notably, all sequences were double‐stranded circular DNA molecules containing 37 genes and one control region. We then compared and analyzed the mitochondrial genome characteristics of phytophagous and predatory bugs. Notably, no significant difference was observed in the length of the mitochondrial genomes between the predatory and phytophagous bugs. However, the AT content was higher in the mitochondrial genomes of phytophagous bugs than that of predatory bugs. Moreover, phytophagous bugs prefer codon usage patterns ending in A/T compared with predatory bugs. The evolution rate of predatory bugs was lower than that of phytophagous bugs. The phylogenetic relationships across phytophagous bugs' lineages were largely consistent at depth nodes based on different datasets and tree‐reconstructing methods, and strongly supported the monophyly of predatory bugs. Additionally, the estimated divergence times indicated that Pentatomidae explosively radiated in the Early Cretaceous. Subsequently, the subfamily Asopinae and the genus Menida diverged in the Late Cretaceous. Our research results provide data supporting for the evolutionary patterns and classification of Pentatomidae.

Abstract Cycle‐cup oaks (Quercus section Cyclobalanopsis) are one of the principal components of forests in the tropical and subtropical climates of East and Southeast Asia. They have experienced relatively recent increases in the diversification rate, driven by changing climates and the Himalayan orogeny. However, the evolutionary history and adaptive mechanisms at the chloroplast genome level in cycle‐cup oaks remain largely unknown. Therefore, we studied this problem by conducting chloroplast genomics on 50 of the ca. 90 species. Comparative genomics and other analyses showed that Quercus section Cyclobalanopsis had a highly conserved chloroplast genome structure. Highly divergent regions, such as the ndhF and ycf1 gene regions and the petN—psbM and rpoB—trnC‐GCA intergenic spacer regions, provided potential molecular markers for subsequent analysis. The chloroplast phylogenomic tree indicated that Quercus section Cyclobalanopsis was not monophyletic, which mixed with the other two sections of subgenus Cerris. The reconstruction of ancestral aera inferred that Palaeotropics was the most likely ancestral range of Quercus section Cyclobalanopsis, and then dispersed to Sino‐Japan and Sino‐Himalaya. Positive selection analysis showed that the photosystem genes had the lowest ω values among the seven functional gene groups. And nine protein‐coding genes containing sites for positive selection: ndhA, ndhD, ndhF, ndhH, rbcL, rpl32, accD, ycf1, and ycf2. This series of analyses together revealed the phylogeny, evolutionary history, and ecological adaptation mechanism of the chloroplast genome of Quercus section Cyclobalanopsis in the long river of earth history. These chloroplast genome data provide valuable information for deep insights into phylogenetic relationships and intraspecific diversity in Quercus.

AbstractCurcuma viridiflora Roxb., a plant species of significant pharmaceutical interest, has been the subject of limited chloroplast genomic research. In this study, we present the sequencing and assembly of the C. viridiflora chloroplast genome, which is characterized by a circular chromosome spanning 162,212 base pairs and a GC content of 36.20%. The genome encodes 87 protein-coding genes (PCGs), 38 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. A phylogenetic analysis was conducted, incorporating eight related species, and based on the complete chloroplast genome and protein-coding DNA sequences of six related taxa within the genus. Outgroup species Zingiber zerumbet and Zingiber officinale were also included in the analysis. The results indicate a close relationship between C. viridiflora and Curcuma phaeocaulis, Curcuma sichuanensis, and Curcuma yunnanensis. This study provides the first chloroplast genome of C. viridiflora, thereby contributing a valuable genomic resource for future research on medicinal plants within the Curcuma genus.

Abstract Background Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations in Danxia or Karst habitats in northern Guangdong Province, China. The specialized habitat preference makes it an ideal model species for study of adaptive evolution. Meanwhile, the phylogenetic relationships of F. danxiaensis in four locations under two landforms are unclear. Therefore, we sequenced its complete chloroplast (cp.) genomes and conducted comprehensive interspecific and intrageneric plastome studies. Results The F. danxiaensis plastomes in four locations showed a typical quadripartite and circular structure that ranged from 160,832 to 161,206 bp in size, with 112 unique genes encoded. Comparative genomics showed that the plastomes of F. danxiaensis were relatively conserved with high similarity of genome organization, gene number, GC content and SSRs. While the genomes revealed higher biased codon preferences in Karst habitat than those in Danxia habitats. Eighteen and 11 divergent hotpots were identified at interspecific and intrageneric levels for species identification and further phylogenetic studies. Seven genes (clpP, accD, ccsA, ndhH, rpl20, rpoC2, and rps4) were under positive selection and may be related to adaptation. Phylogenetic analysis revealed that F. danxiaensis is sister to F. major and F. simplex. However, the interspecific relationships are not consistent with the habitat types. Conclusions The characteristics and interspecific relationship of F. danxiaensis plastomes provide new insights into further integration of geographical factors, environmental factors, and genetic variations on the genomic study of F. danxiaensis. Together, our study will contribute to the study of species identification, population genetics, and conservation biology of F. danxiaensis.

AbstractDiscogobio brachyphysallidos Huang 1989 is a Cyprinidae fish species that is endemic to the upper Pearl River. In the present study, the complete mitochondrial genome of D. brachyphysallidos collected from the Nanpanjiang River was sequenced and annotated. The mitochondrial genome encompassed 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and the control region (D-loop). The total length of the mitochondrial genome was determined to be 16,594 base pairs (bp), with a GC content of 41.7%. Phylogenetic analyses revealed that D. brachyphysallidos may be a sister to D. longibarbatus and D. macrophysallidos. These findings provide insight into the genetic information and phylogenetic relationships of D. brachyphysallidos.

Abstract Background Costaceae, commonly known as the spiral ginger family, consists of approximately 120 species distributed in the tropical regions of South America, Africa, and Southeast Asia, of which some species have important ornamental, medicinal and ecological values. Previous studies on the phylogenetic and taxonomic of Costaceae by using nuclear internal transcribed spacer (ITS) and chloroplast genome fragments data had low resolutions. Additionally, the structures, variations and molecular evolution of complete chloroplast genomes in Costaceae still remain unclear. Herein, a total of 13 complete chloroplast genomes of Costaceae including 8 newly sequenced and 5 from the NCBI GenBank database, representing all three distribution regions of this family, were comprehensively analyzed for comparative genomics and phylogenetic relationships. Result The 13 complete chloroplast genomes of Costaceae possessed typical quadripartite structures with lengths from 166,360 to 168,966 bp, comprising a large single copy (LSC, 90,802 − 92,189 bp), a small single copy (SSC, 18,363 − 20,124 bp) and a pair of inverted repeats (IRs, 27,982 − 29,203 bp). These genomes coded 111 − 113 different genes, including 79 protein-coding genes, 4 rRNA genes and 28 − 30 tRNAs genes. The gene orders, gene contents, amino acid frequencies and codon usage within Costaceae were highly conservative, but several variations in intron loss, long repeats, simple sequence repeats (SSRs) and gene expansion on the IR/SC boundaries were also found among these 13 genomes. Comparative genomics within Costaceae identified five highly divergent regions including ndhF, ycf1-D2, ccsA-ndhD, rps15-ycf1-D2 and rpl16-exon2-rpl16-exon1. Five combined DNA regions (ycf1-D2 + ndhF, ccsA-ndhD + rps15-ycf1-D2, rps15-ycf1-D2 + rpl16-exon2-rpl16-exon1, ccsA-ndhD + rpl16-exon2-rpl16-exon1, and ccsA-ndhD + rps15-ycf1-D2 + rpl16-exon2-rpl16-exon1) could be used as potential markers for future phylogenetic analyses and species identification in Costaceae. Positive selection was found in eight protein-coding genes, including cemA, clpP, ndhA, ndhF, petB, psbD, rps12 and ycf1. Maximum likelihood and Bayesian phylogenetic trees using chloroplast genome sequences consistently revealed identical tree topologies with high supports between species of Costaceae. Three clades were divided within Costaceae, including the Asian clade, Costus clade and South American clade. Tapeinochilos was a sister of Hellenia, and Parahellenia was a sister to the cluster of Tapeinochilos + Hellenia with strong support in the Asian clade. The results of molecular dating showed that the crown age of Costaceae was about 30.5 Mya (95% HPD: 14.9 − 49.3 Mya), and then started to diverge into the Costus clade and Asian clade around 23.8 Mya (95% HPD: 10.1 − 41.5 Mya). The Asian clade diverged into Hellenia and Parahellenia at approximately 10.7 Mya (95% HPD: 3.5 − 25.1 Mya). Conclusion The complete chloroplast genomes can resolve the phylogenetic relationships of Costaceae and provide new insights into genome structures, variations and evolution. The identified DNA divergent regions would be useful for species identification and phylogenetic inference in Costaceae.

Maize (Zea mays L.) is one of the most widely planted crops globally with Argentina leading world production and exportation. Santiago del Estero province, east of Tucumán and north of Córdoba encompasses eight agro-climatic zones in the Chaco Semi-arid region, agro-ecologically characterized by a wide temperature range and frequent drought periods that expose the crop to pathogens, particularly Aspergillus flavus. This pathogen is responsible for ear rot and grain contamination with mycotoxins such as aflatoxin B1 and cyclopiazonic acid. This study obtained fungal isolates from ears of maize and characterized them according to toxigenic capability and morphotype of sclerotia (S < 400 μm, associated with high levels of aflatoxins and L > 400 μm, related to variable levels of aflatoxins). In addition, those not producing aflatoxins were studied to determine phylogenetic relationships based on sequences of a segment of the CaM gene. Fifty-eight isolates were obtained in eight localities representing each agro-climatic zone, 30 of which were non-aflatoxigenic, 28 aflatoxigenic, and all producers of ciclopiazonic acid. Six isolates did not produce sclerotia, 51 were L and only one was S, the latter being a non-producer of aflatoxins. The number of sclerotia was positively correlated with the production of aflatoxin B1, while size was negatively correlated. The CaM gene sequences corroborated that the isolates belonged to the A. flavus clade and the high nucleotide similarity among them (99.4% to 100%) revealed almost zero genetic diversity in this geographic region. No significant differences were observed in the proportion of isolates between growing seasons or among agroclimatic districts. This research revealed characteristics of fungus populations in this agricultural region of north Argentina. Highlights: • Aspergillus flavus isolates from ears of maize were characterized according to toxigenic capability, morphotype of sclerotia and phylogenetic relationships. • Fifty-eight isolates were obtained, 30 non-aflatoxigenic, 28 aflatoxigenic, and all producers of ciclopiazonic acid. • Six isolates did not produce sclerotia, 51 were L and only one was S, the latter being a non-producer of aflatoxins. • All isolates belonged to the flavus clade. High nucleotide similarity among the isolates (99.4% to 100%) revealed almost zero genetic diversity in the region.

Background Despite the Caridean shrimps’ vast species richness and ecological diversity, controversies persist in their molecular classification. Within Caridea, the Pandalidae family exemplifies significant taxonomic diversity. As of June 25, 2023, GenBank hosts only nine complete mitochondrial genomes (mitogenomes) for this family. The Plesionika genus within Pandalidae is recognized as polyphyletic. To improve our understanding of the mitogenome evolution and phylogenetic relationships of Caridea, this study introduces three novel mitogenome sequences from the Plesionika genus: P. ortmanni, P. izumiae and P. lophotes. Methods The complete mitochondrial genomes of three Plesionika species were sequenced utilizing Illumina’s next-generation sequencing (NGS) technology. After assembling and annotating the mitogenomes, we conducted structural analyses to examine circular maps, sequence structure characteristics, base composition, amino acid content, and synonymous codon usage frequency. Additionally, phylogenetic analysis was performed by integrating existing mitogenome sequences of true shrimp available in GenBank. Results The complete mitogenomes of the three Plesionika species encompass 37 canonical genes, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). The lengths of these mitogenomes are as follows: 15,908 bp for P. ortmanni, 16,074 bp for P. izumiae and 15,933 bp for P. lophotes. Our analyses extended to their genomic features and structural functions, detailing base composition, gene arrangement, and codon usage. Additionally, we performed selection pressure analysis on the PCGs of all Pandalidae species available in Genbank, indicating evolutionary purification selection acted on the PCGs across Pandalidae species. Compared with the ancestral Caridea, translocation of two tRNA genes, i.e., trnP or trnT, were found in the two newly sequenced Plesionika species—P. izumiae and P. lophotes. We constructed a phylogenetic tree of Caridea using the sequences of 13 PCGs in mitogenomes. The results revealed that family Pandalidae exhibited robust monophyly, while genus Plesionika appeared to be a polyphyletic group. Conclusions Gene rearrangements within the Pandalidae family were observed for the first time. Furthermore, a significant correlation was discovered between phylogenetics of the Caridea clade and arrangement of mitochondrial genes. Our findings offer a detailed exploration of Plesionika mitogenomes, laying a crucial groundwork for subsequent investigations into genetic diversity, phylogenetic evolution, and selective breeding within this genus.

Rana hanluica: an endemic amphibian of China, is found in the hills and mountains south of the Yangtze River. In this comprehensive study, we collected 162 samples from 14 different localities to delve into the genetic diversity of Rana hanluica using mitochondrial Cytb and nuclear RAG2 as genetic markers. Our findings reveal that the Nanling Mountains, specifically regions like Jiuyi Shan, Jinggang Shan, Mang Shan, and Qiyun Shan, are genetic hotspots harboring remarkable diversity. The research results also indicate that there is gene flow among the various populations of the species, and no distinct population structure has formed, which may be due to migration. Moreover, populations in some regions, as well as the overall population, show signs of a possible genetic bottleneck, which we speculate may have been caused by climate change. However, given the exploratory nature of our study, further investigations are warranted to confirm these observations. Through phylogenetic analyses, we uncovered indications that R. hanluica might have originated within the Nanling region, dispersing along the east-west mountain ranges, with a significant contribution originating from Jiuyi Shan. The genetic distributions uncovered through our research reflect historical migratory patterns, evident in the distinct haplotypes of the RAG2 gene between the western and eastern parts of the studied area. Moreover, Heng Shan and Yangming Shan exhibited unique genetic signatures, possibly influenced by geographic isolation, which has shaped their distinct genotypes. The insights gained from this study hold profound implications for conservation efforts. By identifying regions rich in genetic diversity and crucial gene flow corridors, we can develop more effective conservation strategies. Preserving these genetically diverse areas, especially within the Nanling Mountains, is vital for maintaining the evolutionary potential of R. hanluica. In conclusion, our research has laid a solid foundation for understanding the genetic landscape of R. hanluica, shedding light on its origins, population structures, and evolutionary trajectories. This knowledge will undoubtedly guide future research endeavors and inform conservation strategies for this endemic amphibian.

Introduction“Baizhi” is a famous herbal medicine in China, and it includes four landraces named as ‘Hangbaizhi’, ‘Chuanbaizhi’, ‘Qibaizhi’, and ‘Yubaizhi’. Long-term artificial selection had caused serious degradation of these germplasms. Determining the wild progenitor of the landraces would be benefit for their breed improvements. Previous studies have suggested Angelica dahurica var. dahurica, A. dahurica var. formosana, or A. porphyrocaulis as potential candidates, but the conclusion remains uncertain, and their phylogenetic relationships are still in controversy.MethodsIn this study, the genetic variation and phylogenetic analyses of these species and four landraces were conducted on the basis of both the nrITS and plastome datasets.ResultsGenetic variation analysis showed that all 8 population of four landraces shared only one ITS haplotype, meanwhile extremely low variation occurred within 6 population at plastid genome level. Both datasets supported the four landraces might be originated from a single wild germplasm. Phylogenetic analyses with both datasets revealed largely consistent topology using Bayesian inference and Maximum likelihood methods. Samples of the four landraces and all wild A. dahurica var. dahurica formed a highly supported monophyletic clade, and then sister to the monophyly clade comprised by samples of A. porphyrocaulis, while four landraces were clustered into one clade, which further clustered with a mixed branches of A. porphyrocaulis and A. dahurica var. dahurica to form sister branches for plastid genomes. Furthermore, the monophyletic A. dahurica var. formosana was far distant from the A. dahurica var. dahurica-“Baizhi” clade in Angelica phylogeny. Such inferences was also supported by the evolutionary patterns of nrITS haplotype network and K2P genetic distances. The outcomes indicated A. dahurica var. dahurica is most likely the original plant of “Baizhi”.DiscussionConsidering of phylogenetic inference and evolutionary history, the species-level status of A. dahurica var. formosana should be accepted, and the taxonomic level and phylgenetic position of A. porphyrocaulis should be further confirmed. This study preliminarily determined the wild progenitor of “Baizhi” and clarified the phylogenetic relationships among A. dahurica var. dahurica, A. dahurica var. formosana and A. porphyrocaulis, which will provide scientific guidance for wild resources protections and improvement of “Baizhi”.

Amygdalus species have considerable ecological and economic value, however, the phylogenetic relationships among Amygdalus remain controversy. In this study, we sequenced and assembled the chloroplast (cp) genomes of five Amygdalus species: Prunus communis, P. mongolica, P. pedunculata, P. triloba, and P. mira. We then conducted comparative genomic analyses and constructed their phylogenetic relationships. The genome length ranged from 157,870 to 158,451 bp, and 131 genes were annotated (86 protein-coding genes, 37 tRNAs, and 8 rRNAs). Additionally, 49–57 simple sequence repeats were detected, with most in the large single-copy region and with AT base preferences. Comparative genomic analyses revealed high similarities in structure, order, and gene content. However, we identified four highly divergent sequences: trnR-UCU-atpA, nbdhC-trnV-UAC, ycf4-cemA, and rpl32-trnL-UAG. The phylogenomic relationship analysis suggested that the Amygdalus species were grouped together, in which P. pedunculata, P. triloba, and Prunus tangutica were categorized into a branch, P. mongolica and Prunus davidiana were clustered a branch. This study provides an improved understanding of the genetic relationships among the Amygdalus and provides a basis for the development and utilization of Amygdalus resources.

Abstract Background Date palm (Phoenix dactylifera L.) is the most widespread crop in arid and semi-arid regions and has great traditional and socioeconomic importance, with its fruit well-known for its high nutritional and health value. However, the genetic variation of date palm cultivars is often neglected. The advent of high-throughput sequencing has made possible the resequencing of whole organelle (mitochondria and chloroplast) genomes to explore the genetic diversity and phylogenetic relationships of cultivated plants with unprecedented detail. Results Whole organelle genomes of 171 Tunisian accessions (135 females and 36 males) were sequenced. Targeted bioinformatics pipelines were used to identify date palm haplotypes and genome variants, aiming to provide variant annotation and investigate patterns of evolutionary relationship. Our results revealed the existence of unique haplotypes, identified by 45 chloroplastic and 156 mitochondrial SNPs. Estimation of the effect of these SNPs on genes functions was predicted in silico. Conclusions The results of this study have important implications, in the light of ongoing environmental changes, for the conservation and sustainable use of the genetic resources of date palm cultivars in Tunisia, where monoculture threatens biodiversity leading to genetic erosion. These data will be useful for breeding and genetic improvement programs of the date palm through selective cross-breeding.

AbstractCallicarpa dichotoma (Lour.) K.Koch is a shrub species with distribution from East Asia to Southeast Asia. We assembled and annotated for the first time the complete chloroplast (cp) genome of C. dichotoma. The cp genome of C. dichotoma is 154,110 bp long with the GC content of 38.09% and consists of four subregions: a large single-copy (LSC) region of 84,915 bp, a small single-copy (SSC) region of 17,783 bp and a pair of inverted repeats (IRs) of 25,706 bp each. The cp genome of C. dichotoma encodes a total of 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic trees based on the coding sequences strongly support the position of C. dichotoma within the genus Callicarpa, confirming the previously reported monophyly of the genus.

AbstractSwertia japonica (Schult.) Makino is a traditional medicinal plant in Japan for which the chloroplast genome has not been previously reported. The complete chloroplast genome of S. japonica was determined using a high-throughput sequencing technique. The total length of the S. japonica chloroplast genome was 153,208 bp, and comprised a large single-copy region of 83,319 bp, and a small single-copy region of 18,375 bp, separated by a pair of 25,757 bp inverted repeat regions. A phylogenetic analysis, based on the obtained chloroplast genome, indicated that S. japonica is closely related to S. diluta, S. franchetiana, S. kouitchensis, S. mussotii, and S. punicea. The presented chloroplast genome will be useful for further taxonomic, pharmacological and evolutionary studies of Swertia.

Scutellaria barbata D. Don 1825 is an important medicinal plant distributed in wetlands about 2000 m above sea level and used to treat various diseases. The complete chloroplast genome of S. barbata is 152,050 bp with four subregions consisting of a large single-copy region (84,053 bp), a small single-copy region (17,517 bp), and a pair of inverted repeats (25,240 bp). In the chloroplast genome of S. barbata, 131 genes were detected, comprising 87 protein-encoding genes, eight ribosomal RNA (rRNA) genes, and 36 transfer RNA (tRNA) genes. Phylogenetic analysis based on the complete chloroplast genome and protein-coding DNA sequences of 27 related taxa of the genus (out group included Holmskioldia sanguinea and Tinnea aethiopica) indicates that S. barbata was made a clade with S. orthocalyx, and S. meehanioides was a sister to them. The first chloroplast genome of S. barbata was reported in this work, serving as a potential reference for important medicinal plants within the Scutellaria genus.

Circinaria pakistanica sp. nov. is described from the Himalayan moist temperate forests in Pakistan. The morphology, chemistry and ITS sequence support its distinction from other species of this genus. The taxon is characterised by a whitish to blackish grey thallus, greyish white epruinose apothecia, flat to slightly concave areoles, a hymenium 110–200 μm high, large ascospores (22–38 × 18–32 μm) and the absence of pycnidia; it also differs from related species in the ITS region.

Procypris mera (Lin, 1933), also known as the Chinese ink carp, currently has a second-class protection status in China. Understanding the structure and characteristics of mitochondrial genes provides essential information for resource conservation and phylogenetic studies of P. mera. Here, we sequenced the mitochondrial genomes of three P. mera (WYL1-3) from three sites and performed phylogenetic analysis. The generated three genomes were 16,587 bp in length, comprising 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and two non-coding regions (control region (CR), D-loop, and light-stranded replication start OL), with a preference for codons ending in A or C. The mitochondrial genomes of WYL2 and WYL3 were identical, differing from that of WYL1 by only five single-nucleotide polymorphisms (SNPs). All mitochondrial PCGs had Ka/Ks ratios of less than one, suggesting purifying selection. Phylogenetic tree analysis based on amino acid sequences suggested that the genus Puntioplites is sister to all other genera of the subfamily Cyprinidae of China; the genus Procypris forms a monophyletic group; and the genera Carassioides, Carassius, and Cyprinus form a monophyletic group. This study contributes to our understanding of the phylogenetic relationships in subfamily Cyprininae in China and lays the foundation for resource conservation and management of P. mera.

The taxonomic classification of the genera Salsola L., Pyankovia Akhani and Roalson, and Xylosalsola Tzvelev within Chenopodiaceae Vent. (Amaranthaceae s.l.) remains controversial, with the precise number of species within these genera still unresolved. This study presents a comparative analysis of the complete plastid genomes of S. foliosa, S. tragus, P. affinis, and X. richteri species collected in Kazakhstan. The assembled plastid genomes varied in length, ranging from 151,177 bp to 152,969 bp for X. richteri and S. tragus. These genomes contained 133 genes, of which 114 were unique, including 80 protein-coding, 30 tRNA, and 4 rRNA genes. Thirteen regions, including ndhC-ndhD, rps16-psbK, petD, rpoC2, ndhA, petB, clpP, atpF, ycf3, accD, ndhF-ndhG, matK, and rpl20-rpl22, exhibited relatively high levels of nucleotide variation. A total of 987 SSRs were detected across the four analyzed plastid genomes, primarily located in the intergenic spacer regions. Additionally, 254 repeats were identified, including 92 tandem repeats, 88 forward repeats, 100 palindromic repeats, and only one reverse repeat. A phylogenetic analysis revealed clear clustering into four clusters corresponding to the Salsoleae and Caroxyloneae tribe clades. These nucleotide sequences obtained in this study represent a valuable resource for future phylogenetic analyses within the Salsoleae s.l. tribe.

Abstract Background Sium L. (Apiaceae) is a small genus distributed primarily in Eurasia, with one species also occurring in North America. Recently, its circumscription has been revised to include 10 species, however, the phylogenetic relationships within its two inclusive clades were poorly supported or collapsed in previous studies based on nuclear ribosomal DNA ITS or cpDNA sequences. To identify molecular markers suitable for future intraspecific phylogeographic and population genetic studies, and to evaluate the efficacy of plastome in resolving the phylogenetic relationships of the genus, the complete chloroplast (cp) genomes of six Sium species were sequenced. Results The Sium plastomes exhibited typical quadripartite structures of Apiaceae and most other higher plant plastid DNAs, and were relatively conserved in their size (153,029–155,006 bp), gene arrangement and content (with 114 unique genes). A total of 61–67 SSRs, along with 12 highly divergent regions (trnQ, trnG-atpA, trnE-trnT, rps4-trnT, accD-psbI, rpl16, ycf1-ndhF, ndhF-rpl32, rpl32-trnL, ndhE-ndhG, ycf1a and ycf1b) were discovered in the plastomes. No significant IR length variation was detected showing that plastome evolution was conserved within this genus. Phylogenomic analysis based on whole chloroplast genome sequences produced a highly resolved phylogenetic tree, in which the monophyly of Sium, as well as the sister relationship of its two inclusive clades were strongly supported. Conclusions The plastome sequences could greatly improve phylogenetic resolution, and will provide genomic resources and potential markers useful for future studies of the genus.

The subfamily Gobioninae is one of the most diverse fish groups within Cyprinidae. Their taxonomy and phylogenetic relationships are not completely resolved. In this study, the complete mitochondrial genomes (mitogenome) of four Gobioninae species (Microphysogobio elongatus, Microphysogobio chinssuensis, Gobio rivuloides and Rhinogobio nasutus) were sequenced and compared. The mitogenomes of four species ranges from 16603 bp to 16609 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. Most PCGs had significant codon usage bias. Except for the tRNASer (GCT), all the nucleotide substitutions of tRNA loops higher than the stems could fold into a stable secondary structure. The nucleotide compositions of Gobioninae mitogenome were biased toward A/T, and NAD4 was subjected to low purification selection and had a faster evolution rate among 13 PCGs. Bayesian inference and maximum likelihood phylogenetic analyses showed the consistent results. The four sequenced species clustered together with their congener species. However, more samples and mitogenome data are needed to untangle the phylogenetic relationships among genera Microphysogobio, Romanogobio, Hugobio, Biwia and Platysmacheilus.

Abstract Background Pinus is the largest genus of Pinaceae and the most primitive group of modern genera. Pines have become the focus of many molecular evolution studies because of their wide use and ecological significance. However, due to the lack of complete chloroplast genome data, the evolutionary relationship and classification of pines are still controversial. With the development of new generation sequencing technology, sequence data of pines are becoming abundant. Here, we systematically analyzed and summarized the chloroplast genomes of 33 published pine species. Results Generally, pines chloroplast genome structure showed strong conservation and high similarity. The chloroplast genome length ranged from 114,082 to 121,530 bp with similar positions and arrangements of all genes, while the GC content ranged from 38.45 to 39.00%. Reverse repeats showed a shrinking evolutionary trend, with IRa/IRb length ranging from 267 to 495 bp. A total of 3,205 microsatellite sequences and 5,436 repeats were detected in the studied species chloroplasts. Additionally, two hypervariable regions were assessed, providing potential molecular markers for future phylogenetic studies and population genetics. Through the phylogenetic analysis of complete chloroplast genomes, we offered novel opinions on the genus traditional evolutionary theory and classification. Conclusion We compared and analyzed the chloroplast genomes of 33 pine species, verified the traditional evolutionary theory and classification, and reclassified some controversial species classification. This study is helpful in analyzing the evolution, genetic structure, and the development of chloroplast DNA markers in Pinus.

This study was performed to determine the phylogenetic relationships in the genus Potentilla L. and to assess the importance of the trnL/trnF intergenic spacer (IGS) region. The selection of DNA barcoding region to provide for more effective, accurate and consistent results in the analysis is one of the most important points in success of the study. For this purpose, 71 Potentilla taxa were examined based on trnL/trnF IGS sequence data of chloroplast DNA acquired from the National Center for Biotechnology Information (NCBI) and a Maximum Parsimony (MP) dendrogram was drawn. The trnL/trnF IGS region has the convenient sequence length for barcoding region, and it is also proposed the use of this region which has highly variable and parsimony informative sites. When the probabilities of substitutions from one base to another base for trnL/trnF IGS region were examined, it was assigned that the rate of transitional substitutions with 57.13% is higher than the transversional substitutions. The MP dendrogram revealed that the studies taxa were placed in six groups as Fragarioides, Reptans, Anserina, Alba, Himalayan and Argentea. Phylogenetic relationships within the Argentea clade, represented by the highest species number in this study, were observed as quite confusing compared to other clades. In order to get the most accurate results, it is necessary to determine the regions giving the best results, and then to use these regions together with as many taxa as possible. In conclusion, the using of trnL/trnF IGS sequence information that have high variable sites and grouping ability for studies taxa is strongly recommended.

The persistence of the human papillomavirus type 16 (HPV16) infection on the cervical epithelium contributes to the progression of cervical cancer. Studies have demonstrated that HPV16 genetic variants may be associated with different risks of developing cervical cancer. However, the E5 oncoprotein of HPV16, which is related to several cellular mechanisms in the initial phases of the infection and thus contributes to carcinogenesis, is still little studied. Here we investigate the HPV16 E5 oncogene variants to assess the effects of different mutations on the biological function of the E5 protein. We detected and analyzed the HPV16 E5 oncogene polymorphisms and their phylogenetic relationships. After that, we proposed a tertiary structure analysis of the protein variants, preferential codon usage, and functional activity of the HPV16 E5 protein. Intra-type variants were grouped in the lineages A and D using in silico analysis. The mutations in E5 were located in the T-cell epitopes region. We therefore analyzed the interference of the HPV16 E5 protein in the NF-kB pathway. Our results showed that the variants HPV16E5_49PE and HPV16E5_85PE did not increase the potential of the pathway activation capacity. This study provides additional knowledge about the mechanisms of dispersion of the HPV16 E5 variants, providing evidence that these variants may be relevant to the modulation of the NF-κB signaling pathway.

Four new species of freshwater crab are described from material collected in northern and southwestern Cameroon and assigned to Sudanonautes Bott, 1955. Sudanonautes cameroonensis sp. n., S. eyimba sp. n., S. ngaoundere sp. n. and S. nkam sp. n., are distinguished by characters of the carapace, thoracic sternum, chelipeds, mandibles, adult male gonopods, and in addition by genetic analyses using the mitochondrial CO1 and 16S rRNA genes. Diagnoses, illustrations, and a phylogenetic tree based on mtDNA sequences are provided, as well as a discussion of the threats and conservation of all species.

The family Chenopodiaceae Vent. (Amaranthaceae s.l.) is known for its taxonomic complexity, comprising species of significant economic and ecological importance. Despite its significance, the availability of plastid genome data for this family remains limited. This study involved assembling and characterizing the complete plastid genomes of four Caroxylon Thunb. species within the tribe Salsoleae s.l., utilizing next-generation sequencing technology. We compared genome features, nucleotide diversity, and repeat sequences and conducted a phylogenetic analysis of ten Salsoleae s.l. species. The size of the plastid genome varied among four Caroxylon species, ranging from 150,777 bp (C. nitrarium) to 151,307 bp (C. orientale). Each studied plastid genome encoded 133 genes, including 114 unique genes. This set of genes includes 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Eight divergent regions (accD, atpF, matK, ndhF-ndhG, petB, rpl20-rpl22, rpoC2, and ycf3) were identified in ten Salsoleae s.l. plastid genomes, which could be potential DNA-barcoding markers. Additionally, 1106 repeat elements were detected, consisting of 814 simple sequence repeats, 92 tandem repeats, 88 forward repeats, 111 palindromic repeats, and one reverse repeat. The phylogenetic analysis provided robust support for the relationships within Caroxylon species. These data represent a valuable resource for future phylogenetic studies within the genus.

The B-box proteins (BBXs) encode a family of zinc-finger transcription factors that regulate the plant circadian rhythm and early light morphogenesis. The double B-box (DBB) family is in the class of the B-box family, which contains two conserved B-box domains and lacks a CCT (CO, CO-like and TOC1) motif. In this study, the identity, classification, structures, conserved motifs, chromosomal location, cis elements, duplication events, and expression profiles of the PtrDBB genes were analyzed in the woody model plant Populus trichocarpa. Here, 12 PtrDBB genes (PtrDBB1–PtrDBB12) were identified and classified into four distinct groups, and all of them were homogeneously spread among eight out of seventeen poplar chromosomes. The collinearity analysis of the DBB family genes from P. trichocarpa and two other species (Z. mays and A. thaliana) indicated that segmental duplication gene pairs and high-level conservation were identified. The analysis of duplication events demonstrates an insight into the evolutionary patterns of DBB genes. The previously published transcriptome data showed that PtrDBB genes represented distinct expression patterns in various tissues at different stages. In addition, it was speculated that several PtrDBBs are involved in the responsive to drought stress, light/dark, and ABA and MeJA treatments, which implied that they might function in abiotic stress and phytohormone responses. In summary, our results contribute to the further understanding of the DBB family and provide a reference for potential functional studies of PtrDBB genes in P. trichocarpa.

IntroductionRanavirus disease, caused by viruses within the genus Ranavirus (Iridoviridae), is considered a globally emerging infectious disease linked to mass mortality events in both wild and cultured ectothermic vertebrates. Surveillance work is, however, limited in Asia hence prevalence and the dynamics of the disease remain poorly understood. To understand disease burden and the potential biotic and abiotic drivers in southern China region, we conducted a systematic surveillance of the ranavirus across Guangxi Zhuang Autonomous region (GAR).MethodsFor this, we used a multifaceted approach involving screening of amphibians and other potential hosts, diagnostic tests, phylogenetic analyses, prevalence estimation, co-infection assessments, and climatic niche analyses. Over one thousand individuals were sampled across 25 sampling sites.ResultsWe found ninety-two individuals from 18 species of ectothermic vertebrates to be infected with ranavirus. Two lineages were responsible – Rana nigromaculata ranavirus and tiger frog virus were identified using phylogenetic analysis based on the major capsid protein (MCP) gene fragment. Out of these two lineages, the presence of tiger frog virus is rare as we came across only one case. We also found evidence of a co-infection with ranavirus and Batrachochytrium dendrobatidis that can be highly detrimental to host populations; possibly the first such documentation in Asia. Our niche modelling analysis suggests that precipitation seasonality plays an important role in ranavirus prevalence in GAR – southwestern, southeastern, central and northeastern regions of GAR can be considered to be optimum habitats for ranaviruses. Infection rates in wild frog species have reached 100% in some areas, even in nature reserves.DiscussionOur research also indicates that culture facilities and pet markets are frequently infected, serving as likely vectors for the regional and global spread of ranaviruses. The knowledge generated suggests the need for systematic surveillance, stringent biosecurity measures, and control of international animal trade to prevent further transmission and protection of biodiversity and aquaculture industries across Asia.

Trollius, a genus in the Ranunculaceae family, has significant medicinal and ornamental value. It is widely distributed in China with 16 different species accepted. However, due to the lack of enough samples and information sites, the molecular phylogenetic relationships of Trollius have been unresolved till now. Here we sequenced, assembled and annotated the plastomes of 16 Trollius species to investigate their genomic characteristics, inverted repeat (IR) boundaries, sequence repeats, and hypervariable loci. In addition, the phylogenetic relationships of this genus was reconstructed based on the whole plastomes and the protein-coding sequences data-sets. The plastomes of Trollius ranged between 159,597 bp and 160,202 bp in length, and contained 113 unique genes, including 79 protein coding, 30 tRNA, and 4 rRNA. The IR boundaries were relatively conserved within the genus Trollius. 959 simple sequence repeats and 657 long sequence repeats were detected in the Trollius plastomes. We identified 12 highly polymorphic loci (Pi > 0.0115) that can be used as plastid markers in molecular identification and phylogenetic investigation of the genus. Besides, Trollius was a monophyletic group with the earliest divergence clade being Trollius lilacinus Bunge, and the remaining species were divided into two strongly-supported clades. The phylogeny in our study supported the traditional classification systems based on the color of sepal, but not the previous classification system based on the types and relative lengths of the nectaries, and distribution. The genomic resources provided in our study can be used in the taxonomy of the genus Trollius, promoting the development and utilization of this genus.

The moss family Pottiaceae is one of the most diverse lineages of the subclass Dicranidae (haplolepideous mosses). Nevertheless, the phylogenetic relationships of Pottiaceae with other Dicranidae families remain unclear. To better understand the ancestral genomic structure and evolution of the Pottiaceae, herein, we present the chloroplast and mitochondrial genomes of Ditrichum rhynchostegium (Ditrichaceae, Bryophyta). The chloroplast genome is 124,628 bp long and displayed a circular structure composed of a large single-copy region, a small single-copy region, and a pair of inverted repeats. It has 118 genes, including 82 protein-coding genes, 32 tRNA genes, and four rRNA genes. The mitochondrial genome is 106,246 bp long and has a circular structure. It contains 67 genes, including 40 protein-coding genes, 24 tRNA genes, and three rRNA genes. Phylogenetic trees based on the coding sequences strongly support the sister relationship of D. rhynchostegium with all Pottiaceous accessions, and the dextrosely arranged operculum cells suggest its affinity for Pottiaceae. This study also demonstrates that long-read sequencing employing the Nanopore platform facilitates the repair of unassembled or misassembled organellar genomic regions.

Background Short tandem repeats (STR) are highly polymorphic DNA markers utilised in forensic personal identification and human population genetic research. Guizhou Tujia is one of the ancient minority groups in southwest China, however, the population has not been studied using the highly discriminating 23 STR Huaxia Platinum Kit. Aim To obtain genetic data from 23 autosomal STRs in Guizhou Tujia and examine the population’s relationship with others. Subjects and methods A total of 480 individuals from the Guizhou Tujia population were analysed using 23 STR loci of Huaxia Platinum Kit. Allele frequencies and forensic parameters were estimated. Population genetic relationships were calculated by Nei’s genetic distances and visualised using a variety of biostatistical methods. Results A total of 264 alleles were found, with allelic frequencies ranging from 0.0010 to 0.5104. The combined discrimination power (CDP) and the combined probability of paternity (CPE) of 23 STR loci were 0.9999999999999999999999999996 and 0.999999999710422, respectively. Guizhou Tujia showed closer genetic relationships with Hubei Tujia, Guizhou Gelao, and Guizhou Miao than with other populations. Conclusion We first obtained the population genetic data of Guizhou Tujia using the 23 STR system and demonstrated its value in forensic applications. Comprehensive population comparisons showed an evident genetic affinity pattern between populations that are geographically, ethnically and linguistically related.

Abstract Background Eriocaulon is a wetland plant genus with important ecological value, and one of the famous taxonomically challenging groups among angiosperms, mainly due to the high intraspecific diversity and low interspecific variation in the morphological characters of species within this genus. In this study, 22 samples representing 15 Eriocaulon species from China, were sequenced and combined with published samples of Eriocaulon to test the phylogenetic resolution using the complete chloroplast genome. Furthermore, comparative analyses of the chloroplast genomes were performed to investigate the chloroplast genome evolution of Eriocaulon. Results The 22 Eriocaulon chloroplast genomes and the nine published samples were proved highly similar in genome size, gene content, and order. The Eriocaulon chloroplast genomes exhibited typical quadripartite structures with lengths from 150,222 bp to 151,584 bp. Comparative analyses revealed that four mutation hotspot regions (psbK-trnS, trnE-trnT, ndhF-rpl32, and ycf1) could serve as effective molecular markers for further phylogenetic analyses and species identification of Eriocaulon species. Phylogenetic results supported Eriocaulon as a monophyletic group. The identified relationships supported the taxonomic treatment of section Heterochiton and Leucantherae, and the section Heterochiton was the first divergent group. Phylogenetic tree supported Eriocaulon was divided into five clades. The divergence times indicated that all the sections diverged in the later Miocene and most of the extant Eriocaulon species diverged in the Quaternary. The phylogeny and divergence times supported rapid radiation occurred in the evolution history of Eriocaulon. Conclusion Our study mostly supported the taxonomic treatment at the section level for Eriocaulon species in China and demonstrated the power of phylogenetic resolution using whole chloroplast genome sequences. Comparative analyses of the Eriocaulon chloroplast genome developed molecular markers that can help us better identify and understand the evolutionary history of Eriocaulon species in the future.

Abstract Background The Ferula genus encompasses 180–185 species and is one of the largest genera in Apiaceae, with many of Ferula species possessing important medical value. The previous studies provided more information for Ferula, but its infrageneric relationships are still confusing. In addition, its genetic basis of its adaptive evolution remains poorly understood. Plastid genomes with more variable sites have the potential to reconstruct robust phylogeny in plants and investigate the adaptive evolution of plants. Although chloroplast genomes have been reported within the Ferula genus, few studies have been conducted using chloroplast genomes, especially for endemic species in China. Results Comprehensively comparative analyses of 22 newly sequenced and assembled plastomes indicated that these plastomes had highly conserved genome structure, gene number, codon usage, and repeats type and distribution, but varied in plastomes size, GC content, and the SC/IR boundaries. Thirteen mutation hotspot regions were detected and they would serve as the promising DNA barcodes candidates for species identification in Ferula and related genera. Phylogenomic analyses with high supports and resolutions showed that Talassia transiliensis and Soranthus meyeri were nested in the Ferula genus, and thus they should be transferred into the Ferula genus. Our phylogenies also indicated the monophyly of subgenera Sinoferula and subgenera Narthex in Ferula genus. Twelve genes with significant posterior probabilities for codon sites were identified in the positively selective analysis, and their function may relate to the photosystem II, ATP subunit, and NADH dehydrogenase. Most of them might play an important role to help Ferula species adapt to high-temperatures, strong-light, and drought habitats. Conclusion Plastome data is powerful and efficient to improve the support and resolution of the complicated Ferula phylogeny. Twelve genes with significant posterior probabilities for codon sites were helpful for Ferula to adapt to the harsh environment. Overall, our study supplies a new perspective for comprehending the phylogeny and evolution of Ferula.

Mitochondrial genome (mitogenome) is a frequently-used tool for phylogenetic and evolutionary studies among metazoans, however, it was still poorly represented in some invertebrate groups, including holothurians. Apodida is one of the most ancient orders of Holothuroidea, with unique characteristics in lacking tube feet and the respiratory tree. Here, we sequenced six mitogenomes from the holothurian order Apodida (Synaptidae and Chiridotidae) and compared them with other available holothurian mitogenomes. The apodan mitogenomes present positive GC skews and negative AT skews, a pattern diametrically opposite to that found in the mitogenomes of other holothurians. The amino acid genetic distances of the 13 protein-coding genes (PCGs) were the highest between Apodida and other holothurians. The mitochondrial gene orders within Apodida were extensively rearranged at the species level, and also were unique from the arrangement patterns of other holothurians. Phylogenetic relationships based on two different criteria: (i) nucleotides sequences with all codon positions (PCG123) and (ii) Neutral Transitions Excluded model (NTE) confirmed the monophyly and basal position of the order Apodida with a long branch. The NTE phylogeny generated a low variation of branch length, but it did not ameliorate the long branch length of Apodida. The divergence time estimation suggested that the Apodida originated in the Middle Carboniferous, implying that they survived the extinction event that occurred in the boundary of the Permian and Triassic. The NTE dataset revealed younger age than that generated by PCG123 dataset. Apodida is accompanied by a faster evolutionary rate than other holothurians (0.0069 vs 0.0043 subs/s/my). The absence of tube feet and the respiratory tree may play an important role in the dramatic evolutionary changes of apodan mitogenomes.

Taxodium “Zhongshanshan” are a group of intraspecific Taxodium hybrids with superparental dominance and high ecological and economic value in southern China. Identifying the parentage of hybrids, especially the male parent, is critically important for genetic studies. However, the large nuclear genomes of members of the genus Taxodium pose a major challenge for the development of molecular markers. Here, we developed novel molecular markers by conducting a comparative analysis of the chloroplast genomes of four artificial Taxodium hybrids and their parents. The lengths of the whole chloroplast genome ranged from 131,942 to 132,128 bp, and the total guanine (GC) content of the chloroplast genomes ranged from 34.6% to 35.81%. A total of 120 unique genes were identified, including 83 protein-coding genes, 33 transfer RNAs, and four ribosomal RNAs. There were 69‐71 simple sequence repeats were detected in the four hybrids. Phylogenetic analysis revealed that these hybrids clustered with their paternal parents. Similar findings were obtained by analysis of the GC content of protein-coding genes. Molecular markers were developed using the highly variable regions of the chloroplast genomes, and polymerase chain reaction (PCR) assays revealed that these markers were effective for identifying the male parents of these hybrids. Our findings indicate for the first time that the chloroplast genomes of Taxodium are paternally inherited. Generally, these molecular markers could facilitate breeding and genetic studies of Taxodium.

We sequenced and analyzed the complete mitochondrial genome of Lentipes ikeae and explored the phylogenetic relationships among Sicydiinae based on mitochondrial genome sequences. The complete mitochondrial genome sequence of L. ikeae was determined using the Illumina HiSeq X Ten sequencing platform, and the gene structural characteristics and base composition were analyzed. Based on the mitochondrial genome sequences of 28 Sicydiinae species published in GenBank and mitochondrial protein-coding genes (PCGs), Acanthogobius flavimanus (Gobionellinae) was selected as an outgroup to construct phylogenetic trees of Sicydiinae using the maximum likelihood and Bayesian inference methods. The mitochondrial genome of L. ikeae (GenBank number: OP764680) has a total length of 16,498 bp and encodes 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes, and a D-loop (control) region. Gene rearrangement is not observed. The mitochondrial genome of L. ikeae exhibits an AT preference, with AT skew > 0 and GC skew < 0 across the entire genome. The phylogenetic relationships of Sicydiinae based on 13 mitochondrial PCG sequences are Sicydium + (Stiphodon + (Sicyopus + Lentipes)) + Sicyopterus, indicating that Sicydium, Sicyopterus, Lentipes, and Stiphodon are all monophyletic groups.

Astroviruses (AstVs) are small RNA viruses characterized by a high mutation rate, the ability to recombine, and interspecies transmission, which allows them to infect a multitude of hosts including humans, companion animals, and farmed animals as well as wildlife. AstVs are stable in the environment, and their transmission is usually through the fecal–oral route or via contaminated water and food. Although direct zoonotic transmission was not confirmed, interspecies transmission events have occurred or have been indicated to occur in the past between wild and domestic animals and humans. They cause large economic losses, mainly in the poultry sector, due to gastroenteritis and mortality. In young children, they are the second most common cause of diarrhea. This study involved 166 intestine samples and pools of spleen, lymph node, and kidney samples collected from 352 wild animals, 52 pigs, and 31 companion animals. Astroviruses were detected in the intestine samples and were separately detected in pools of tissue samples prepared for individual animals using a heminested RT-PCR protocol. Amplicons were subjected to Sanger sequencing, and a phylogenetic analysis of 320 nt RNA-dependent RNA polymerase (RdRp) fragments referring to known nt sequences of astroviruses was performed. Astroviral RNA was detected in the intestine samples and/or tissue pools of red foxes (nine positive intestines and six positive tissue pools), rats (two positive intestines and three positive tissue pools), a cat (one AstV detected in an intestine sample), pigs (eight positive tissue pools), and wild boars (two positive pools of spleens, kidneys, and lymph nodes). No astroviral RNA was detected in wild mustelids, dogs, or other small wild animals including rodents. A phylogenetic analysis revealed that the astroviruses detected during this study were mostly host-specific, such as porcine, canine, and rat astroviruses that were highly homologous to the sequences of reference strains. In one of two wild boars, an AstV distinct to porcine species was found with the highest nt identity to Avastroviruses, i.e., turkey astroviruses, which suggests potential cross-species transmission of the virus, as previously described. Here, we present the first detection of astroviruses in the population of wild animals, companion animals, and pigs in Poland, confirming that astroviruses are frequent pathogens circulating in animals in the field. Our study also suggests potential cross-species transmission of Avaastrovirus to wild boars; however, further molecular characterization is needed.

Abstract 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.

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.

Abstract 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.

IntroductionFungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns.MethodsThe complete mitochondrial genome sequence of the mycoparasitic fungus Trichoderma koningiopsis was determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project of T. koningiopsis genome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes.ResultsT. koningiopsis strain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such as atp6, atp8, atp9, cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in the T. koningiopsis POS7 mitogenome, one of them in cox3 gene and the other in rnl gene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes of T. koningiopsis strain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina. T. koningiopsis strain POS7 was clustered together with other representatives of Trichoderma lineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers.DiscussionThe mitochondrial genome of T. koningiopsis POS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.