Gene redundancy and gene compensation of insulin-like peptides in the oocyte development of bean beetle.

Bean beetle (Callosobruchus maculatus) exhibits clear phenotypic plasticity depending on population density; However, the underlying molecular mechanism remains unknown. Compared to low-density individuals, high-density individuals showed a faster terminal oocyte maturity rate. Four insulin-like peptide (ILP) genes were identified in the bean beetle, which had higher expression levels in the head than in the thorax and abdomen. The population density could regulate the expression levels of CmILP1-3, CmILP2-3, and CmILP1 as well as CmILP3 in the head, thorax, and abdomen, respectively. RNA interference results showed that each CmILP could regulate terminal oocyte maturity rate, indicating that there was functional redundancy among CmILPs. Silencing each CmILP could lead to down-regulation of some other CmILPs, however, CmILP3 was up-regulated in the abdomen after silencing CmILP1 or CmILP2. Compared to single gene silencing, silencing CmILP3 with CmILP1 or CmILP2 at the same time led to more serious retardation in oocyte development, suggesting CmILP3 could be up-regulated to functionally compensate for the down-regulation of CmILP1 and CmILP2. In conclusion, population density-dependent plasticity in terminal oocyte maturity rate of bean beetle was regulated by CmILPs, which exhibited gene redundancy and gene compensation.

Genome analysis and classification of Xanthomonas bacteriophage AhaSv, a new member of the genus Salvovirus.

Xanthomonas phage AhaSv was isolated from lake water. Genome sequencing showed that its genome is a linear dsDNA molecule with a length of 55,576 bp and a G+C content of 63.23%. Seventy-one open reading frames (ORFs) were predicted, and no tRNAs were found in the genome. Phylogenetic analysis showed that AhaSv is closely related to members of the genus Salvovirus of the family Casjensviridae. Intergenomic similarity values between phage AhaSv and homologous phages were up to 90.6%, suggesting that phage AhaSv should be considered a member of a new species in the genus Salvovirus.

Partial Alleviation of Homologous Superinfection Exclusion of SeMNPV Latently Infected Cells by G1 Phase Infection and G2/M Phase Arrest.

Viral infection can regulate the cell cycle, thereby promoting viral replication. Hijacking and altering the cell cycle are important for the virus to establish and maintain a latent infection. Previously, Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV)-latently infected P8-Se301-C1 cells, which grew more slowly than Se301 cells and interfered with homologous SeMNNPV superinfection, were established. However, the effects of latent and superinfection with baculoviruses on cell cycle progression remain unknown. In this study, the cell cycle profiles of P8-Se301-C1 cells and SeMNPV or Autographa californica multiple nucleopolyhedrovirus (AcMNPV)-infected P8-Se301-C1 cells were characterized by flow cytometry. The results showed that replication-related genes MCM4, PCNA, and BAF were down-regulated (p < 0.05) in P8-Se301-C1 cells, and the S phase of P8-Se301-C1 cells was longer than that of Se301 cells. P8-Se301-C1 cells infected with SeMNPV did not arrest in the G2/M phase or affect the expression of Cyclin B and cyclin-dependent kinase 1 (CDK1). Furthermore, when P8-Se301-C1 cells were infected with SeMNPV after synchronized treatment with hydroxyurea and nocodazole, light microscopy and qRT-PCR analysis showed that, compared with unsynchronized cells and S and G2/M phase cells, SeMNPV-infected P8-Se301-C1 cells in G1 phase induced G2/M phase arrest, and the amount of virus adsorption and intracellular viral DNA replication were significantly increased (p < 0.05). In addition, budded virus (BV) production and occlusion body (OB)-containing cells were both increased at 120 h post-infection (p < 0.05). The expression of Cyclin B and CDK1 was significantly down-regulated at 48 h post-infection (p < 0.05). Finally, the arrest of SeMNPV-infected G1 phase cells in the G2/M phase increased BV production (p < 0.05) and the number of OB-containing cells. In conclusion, G1 phase infection and G2/M arrest are favorable to SeMNPV proliferation in P8-Se301-C1 cells, thereby alleviating the homologous superinfection exclusion. The results contribute to a better understanding of the relationship between baculoviruses and insect cell cycle progression and regulation.

Characteristics and whole-genome analysis of a novel Pseudomonas syringae pv. tomato bacteriophage D6 isolated from a karst cave.

Pseudomonas syringae is a gram-negative plant pathogen that infects plants such as tomato and poses a threat to global crop production. In this study, a novel lytic phage infecting P. syringae pv. tomato DC3000, named phage D6, was isolated and characterized from sediments in a karst cave. The latent period of phage D6 was found to be 60 min, with a burst size of 16 plaque-forming units per cell. Phage D6 was stable at temperatures between 4 and 40 °C but lost infectivity when heated to 70 °C. Its infectivity was unaffected at pH 6-10 but became inactivated at pH ≤ 5 or ≥ 12. The genome of phage D6 is a linear double-stranded DNA of 307,402 bp with a G + C content of 48.43%. There is a codon preference between phage D6 and its host, and the translation of phage D6 gene may not be entirely dependent on the tRNA library provided by the host. A total of 410 open reading frames (ORFs) and 14 tRNAs were predicted in its genome, with 92 ORFs encoding proteins with predicted functions. Phage D6 showed low genomic similarity to known phage genomes in the GenBank and Viral sequence databases. Genomic and phylogenetic analyses revealed that phage D6 is a novel phage. The tomato plants were first injected with phage D6, and subsequently with Pst DC3000, using the foliar spraying and root drenching inoculum approach. Results obtained after 14 days indicated that phage D6 inoculation decreased P. syringae-induced symptoms in tomato leaves and inhibited the pathogen's growth in the leaves. The amount of Pst DC3000 was reduced by 150- and 263-fold, respectively. In conclusion, the lytic phage D6 identified in this study belongs to a novel phage within the Caudoviricetes class and has potential for use in biological control of plant diseases.

First Report of Powdery Mildew on Viburnum chinshanense Caused by Erysiphe pseudoviburni in China.

Viburnum chinshanense, a deciduous shrub in the family Caprifoliaceae, is a dominant tree distributed mainly in the North-Central and South-Central regions of China (Zhu et al. 2023). Because of its lush white flowers and vibrant red fruits, V. chinshanense is used widely as ornamental tree in China. In May 2022, severe powdery mildew symptoms were observed on V. chinshanense on the Huaxi Campus of Guizhou Normal University, Guiyang, China. The incidence was approximately 75% among 80 V. chinshanense plants observed. White mycelia were present on both adaxial and abaxial leaf sides, but not on fruits, petioles, or stems. Infected leaves showed slight chlorosis and twisting. The mycelia were amphigenous, forming small-to-large patches, often sparse on the upper leaf surface, but mostly confluent on the lower leaf surface. Hyphae were hyaline, 4-7 µm wide. Hyphal appressoria were lobed to multilobed, in opposite pairs or solitary. Conidiophores were erect, straight, or somewhat flexuous, 60-130 µm long (n = 30). Foot cells were subcylindrical to slightly curved-sinuous at the base, 20-40 × 6-10 µm (n = 30) in size, followed by 1-3 shorter cells. Conidia formed singly, occasionally two to three in a chain. Conidia were ellipsoid to ovoid, cylindrical, and 24-40 × 16-20 µm (n = 50). No fibrosin bodies were observed on the conidia. Chasmothecia were subglobose, 56-115 µm in diameter. The appendages were 35-70 µm long. Based on these morphological characteristics, the powdery mildew fungus was identified as Erysiphe pseudoviburni (Bradshaw et al. 2020). To confirm the identification, the ribosomal DNA internal transcribed spacer (ITS) and the ribosomal large subunit (LSU) region were amplified and sequenced using the ITS1/ITS4 primer pair (White et al. 1990) and the NL1/NL4 primer pair (Ziemiecki et al. 1990), respectively. The obtained 643-bp ITS sequence (GenBank accession no. ON729292) had 99.84% identity with E. pseudoviburni strains KUS-F27310 (MN431595) and MUMH0001 (LC009904). The obtained 593-bp LSU sequence (ON729293) had 99.83% identity with E. pseudoviburni (LC009904 and MN431595). Based on the phylogenetic analysis of the combined ITS and LSU dataset (Bradshaw et al. 2020), the isolate (GZVD-1) was grouped in a clade with the E. pseudoviburni strains KUS-F27319, KUS-F27310, and MUMH0001. To fulfill Koch's postulates, leaves of three healthy potted V. chinshanense plants were inoculated by gently pressing with diseased leaves. Non-contact plants were used as controls. All plants were incubated in a greenhouse at 25 ± 2°C, 80% relative humidity. Similar powdery mildew symptoms were observed on the inoculated plants 12 days after inoculation, whereas the control plants remained symptomless. The reisolated fungus from the inoculated plants was morphologically identical to that on originally diseased plants. ITS and LSU sequences of the reisolated fungus showed 100% identity with ON729292 and ON729293, respectively. E. pseudoviburni has previously been reported to infect some Viburnum species, including V. sieboldii in Japan (Takamatsu et al. 2015) and V. odoratissimum in South Korea (Bradshaw et al. 2020). To the best of our knowledge, this is the first report of powdery mildew caused by E. pseudoviburni on V. chinshanense in China. This work expands the known host range of E. pseudoviburni in the Viburnum genus.

Prediction and characterization of prophages of Stenotrophomonas maltophilia reveals a remarkable phylogenetic diversity of prophages.

Prophages, which enables bacterial hosts to acquire novel traits, and increase genetic variation and evolutionary innovation, are considered to be one of the greatest drivers of bacterial diversity and evolution. Stenotrophomonas maltophilia is widely distributed and one of the most important multidrug resistant bacteria in hospitals. However, the distribution and genetic diversity of S. maltophilia prophages have not been elucidated. In this study, putative prophages were predicted in S. maltophilia genomes by using virus prediction tools, and the genetic diversity and phylogeny of S. maltophilia and the prophages they harbor were further analyzed. A total of 356 prophage regions were predicted from 88 S. maltophilia genomes. Among them, 144 were intact prophages, but 77.09% of the intact prophages did not match any known phage sequences in the public database. The number of prophage carried by S. maltophilia is related to its host habitat and is an important factor affecting the size of the host genome, but it is not related to the genetic diversity of the prophage. The prediction of auxiliary genes encoded by prophage showed that antibiotic resistance genes was not predicted for any of the prophages except for one questionable prophage, while 53 virulence genes and 169 carbohydrate active enzymes were predicted from 11.24 and 44.1% prophages, respectively. Most of the prophages (72.29%) mediated horizontal gene transfer of S. maltophilia genome, but only involved in 6.25% of the horizontal gene transfer events. In addition, CRISPR prediction indicated 97.75% S. maltophilia strains contained the CRISPR-Cas system containing 818 spacer sequences. However, these spacer sequences did not match any known S. maltophilia phages, and only a few S. maltophilia prophages. Comparative genomic analysis revealed a highly conserved and syntenic organization with genomic rearrangement between the prophages and the known related S. maltophilia phages. Our results indicate a high prevalence and genetic diversity of prophages in the genome of S. maltophilia, as well as the presence of a large number of uncharacterized phages. It provides an important complement to understanding the diversity and biological characteristics of phages, as well as the interactions and evolution between bacteria and phages.

Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage.

Acid mine drainage (AMD) is usually acidic (pH < 4) and contains high concentrations of dissolved metals and metalloids, making AMD a typical representative of extreme environments. Recent studies have shown that microbes play a key role in AMD bioremediation, and secondary metabolite biosynthetic gene clusters (smBGCs) from AMD microbes are important resources for the synthesis of antibacterial and anticancer drugs. Here, 179 samples from 13 mineral types were used to analyze the putative novel microorganisms and secondary metabolites in AMD environments. Among 7,007 qualified metagenome-assembled genomes (MAGs) mined from these datasets, 6,340 MAGs could not be assigned to any GTDB species representative. Overall, 11,856 smBGCs in eight categories were obtained from 7,007 qualified MAGs, and 10,899 smBGCs were identified as putative novel smBGCs. We anticipate that these datasets will accelerate research in the field of AMD bioremediation, aid in the discovery of novel secondary metabolites, and facilitate investigation into gene functions, metabolic pathways, and CNPS cycles in AMD.

Heterologous Expression and Characterization of Tea (Camellia sinensis) Polyamine Oxidase Homologs and Their Involvement in Stresses.

Polyamine oxidase (PAO) is a key enzyme maintaining polyamine homeostasis, which affects plant physiological activities. Until now, the gene members and function of PAOs in tea (Camellia sinenesis) have not been fully identified. Here, through the expression in Escherichia coli and Nicotiana benthamiana, we identified six genes annotated as CsPAO in tea genome and transcriptome and determined their enzyme reaction modes and gene expression profiles in tea cultivar 'Yinghong 9'. We found that CsPAO1,2,3 could catalyze spermine, thermospermine, and norspermidine, and CsPAO2,3 could catalyze spermidine in the back-conversion mode, which indicated that the precursor of γ-aminobutyric acid might originate from the oxidation of putrescin but not spermidine. We further investigated the changes of CsPAO activity with temperature and pH and their stability. Kinetic parameters suggested that CsPAO2 was the major PAO modifying polyamine composition in tea, and it could be inactivated by ß-hydroxyethylhydrazine and aminoguanidine. Putrescine content and CsPAO2 expression were high in tea flowers. CsPAO2 responded to wound, drought, and salt stress; CsPAO1 might be the main member responding to cold stress; anoxia induced CsPAO3. We conclude that in terms of phylogenetic tree, enzyme characteristics, and expression profile, CsPAO2 might be the dominant CsPAO in the polyamine degradation pathway.

First Report of Powdery Mildew on Photinia × fraseri Caused by Podosphaera leucotricha in Guizhou Province, China.

The evergreen shrub Photinia × fraseri is a Photinia glabra × Photinia serrulata hybrid belonging to the family Rosaceae that is widely used in ornamental landscaping. In March 2022, severe powdery mildew symptoms were observed on shrubs of Photinia × fraseri in Huaxi University Town, Guiyang, Guizhou Province, China. All observed Photinia × fraseri plants in the green belts of both roads and parks in University Town showed powdery mildew symptoms. Almost all young branches of each Photinia × fraseri individual was infected. Powdery mildew colonies covered twig tips entirely, including the stems, petioles, and the adaxial and abaxial surfaces of leaves. Infected leaves were rolled up and had irregular, dark red spots. Fungal hyphae were straight to flexuous, branched, septate, 3 to 6 µm in width, and had nipple-shaped appressoria. Conidiophores were erect, straight or somewhat flexuous, and measured 90 to 300 µm × 7 to 10.5 µm (n = 30). Foot-cells were cylindrical or subcylindrical, straight or somewhat flexuous, and measured 25 to 50 × 7 to 9.5 µm (n = 30). Foot-cells were followed by one to two shorter cells, these being 10 to 16 × 7 to 9.5 µm in size (n = 50). Shorter cells were followed by one to six conidia (most often five conidia). Conidia formed in chains, ellipsoid to ovoid in shape, having dimensions of 22.5 to 30 × 12.5 to 16 µm (n = 50), and containing fibrosin bodies. No chasmothecia (fruiting bodies) were observed. Based on these morphological characteristics, the pathogen was identified as Podosphaera leucotricha (Ellis & Everh.) E.S. Salmon (Braun & Cook 2012). To confirm this species-level identification, the ribosomal DNA internal transcribed spacer (ITS) was amplified using the primers ITS1/ITS4 (White et al. 1990). The resulting sequence was deposited in GenBank (Accession No. ON325389). When the query coverage is 100%, the obtained ITS sequence showed 99.8% identity with P. leucotricha (AB027231, MT180425, MZ298746, KX842350, and KY661036) and 100% with P. leucotricha (HM242221, KY661017, KY661028, KY661050, KY661076, KR048110, MW364489, MW364490, MZ343479, OM022112, ON073894, and ON325389), respectively. Based on the ITS sequences of Podosphaera spp., phylogenetic tree was constructed with MEGA7.0 using the Maximum Likelihood method. The ML analysis supported our isolate's putative identification as P. leucotricha. To fulfill Koch's postulates, pathogenicity testing was conducted by gently pressing naturally diseased leaves onto young leaves of three healthy, potted 1-year-old Photinia × fraseri plants; three non-inoculated healthy plants served as control. Powdery mildew symptoms were observed on 100% inoculated Photinia × fraseri plants after 12 days (in a growth chamber at 21°C under a 12 h/12 h light/dark cycle), whereas the control plants remained symptomless. The powdery mildew colonies on inoculated leaves were morphologically identical to those observed on the original diseased leaves. It is known that P. leucotricha causes powdery mildew on Photinia × fraseri in Italy (Garibaldi et al. 2005). Moreover, this fungus reportedly infected Photinia serrulata in New Zealand, Ukraine, Italy, the United States, Japan, and in East China's Shandong Province (Liang et al. 2012). To the best of our knowledge, this is the first report of powdery mildew caused by P. leucotricha on Photinia × fraseri in Southwest China's Guizhou Province. This finding is significant as P. leucotricha is the causal agent of powdery mildew on apple and pear (Strickland et al. 2021). The occurrence of said disease on Photinia × fraseri could pose a potential disease threat to these fruit crops if nearby ornamental shrubs were able to act as reservoirs for the fungus, and a means to escape agricultural management efforts.

First Report of Leaf Blight on Dumasia villosa Caused by Boeremia exigua in China.

Dumasia (Fabaceae, tribe Phaseoleae, subtribe Glycininae), a genus of trifoliate vines, is widely distributed in tropical and subtropical regions of Asia and Africa (Pan & Zhu 2010). In October 2021, lesions were observed on Dumasia villosa leaves on Longwen mountain of Guizhou Normal University, Guiyang City, Guizhou Province, China. The incidence of leaf blight on observed D. villosa leaves was 10%. All necrotic spots were close to insect-feeding sites. Necrotic spots were grey or black, and circular (2 to 10 mm in diameter) or irregular (2 to 20 mm long) in shape. Stems and pods showed no disease symptoms. Pathogen isolation was conducted following surface sterilization with ethanol. After growth for 5 days on potato dextrose agar in a moist climate chamber at 26°C under a 16 h/8 h light/dark cycle, colonies were 5.2 to 5.6 cm in diameter, olivaceous grey in colour, and sparse, white, aerial mycelia with irregular margins were evident. Conidia were hyaline, ellipsoidal to oblong, mostly 1-septate, and occasionally aseptate with dimensions ranging from 3.5 to 7.0 × 1.5 to 3.5 µm (n = 30). To confirm the species of the isolate, ribosomal DNA internal transcribed spacer (ITS) and ß-tubulin (tub2) genes were amplified and sequenced using primers ITS1/ITS4 and Btub2Fd/Btub4Rd (White et al. 1990), respectively. The obtained 529 bp ITS sequence (GenBank accession no. OL872186) shares 99.61% identity with the sequences of Boeremia exigua (MF662797 and GU395499). The obtained 299 bp tub2 sequence (OM830712) shares 100% identity with the sequence of B. exigua (KR653201). Based on morphology and DNA sequence analysis, the isolate was identified as B. exigua. To fulfil Koch's postulates, healthy leaves of 8-week-old D. villosa plants (n = 6) were wounded with a sterilized hypodermic needle and inoculated with 2 µL of a conidial suspension (106 conidia/mL). Six plants were inoculated with 2 µL of sterile distilled water as controls. After 3 days in a moist climate chamber at 26°C under a 16 h/8 h light/dark cycle, dark spots were only present on conidia-inoculated leaves, while controls remained healthy. Boeremia exigua was reisolated from disease spots and confirmed using the same morphological and molecular methods described above. To our knowledge, this is the first report of leaf blight on D. villosa caused by B. exigua, although this fungus has been reported to infect leguminous plants, including field pea (Li et al. 2012), white clover (Wang et al. 2020), and soybean (Schaffrath et al. 2020). In China, B. exigua has also been reported to infect other plants, such as walnut (Cai et al. 2021; Wang et al. 2021) and Japanese ginseng (You et al. 2015). This identification suggests that D. villosa could be a potential reservoir for the pathogen affecting other leguminous crops that might be economically important.

First Report of Powdery Mildew on Rosa cymosa Caused by Podosphaera pannosa in Guizhou Province, China.

Rosa cymosa is a traditional Chinese medicine and an ornamental plant in China (Fan et al. 2020). In April 2022, powdery mildew symptoms were observed on R. cymosa in Guiyang, Guizhou Province, China. The incidence was approximately 5% among all observed one hundred R. cymosa plants. On average, 20% of the twig tips per diseased R. cymosa plant were affected. Powdery mildew colonies covered the adaxial and abaxial surfaces of leaves. Infected young leaves rolled up along the main vein. Stems and mature leaves occasionally had signs of powdery mildew. The hyphae were straight to flexuous, branched, septate, 3 to 6 µm in width. Conidiophores were erect, straight or somewhat flexuous, and 100 to 235 µm long. Foot cells (n = 30) were cylindrical or subcylindrical, straight or somewhat flexuous, and measured 20 to 48 µm (length) × 4.5 to 5.5 µm (width). Foot cells were followed by one to two shorter cells (n = 30) that measured 8 to 12 µm (length) × 4.5 to 5.8 µm (width). The shorter cells were followed by a chain of four to eight conidia. The conidia (n = 50) were hyaline, cylindrical to ovoid, with fibrosin bodies, and measured 20 to 28 µm (length) × 10.5 to 16.5 µm (width). No chasmothecia were observed on the surface of diseased leaves. For molecular identification, the ribosomal DNA internal transcribed spacer (ITS) was amplified and sequenced using primers ITS1/ITS4 (White et al. 1990). The obtained 508-bp ITS sequence was deposited in GenBank (Accession No. ON316871). The subsequent phylogeny grouped the ITS sequence within a clade of Podosphaera pannosa sequences. Based on both morphological and phylogenetic characteristics, the powdery mildew pathogen was identified as P. pannosa (Braun et al. 2002). The voucher specimen (Accession No. GZNU-RCPP/0804/2022) were deposited at the School of Life Sciences, Guizhou Normal University, China. Pathogenicity was assessed by gently pressing naturally diseased leaves onto young leaves of three healthy, potted 2-year-old R. cymosa plants, with three non-inoculated plants as controls. Powdery mildew symptoms were observed on all inoculated plants after incubation for 10 days at 21°C, 75% relative humidity, and 12 h/12 h light/dark cycle in a greenhouse. The control plants remained symptomless. The re-isolated powdery mildew colonies on inoculated leaves were morphologically identical to those observed on the original diseased leaves, fulfilling Koch's postulates. Podosphaera pannosa has been described as the most frequent species causing powdery mildew on the Rosaceae family, particularly on Rosa spp. and Prunus spp. (Hubert et al. 2012; Félix-Gastélum et al. 2014). The occurrence of powdery mildew on R. cymosa caused by P. pannosa could pose a potential disease threat to other Rosa crops or Prunus spp.

Arthrobacter cavernae sp. nov., a novel actinobacterium isolated from sediment of karst cave.

A novel, Gram-stain-positive, aerobic, non-endospore-forming, non-motile and rod-shaped bacterium designated PO-11T was isolated from sediment of karst cave collected in Libo county, Guizhou Province, PR China. The isolate grew optimally on R2A agar at 25 °C, pH 8.0 and with 0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that PO-11T belonged to the genus Arthrobacter and was most closely related to Arthrobacter methylotrophus TGAT (98.3 % sequence similarity), Arthrobacter alkaliphilus LC6T (97.7 %) and Arthrobacter ramosus CCM1646T (97.1 %). Genome sequencing revealed a genome size of 4 073 119 bp and the genomic DNA G+C content was 66.16 mol%. Its DNA-DNA relatedness values with A. methylotrophus TGAT, A. alkaliphilus LC6T and A. ramosus CCM1646T were 23.0, 22.9 and 23.2 %, respectively. The main fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The major respiratory quinone was MK-9(H2). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, glycolipid, phosphatidylethanolamine, phosphatidylinositol and unidentified lipids. Thus, based on phylogenetic and phenotypic and chemotaxonomic data, strain PO-11T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter cavernae sp. nov. is proposed. The type strain is strain PO-11T (=CCTCC AB 2021070T=LMG 32459T).

Complete chloroplast genome features of the model heavy metal hyperaccumulator Arabis paniculata Franch and its phylogenetic relationships with other Brassicaceae species.

Arabis paniculata Franch (Brassicaceae) has been widely used for the phytoremediation of heavy mental, owing to its hyper tolerance of extreme Pb, Zn, and Cd concentrations. However, studies on its genome or plastid genome are scarce. In the present study, we obtained the complete chloroplast (cp) genome of A. paniculata via de novo assembly through the integration of Illumina reads and PacBio subreads. The cp genome presents a typical quadripartite cycle with a length of 153,541 bp, and contains 111 unigenes, with 79 protein-coding genes, 28 tRNAs and 4 rRNAs. Codon usage analysis showed that the codons for leucine were the most frequent codons and preferentially ended with A/U. Synonymous (Ks) and non-synonymous (Ka) substitution rate analysis indicated that the unigenes, ndhF and rpoC2, related to "NADH-dehydrogenase" and "RNA polymerase" respectively, underwent the lowest purifying selection pressure. Phylogenetic analysis demonstrated that Arabis flagellosa and A. hirsuta are more similar to each other than to A. paniculata, and Arabis is the closest relative of Draba among all Brassicaceae genera. These findings provide valuable information for the optimal exploitation of this model species as a heavy-metal hyperaccumulator. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01151-1.

Characterization of the chloroplast genome of Lonicera ruprechtiana Regel and comparison with other selected species of Caprifoliaceae.

Lonicera ruprechtiana Regel is widely used as a greening tree in China and also displays excellent pharmacological activities. The phylogenetic relationship between L. ruprechtiana and other members of Caprifoliaceae remains unclear. In this study, the complete cp genome of L. ruprechtiana was identified using high-throughput Illumina pair-end sequencing data. The circular cp genome was 154,611 bp long and has a large single-copy region of 88,182 bp and a small single-copy region of 18,713 bp, with the two parts separated by two inverted repeat (IR) regions (23,858 bp each). A total of 131 genes were annotated, including 8 ribosomal RNAs, 39 transfer RNAs, and 84 protein-coding genes (PCGs). In addition, 49 repeat sequences and 55 simple sequence repeat loci of 18 types were also detected. Codon usage analysis demonstrated that the Leu codon is preferential for the A/U ending. Maximum-likelihood phylogenetic analysis using 22 Caprifoliaceae species revealed that L. ruprechtiana was closely related to Lonicera insularis. Comparison of IR regions revealed that the cp genome of L. ruprechtiana was largely conserved with that of congeneric species. Moreover, synonymous (Ks) and non-synonymous (Ka) substitution rate analysis showed that most genes were under purifying selection pressure; ycf3, and some genes associated with subunits of NADH dehydrogenase, subunits of the cytochrome b/f complex, and subunits of the photosystem had been subjected to strong purifying selection pressure (Ka/Ks < 0.1). This study provides useful genetic information for future study of L. ruprechtiana evolution.

Gut bacteria reflect the adaptation of Diestrammena japanica (Orthoptera: Rhaphidophoridae) to the cave.

The gut microbiota is essential for the nutrition, growth, and adaptation of the host. Diestrammena japanica, a scavenger that provides energy to the cave ecosystem, is a keystone species in the karst cave in China. It inhabits every region of the cave, regardless of the amount of light. However, its morphology is dependent on the intensity of light. Whether the gut bacteria reflect its adaptation to the cave environment remains unknown. In this research, D. japanica was collected from the light region, weak light region, and dark region of three karst caves. The gut bacterial features of these individuals, including composition, diversity, potential metabolism function, and the co-occurrence network of their gut microbiota, were investigated based on 16S rRNA gene deep sequencing assay. The residues of amino acids in the ingluvies were also evaluated. In addition, we explored the contribution of gut bacteria to the cave adaptation of D. japanica from three various light zones. Findings showed that gut bacteria were made up of 245 operational taxonomic units (OTUs) from nine phyla, with Firmicutes being the most common phylum. Although the composition and diversity of the gut bacterial community of D. japanica were not significantly different among the three light regions, bacterial groups may serve different functions for D. japanica in differing light strengths. D. japanica has a lower rate of metabolism in cave habitats than in light regions. We infer that the majority of gut bacteria are likely engaged in nutrition and supplied D. japanica with essential amino acids. In addition, gut bacteria may play a role in adapting D. japanica's body size. Unveiling the features of the gut bacterial community of D. japanica would shed light on exploring the roles of gut bacteria in adapting hosts to karst cave environments.

The complete mitochondrial genome of Brevicoryne brassicae (Hemiptera: Aphididae).

The mitochondrial genome of Brevicoryne brassicae (Hemiptera: Aphididae) was determined by Illumina paired-end sequencing. The genome size is 15,927 bp with 45.19% A, 39.03% T, 9.92% C and 5.86% G. It is encoded with 13 protein-coding genes, 22 transfer RNAs and two ribosome RNAs. The phylogenetic tree showed that B. brassicae clustered within clade of Aphididae, had a closer relationship with genus Diuraphis than the rest genera. This study provides important information for future study on the evolution, genetic and molecular biology of Brevicoryne.

The complete chloroplast genome of Viburnum sargentii Koehne (Adoxaceae).

Viburnum sargentii Koehne is widely used for garden greening and also displays excellent medicinal value in China. However, the phylogenetic relationship between V. sargentii and other Adoxaceae members remains unknown. In this research, the complete chloroplast genome of V. sargentii was obtained by the high-throughput Illumina pair-end sequencing data. The chloroplast genome shows a typically quadripartite structure with 158,524 bp in size, including a large single-copy (LSC) region of 87,087 bp and a small single-copy (SSC) region of 18,489 bp, which were separated by two inverted repeat (IR) regions (26,474 bp each). A total of 128 genes were predicted, including 8 ribosomal RNAs (rRNAs), 37 transfer RNAs (tRNAs), and 83 protein-coding genes (PCGs). Maximum-likelihood phylogenetic analysis revealed that V. sargentii was clustered in the Viburnum genus and in a sister position to Viburnum japonicum, Viburnum erosum, Viburnum fordiae, and Viburnum betulifolium. This study provides useful information for future genetic study of V. sargentii.

Characterization of the complete chloroplast genome of China Viburnum burejaeticum Regel et Herd and intra-species diversity.

Viburnum burejaeticum Regel et Herd is widely cultivated in botanical gardens. However, as a member of Adoxaceae, few studies have been carried out on its phylogenetic relationship with other family members. Here we report the first complete chloroplast (cp) genome sequence of V. burejaeticum collected from China. The circular cp genome is 158,381 bp in size, including a large single-copy (LSC) region of 87,067 bp and a small single-copy (SSC) region of 18,212 bp, which were separated by two inverted repeat (IR) regions (26,551 bp each). A total of 126 genes were annotated, including 8 ribosomal RNAs (rRNAs), 36 transfer RNAs (tRNAs), and 82 protein-coding genes (PCGs). The sequence comparison of two V. burejaeticum collected from Korea and China revealed 101 single nucleotide polymorphisms (SNPs) and 16 insertions/deletions (InDels). In addition, maximum-likelihood (ML) phylogenetic analysis indicated V. burejaeticum species collected in Korea and China are clustered together. This study provides useful information for future genetic study of V. burejaeticum.

The complete mitochondrial genome of Melanostoma orientale (Diptera: Syrphidae).

The mitochondrial genome of Melanostoma orientale has been decoded by Illumina sequencing. The mitogenomic size is 16,229 bp with 40.96% A, 40.29% T, 10.60% C, and 8.15% G. It is encoded with 13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNAs. The phylogenetic tree showed that 10 species of Syrphidae, belonging to six genera, were clustered into two clades. This is the first mitochondrial genome for the genus Melanostoma.

The complete mitochondrial genome of Eysarcoris guttigerus (Hemiptera: Pentatomidae).

The mitochondrial genome of Eysarcoris guttigerus has been decoded using Illumina sequencing. The mitogenomic size is 15,368 bp with 42.97% A, 33.90% T, 13.22% C, and 9.90% G. It encoded 13 protein-coding genes, two ribosomal RNA, and 22 transfer RNAs. Phylogenetic tree showed that genus Eysarcoris had a closer relationship with the genus Carbula than the rest of 20 genera.