Neighbor-joining Tree Research Articles

Genetic Diversity and Population Structure in Ethiopian Mustard (Brassica carinata A. Braun) as Revealed by Single Nucleotide Polymorphism Markers.

Ethiopian mustard (Brassica carinata A. Braun) is currently one of the potential oilseeds dedicated to the production for biofuel and other bio-industrial applications. The crop is assumed to be native to Ethiopia where a number of diversified B. carinata germplasms are found and conserved ex situ. However, there is very limited information on the genetic diversity and population structure of the species. This study aimed to investigate the genetic diversity and population structure of B. carinata genotypes of different origins using high-throughput single nucleotide polymorphism (SNP) markers. We used Brassica 90K Illumina InfiniumTM SNP array for genotyping 90 B. carinata genotypes, and a total of 11,499 informative SNP markers were used for investigating the population structure and genetic diversity. The structure analysis, principal coordinate analysis (PcoA) and neighbor-joining tree analysis clustered the 90 B. carinata genotypes into two distinct subpopulations (Pop1 and Pop2). The majority of accessions (65%) were clustered in Pop1, mainly obtained from Oromia and South West Ethiopian People (SWEP) regions. Pop2 constituted dominantly of breeding lines and varieties, implying target selection contributed to the formation of distinct populations. Analysis of molecular variance (AMOVA) revealed a higher genetic variation (93%) within populations than between populations (7%), with low genetic differentiation (PhiPT = 0.07) and poor correlation between genetic and geographical distance (R = 0.02). This implies the presence of gene flow (Nm > 1) and weak geographical structure of accessions. Genetic diversity indices showed the presence of moderate genetic diversity in B. carinata populations with an average genetic diversity value (HE = 0.31) and polymorphism information content (PIC = 0.26). The findings of this study provide important and relevant information for future breeding and conservation efforts of B. carinata.

First report of cucumber mosaic virus infecting Azorina vidalii in Azores Islands.

Virus diseases that occur in crops pose a major threat not only to global food security but also to wild plant communities growing in natural ecosystems (Jones, 2020, and references therein). In Azores (Portugal) little is known about viruses present on native flora and therefore, they have not been taken into consideration in conservation programs. Considering this, we selected Azorina vidalii (Campanulaceae), an endangered (IUCN) plant, endemic to Azores (Bilz, 2011), to survey for plant viruses. A. vidalii, the sole species of its genus, is often found in crevices with no soil accumulation on coastal cliffs, exposed to storms and sea spray, and is used as an ornamental. Leaves from 53 plants of A. vidalii from three populations from Terceira Island and three populations from Flores Island were randomly collected without obvious symptoms of virus infection, between the summer of 2021 and fall of 2022. RNA extraction was performed using the Plant/Fungi Total RNA Purification Kit (Norgen Biotek, Canada). RNA extracts from each population were pooled into six distinct composite samples (AvT1, AvT2, AvT3, AvF1, AvF4 and AvF5) and sent to Lexogen (Austria) for small RNA library preparation and High-Throughput Sequencing. Single-end RNA sequencing using Illumina NextSeq2000 system yielded between 10.1 M and 33.8 M raw reads. Adaptors and low-quality reads were removed with Trim Galore! and PRINSEQ. Trimmed reads were mapped to the genome phylogenetically nearest to A. vidalii available at the NCBI database (Adenophora triphylla). The resulting 2.5 M - 13.5 M unmapped reads were analysed with VirusDetect online version (database v248) (Zheng et al., 2017) for virus detection and identification. Sequences of cucumber mosaic virus (CMV) (contigs of up to 3045 nt for RNA1, 2917 nt for RNA2 and 2086 nt for RNA3) were identified in five (AvT1, AvT2, AvT3, AvF1 and AvF5) of the six composite samples and CMV satellite sequences (two contigs with 145 and 197 nt) were identified in only one (AvT1) of the composite samples. To confirm the presence of CMV, all samples were tested by two-step RT-PCR using primers targeting CMV-specific RdRp gene (513 bp) (Grieco et al., 2000), which retrieved 18 positive samples (34%). Nine samples were selected for Sanger sequencing (six out of 13 from Terceira and three out of five from Flores) based on digestion profile obtained with AluI and MboI. The resulting sequences (OQ176229-OQ176233, OQ732757-OQ732760) share an identity of 97.2-100% and BLASTn showed them to have 98.3-99.6% identity to CMV strain TN (AB176848). A Neighbour-Joining tree (Supplementary material) inferred in MEGA11 (Tamura et al., 2021) with 237 additional CMV-RdRp sequences, showed that A. vidalii CMV-derived isolates clustered together with reference strains of subgroup II, as those used by Roossinck (2002) for phylogenetic analysis of the 2a ORF. Besides CMV, tomato spotted wilt virus and polerovirus-associated RNAs sequences were found in one of the A. vidalii populations, but with lower coverage, and need to be further investigated. To the best of our knowledge, this is the first report of CMV infecting A. vidalli. CMV, genus Cucumovirus, is an agriculturally important virus and one of the most successful viruses known, infecting over 1,200 species of plants (Palukaitis & García-Arenal, 2003). In addition to A. vidalii being a CMV reservoir, which may have implications on adjacent crop fields, further research is needed to investigate the impact of CMV on A. vidalli fitness.

First Report of Fusarium denticulatum Causing Chlorotic Leaf Distortion of Sweetpotato in China.

Sweetpotato (Ipomoea batatas) is one of the most important crops in China. To gain a clearer picture of the occurrence of diseases on sweetpotato, 50 fields (100 plants/field) were randomly surveyed in prominent sweetpotato growing areas of Lulong county, Hebei Province in the years 2021-2022. Plants showing chlorotic leaf distortion with mildly twisted young leaves and stunted vines were observed frequently. It was similar to the symptoms of chlorotic leaf distortion of sweetpotato (Clark et al. 2013). The incidence of disease with patch pattern ranged from 15% to 30%. Ten symptomatic leaves were excised, surface disinfested with 2% sodium hypochlorite for 1 min, rinsed three times in sterilized ddH2O, and cultured on potato dextrose agar (PDA) at 25°C. Nine fungal isolates were obtained. A pure culture of representative isolate FD10 obtained after serial hyphal tip transfer was examined for morphological and genetic characters. Colonies of isolate FD10 on PDA at 25°C were slow growing (4±0.1mm/day) with aerial, white-to-pink mycelium. Lobed colonies had greyish-orange pigmentation in reverse and conidia aggegated in false heads. Conidiophores were prostrate and short. Phialides were mostly monophialidic but occasionally polyphialidic. Polyphialidic openings often denticulate in a rectangular arrangement. Microconidia were abundant, long, oval to allantoid, mostly none or one septate, and 4.79 to 9.53 × 2.08 to 3.22 μm (n = 20). Macroconidia were fusiform to falcate with a beaked apical cell and a footlike basal cell, 3 to 5 septate, and 25.03 to 52.92 × 2.56 to 4.49 µm. Chlamydospores were absent. All in agreement with the morphology of Fusarium denticulatum (Nirenberg and O'Donnell 1998). Genomic DNA of isolate FD10 was extracted. The EF-1α and β-tubulin genes were amplified and sequenced (O'Donnell and Cigelnik 1997; O'Donnell et al. 1998). The obtained sequences were deposited in GenBank (accession nos. OQ555191 and OQ555192). BLASTn revealed that those sequences showed 99.86% (EF-1α) and 99.93% (β-tubulin) homology with the relative sequences of F. denticulatum type strain CBS407.97 (accession nos. MT011002.1 and MT011060.1), respectively. Furthermore, a neighbor-joining phylogenetic tree based on the EF-1α and β-tubulin sequences revealed that the isolate FD10 clustered with F. denticulatum. Based on morphological characteristics and sequence analysis, the isolate FD10 associated with chlorotic leaf distortion of sweetpotato was identified as F. denticulatum. Pathogenicity tests were performed by immersing ten 25-cm-long vine-tip cuttings of cultivar Jifen 1 origin from tissue culture in a conidial suspension (1 × 106 conidia per ml) of isolate FD10. Vines immersed in sterile distilled water used as a control. All inoculated plants in 25-cm plastic pots were incubated in a climate chamber at 28℃ and 80% RH for two and half months and the control were incubated in a separate climate chamber. Nine inoculated plants developed chlorotic terminals, moderate interveinal chlorosis and slight leaf distortion. No symptoms were observed on the control plants. The pathogen was reisolated from inoculated leaves and matched the morphological and molecular characteristics of the original isolates, thus fulfilling Koch's postulates. To our knowledge, this is the first report of F. denticulatum causing chlorotic leaf distortion of sweetpotato in China. Its identification will promote the management of this disease in China.

First report of black patch disease caused by Phyllosticta capitalensis on Litsea cubeba in China.

Litsea cubeba, an economical important tree species originally from China, produces fruit from which essential oils are extracted and extensively used in the chemical industry (Zhang et al. 2020). In August 2021, a large-scale outbreak of black patch disease was first observed on the leaves of Litsea cubeba in Huaihua (27°33'N; 109°57'E), Hunan province, China (disease incidence 78%). A second outbreak in 2022, in the same area, lasted from June to August. Symptoms consisted of irregular lesions that initially appeared as small black patches near the lateral veins. These lesions grew along the lateral veins and formed feathery patches until almost the entire lateral veins of the leaves were infected by the pathogen. The infected plants grew poorly and eventually the leaves desiccated and the tree defoliated. To identify the causal agent, the pathogen was isolated from nine symptomatic leaves from three trees. Symptomatic leaves were washed with distilled water three times. Leaves were cut into small pieces (11 cm), surface sterilized with 75% ethanol for 10s and 0.1% HgCl2 for 3 min, and then washed 3 times in sterile distilled water. Surface disinfected leaf pieces were placed onto potato dextrose agar (PDA) medium with cephalothin (0.2 mg/ml) and incubated at 28°C for 4-8 days (about 16h light, 8h dark). Seven morphologically identical isolates were obtained, from which five were selected for further morphological examination and three for molecular identification and pathogenicity test. Strains from grayish white colonies with a granular surface and grayish black wavy edges; bottom of the colonies turned black over time. Conidia were hyaline and nearly elliptical, unicellular. The sizes of conidia ranged from 8.59 to 15.06 μm (n=50) in length and 3.57 to 6.36 μm (n=50) in width. These morphological characteristics are consistent with the description of Phyllosticta capitalensis (Guarnaccia et al. 2017, Wikee et al. 2013). To further confirm the identity of this pathogen, genomic DNA of three isolates (phy1, phy2 and phy3) were extracted to amplify the internal transcribed spacer (ITS) region, the 18S rDNA region, the transcription elongation factor (TEF), and actin (ACT) gene with ITS1/ITS4 (Cheng et al. 2019), NS1/NS8 (Zhan et al. 2014), EF1-728F/EF1-986R (Druzhinina et al. 2005) and ACT-512F/ACT-783R (Wikee et al. 2013) primers, respectively. Sequence similarity indicated that these isolates were highly homologous to Phyllosticta capitalensis. The ITS (Genbank No. OP863032, ON714650 and OP863033), 18S rDNA (Genbank No. OP863038, ON778575 and OP863039), TEF (Genbank No. OP905580, OP905581 and OP905582) and ACT (Genbank No. OP897308, OP897309 and OP897310) sequences of isolates Phy1, Phy2 and Phy3 shared up to 99%, 99%, 100% and 100% similarities with their counterparts (Genbank No. OP163688, MH051003, ON246258 and KY855652) in Phyllosticta capitalensis, respectively. To further confirm their identity, a neighbor-joining phylogenetic tree was generated using MEGA7. Based on morphological characteristics and sequence analysis, the three strains were identified as P. capitalensis. To fulfill Koch's postulates, conidial suspension (1×105 conidia per mL) collected from three isolates were independently inoculated on artificially wounded detached leaves and leaves on trees of Litsea cubeba. Leaves were inoculated with sterile distilled water as negative controls. The experiment was repeated three times. All pathogen-inoculated wounds exhibited necrotic lesions within 5 days on detached leaves and 10 days on the leaves growing on trees after inoculation, whereas no symptoms were observed on the controls. The pathogen was exclusively re-isolated from the infected leaves and showed identical morphological characteristics to those of the original pathogens. P. capitalensis is a destructive plant pathogen that has been shown to cause leaf spots or black patch symptoms on variety of host plants around the world (Wikee et al. 2013), including oil palm (Elaeis guineensis Jacq.), tea plant (Camellia sinensis), Rubus chingii and castor (Ricinus communis L.). To our knowledge, this is the first report of black patch disease of Litsea cubeba caused by P. capitalensis in China. This disease causes severe leaf abscission in fruit development stage of Litsea cubeba and leads to a large amount of fruit drop.

Stemroton Adenia globosa caused by Lasiodiplodia theobromae in Jiangsu.

Adenia globosa, as an excellent indoor ornamental plant, is planted in Tropical Botanical Museum, Nanjing Zhongshan Botanical Garden, Jiangsu Province, China.In September 2022, a new stembasalrot disease was observed on A. globosa seedlings,being planted here. Stem basalrot were observed on approximately 80% of A. globosa seedlings. The basalstem of cutting seedlings appeared decayed, and stem tip eventually turned dry due to water loss (Figure S1A). To isolate the pathogen, three diseased stems were collected from three cuttings planted in different pots of the Tropical Botanical Museum. The stem sections (3 to 4 mm) were excised from the margins between healthy and diseased tissues, surface sterilized in 75% ethanol for 30 s and 1.5% NaClO for 90 s, rinsed three times in sterilized distilled water, plated on potato dextrose agar (PDA) and incubated at 25℃ in the dark. Pure cultures were obtained by monosporic isolation. Eight isolates were obtained, and all identified as Lasiodiplodia sp.. The colonies morphology of cultures, growing on PDA were cotton-like, the primary mycelia were black gray after 7 days, and the reverse sides of PDA plates were similar to front sides in color (Figure S1B). A representative isolate, QXM1-2 was selected for the further study. Conidia of QXM1-2 were oval or elliptic, with a mean size of 11.6 µm×6.6 µm (n=35). The conidia are colorless and transparent in the early stage, and become dark brown with one-septum in the later stage (Figure S1C). The conidiophores produced conidia after nearly four weeks of cultivation on PDA plate (Figure S1D). The conidiophore was a transparent cylindrical structure, with a size of (6.4-18.2) µm × (2.3-4.5) µm ( n = 35). These characteristics were consistent with the description of Lasiodiplodia sp. (Alves et al. 2008). The internal transcribed spacer regions (ITS), translation elongation factor 1-alpha (TEF1α) and β-tubulin (TUB) genes (GenBank Accession No.OP905639, No.OP921005, and No.OP921006, respectively) were amplified and sequenced with the primer pairs ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Alves et al. 2008) and Bt2a/Bt2b (Glass and Donaldson 1995), respectively. They had 99.8-100% homology to the ITS (504/505 bp) of Lasiodiplodia theobromae strain NH-1 (MK696029), TEF1α (316/316 bp) of strain PaP-3 (MN840491), and TUB (459/459 bp) of isolate J4-1 (MN172230). A neighbor-joining phylogenetic tree was generated by combining all sequenced loci in MEGA7. The isolate QXM1-2 clustered in the L. theobromae clade with 100% bootstrap support (Figure S2). To test pathogenicity, three A. globosa cutting seedlings that previously had been wounded with a sterile needle were inoculated with 20 μL conidia suspension (1×106 conidia/mL) on the stem base. The seedlings inoculated with 20 µL sterile water was used as the control. All plants were covered with clear polyethylene bags to keep moisture in a greenhouse (25℃, 80% relative humidity). The experiment was repeated three times. After 7 days post-inoculation, typical stem rot were found on the treated cutting seedlings and the control seedlings did not have any symptoms (Figure S1E-F). The same fungus, identified by morphological characteristics and sequencing using ITS, TEF1α and TUB genes, was isolated from the diseased tissues of the inoculated stems to complete Koch's postulates. This pathogen has been reported infecting the branch of castor bean (Tang et al. 2021) androot ofCitrus (Al-Sadi et al. 2014). For our knowledge, this is the first report of L. theobromae infecting A. globosa in China. This study provides an important reference for the biology, epidemiology of L. theobromae.

Precision metagenomics sequencing for food safety: hybrid assembly of Shiga toxin-producing Escherichia coli in enriched agricultural water.

Culture-independent metagenomic sequencing of enriched agricultural water could expedite the detection and virulotyping of Shiga toxin-producing Escherichia coli (STEC). We previously determined the limits of a complete, closed metagenome-assembled genome (MAG) assembly and of a complete, fragmented MAG assembly for O157:H7 in enriched agricultural water using long reads (Oxford Nanopore Technologies, Oxford), which were 107 and 105 CFU/ml, respectively. However, the nanopore assemblies did not have enough accuracy to be used in Single Nucleotide Polymorphism (SNP) phylogenies and cannot be used for the precise identification of an outbreak STEC strain. The present study aimed to determine the limits of detection and assembly for STECs in enriched agricultural water by Illumina MiSeq sequencing technology alone, followed by establishing the limit of hybrid assembly with nanopore long-read sequencing using three different hybrid assemblers (SPAdes, Unicycler, and OPERA-MS). We also aimed to generate a genome with enough accuracy to be used in a SNP phylogeny. The classification of MiSeq and nanopore sequencing identified the same highly abundant species. Using the totality of the MiSeq output and a precision metagenomics approach in which the E. coli reads are binned before assembly, the limit of detection and assembly of STECs by MiSeq were determined to be 105 and 107 CFU/ml, respectively. While a complete, closed MAG could not be generated at any concentration, a complete, fragmented MAG was produced using the SPAdes assembler with an STEC concentration of at least 107 CFU/ml. At this concentration, hybrid assembled contigs aligned to the nanopore-assembled genome could be accurately placed in a neighbor-joining tree. The MiSeq limit of detection and assembly was less sensitive than nanopore sequencing, which was likely due to factors including the small starting material (50 vs. 1 μg) and the dilution of the library loaded on the cartridge. This pilot study demonstrates that MiSeq sequencing requires higher coverage in precision metagenomic samples; however, with sufficient concentration, STECs can be characterized and phylogeny can be accurately determined.

First Report of black spot of Shine Muscat fruit caused by Cladosporium allicinum in China.

Shine muscat is a Vitis vinifera hybrid (Akitsu-21 × Hakunan), that has emerged as a popular table grape cultivar in China. In recent years, shine muscat has been widely cultivated with 66,667 ha being cultivated in 2021. In November 2021, symptoms of fruit spot were observed on shine muscat during the storage at 0~3℃ and 85%~90% RH, while stored at National Agricultural Product Preservation Engineering Technology Research Center, in Tianjin (N 116°20', E 39°09'), China. The incidence of this disease was about 35%. Affected grape berries initially had small brown spots. The spots on the fruit expanded to an ellipse or circular sunken area with a black center. The central peel of the diseased spots were ruptured and collapsed. The diseased fruits eventually fell off the vine. To isolate the pathogen, grape peels with typical symptoms were cut into small pieces, sterilized with 75% ethanol for 45-sec, rinsed with sterilized distilled water three times, and then transferred onto potato dextrose agar (PDA) medium.The plates were incubated at 25°C in the dark. After 10 days, 26 single spore isolates with similar morphology were obtained from 30 symptomatic grape berries. Fungal colonies were grayish brown, with abundant conidia on the obverse-side on PDA. Conidiophores were cylindrical, straight with unbranched, solitary or clustered, elongation at the tip and ranged in size from 3.2-6.8 × 35.6-150.9 µm (n=50). Conidia were grew in chains, ovoid, aseptate, and 2.2-6.0 × 8.3-16.8 µm (n=50). The morphological characteristics were consistent with Cladosporium allicinum (Bensch et al. 2012). Molecular data were also used to support the microscopic identification by extracting genomic DNA from 26 isolates using a Plant Genomic DNA kit (Tiangen, China). Amplicons were generated for the internal transcribed spacer (ITS), translation elongation factor 1-alpha(tef1-α), and actin (act) using the following primers ITS1/ITS4, EF1-728F/ EF1-986R and ACT-512F/ ACT-783R, respectively (Bensch et al. 2012). Blast analysis showed that three amplified fragments of 26 isolates were highly similar to C. allicinum, with 98.96~100% sequence identity with Cladosporium allicinum accessions in GenBank (ITS, OK661041; tef1-α, MF473332; act, LN834537). Three amplified fragments of representative isolate YG03 were deposited in GenBank with accession nos. OP799670 for ITS, OP888001 for tef1-α and OP887999 for act, respectively. Neighbor-joining trees based on concatenated sequences of three genes were constructed using MEGA5.2. The results showed that the strain YG03 from shine muscat was closely related to C. allicinum. Pathogenicity tests of 26 isolates were performed on healthy shine muscat berries using pin pricks and a humidor. In each wound, 5 μL of conidial suspension (1×106 conidia/mL) and sterile distilled water were inoculated on 30 berries, and maintained in a dark incubator at 25°C, 90% relative humidity. Each treatment was repeated twice. After 10 days, the wounded berries inoculated with the spore suspension showed dark brown spots, similar to the original diseased fruits, while no symptoms were observed on the control treament. Pathogen re-isolated from inoculated fruits were identical to the original strains on colony and microscopic morphology, and identified to Cladosporium allicinum based on act gene by molecular method, thereby fulfilling Koch's postulates. C.allicinum has been reported causing leaf spot on 11 host plants around the world (Bensch et al. 2012, 2015; Quaedvlieg et al. 2014; Jurisoo et al. 2019). To our knowledge, this is the first report of C. allicinum causing black spot on fruit of Vitis vinifera worldwide. The identification of this disease could establish a foundation for developing management strategies to reduce losses in storage period.

Unexpected mitotype diversity of Simplimorpha promissa (Lepidoptera: Nepticulidae) in Ukraine and Armenia revealing a possible cryptic taxon.

In this paper, the results of a recent molecular study of theCotinus-feeding, leaf-miningSimplimorpha promissa(Staudinger) (Lepidoptera: Nepticulidae) are discussed for the first time on the basis of samples collected in Ukraine and Armenia. Newly obtained mtDNACO1-5'sequences from these countries were compared with previously known sequences from France, Italy, Croatia and Greece. A mitotype network and a Neighbor-Joining tree of twenty-two specimens ofS. promissaare provided.They show that the studied specimens from Ukraine and the rest of the European countries are genetically closer to each other than to the examined specimens from Armenia, thereby suggesting the Armenian specimens could represent a sister taxon to the EuropeanS. promissa. The study also revealed a significantly large genetic diversity ofS. promissain Ukraine.

Population genomic analyses of protected incense trees Aquilaria sinensis reveal the existence of genetically distinct subpopulations

The incense tree Aquilaria sinensis (Thymelaeaceae) can produce agarwood with commercial values and is now under threat from illegal exploitation in Hong Kong, impairing the local population and biodiversity. Together with other species of Aquilaria, it is listed in the CITES Appendix II, which strictly regulates its international trade. To understand the population structure of A. sinensis and to make relevant conservation measures, we have sequenced 346 individuals collected in Hong Kong and southern mainland China. Population genomic analyses including principal component analysis, neighbor-joining tree construction, ADMIXTURE, and hierarchical pairwise-FST analyses suggested that genetically distinct populations are contained in certain areas. Genomic scan analyses further detected single-nucleotide polymorphism (SNP) outliers related to plant defense, including the CYP71BE gene cluster. In addition to the population analyses, we have developed a modified hexadecyltrimethyl-ammonium bromide (CTAB) DNA extraction protocol for obtaining DNA from agarwood samples in this study, and resequencing of DNA extracted from two agarwood samples using this method allows us to successfully map to the sample corresponding localities in the phylogenetic tree. To sum up, this study suggested that there is a genetically distinct subpopulation of incense tree in Hong Kong that would require special conservation measures and established a foundation for future conservation measures.

Comparative Analysis of Genetic Structure and Diversity in Five Populations of Yellowtail Kingfish (Seriola aureovittata)

To clarify the population genetic structure, intrapopulation diversity, and interpopulation differentiation of yellowtail kingfish (Seriola aureovittata), we sampled 143 individuals from five collections of yellowtail kingfish: farmed (n = 30) and wild (n = 33) collections in China, a wild collection in Japan (n = 20), and farmed (n = 31) and wild (n = 29) collections in Australia. Using 2b-RAD simplified genome sequencing, we obtained an average of 287,594 unique tags per population, with an average sequencing depth of 27.13×. Our final genotype dataset included 48,710 SNPs (Single Nucleotide Polymorphisms). The five collections were all in Hardy–Weinberg equilibrium, and the interpopulation differentiation varied among the sample collections. The genetic differentiation coefficients (Fst) between the Chinese and Japanese yellowtail kingfish collections were low and the gene flow (Nm) values were high. These results suggest continuous gene flow occurs frequently between the collections, indicating that they belong to the same population. In contrast, genetic differentiation was high between the Australian collections and the Chinese and Japanese populations, suggesting different evolutionary origins and belonging to different populations. The farmed and wild Australian collections fell into distinct clades in a neighbor-joining phylogeny tree, suggesting farmed fish have begun to differentiate from the wild collection. A similar level of genetic diversity between the wild collections in China and Japan suggests that they originated from the same spawning ground. This, therefore, reminds us that in future aquaculture processes attention is needed regarding implementing targeted breeding strategies. In addition, our data will contribute to Chinese yellowtail kingfish genetic breeding and the sustainable use of Chinese yellowtail kingfish germplasms.

PbWRKY26 positively regulates malate accumulation in pear fruit by activating PbMDH3

Malate is the main organic acid that affects fruit acidity and flavor in pear (Pyrus spp.). However, the regulatory mechanism of malic acid accumulation in pear remains unclear. We identified PbWRKY26 as a candidate gene using mRNA-seq, and quantification analysis verified the expression level. The expression of PbWRKY26 was positively correlated with the malic acid content in two P. pyrifolia cultivars (‘Cuiguan’, ‘Hongsucui’) and two P. ussuriensis cultivars (‘Qiuxiang’, ‘Hanhong’), with respective correlation coefficients of 0.748*, 0.871**, 0.889**, and 0.910** (*, P < 0.05; **, P < 0.01). The expression of PbWRKY26 enhanced the malate content in overexpression transgenic pear fruit and callus. In contrast, silencing PbWRKY26 decreased the pear fruit malic acid content. Analysis of the neighbor-joining phylogenetic tree indicated that PbWRKY26 was a PH3 homolog. The WRKY26 (PH3) has been identified to regulate a proton pump gene, PH5, in a lot of plant species, but the LUC and Y1H assays showed that PbWRKY26 could not bind to PbPH5 promoter in our study. Interestingly, a malate dehydrogenase gene, PbMDH3, was identified to be regulated by PbWRKY26. This study might be valuable to understand the metabolic regulatory network associated with malate accumulation.

Genetic diversity and functional implication of the long control region in human papillomavirus types 52, 58, and 16 from Central China.

High-risk human papillomavirus (HR-HPV) is a main reason for cervical cancer. The long control region (LCR) of the genome plays a variety of roles in the transcription of the virus. LCR sequences were amplified by polymerase chain reaction (PCR) and confirmed by DNA sequencing. MEGA 11.0 software and NCBI blast were used to analyze the sequences and construct the Neighbor-Joining tree. In addition, the JASPAR database was used to predict the potential transcription factor binding sites (TFBS). For HPV-52 LCR, 68 single nucleotide polymorphisms (SNPs), 8 deletions, and 1 insertion were found, 17 of which were novel variations. Most of the variants were clustered in B2 sub-lineage (96.22%). For HPV-58 LCR, 25.43% of samples were prototype. 49 SNPs, 2 deletions, and 1 insertion were observed in the remaining samples. A1 sub-lineage was the most frequent (64.16%). For HPV-16 LCR, 75 SNPs and 2 deletions were identified, 13 of which were newly identified. A total of 55.68% of the variants were distributed in A4 sub-lineage. The JASPAR results suggested that multiple variations occurred in TFBSs, which might affect the function of transcription factors. This study provides experimental data for further studies on the epidemiology and biological function of LCR. Various LCR mutational data may prove useful for exploring the carcinogenic mechanism of HPV.

Nematodes Degrade Extracellular Antibiotic Resistance Genes by Secreting DNase II Encoded by the nuc-1 Gene.

This study investigated the degradation performance and mechanism of extracellular antibiotic resistance genes (eARGs) by nematodes using batch degradation experiments, mutant strain validation, and phylogenetic tree construction. Caenorhabditis elegans, a representative nematode, effectively degraded approximately 99.999% of eARGs (tetM and kan) in 84 h and completely deactivated them within a few hours. Deoxyribonuclease (DNase) II encoded by nuc-1 in the excretory and secretory products of nematodes was the primary mechanism. A neighbor-joining phylogenetic tree indicated the widespread presence of homologs of the NUC-1 protein in other nematodes, such as Caenorhabditis remanei and Caenorhabditis brenneri, whose capabilities of degrading eARGs were then experimentally confirmed. C. elegans remained effective in degrading eARGs under the effects of natural organic matter (5, 10, and 20 mg/L, 5.26-6.22 log degradation), cation (2.0 mM Mg2+ and 2.5 mM Ca2+, 5.02-5.04 log degradation), temperature conditions (1, 20, and 30 °C, 1.21-5.26 log degradation), and in surface water and wastewater samples (4.78 and 3.23 log degradation, respectively). These findings highlight the pervasive but neglected role of nematodes in the natural decay of eARGs and provide novel approaches for antimicrobial resistance mitigation biotechnology by introducing nematodes to wastewater, sludge, and biosolids.

Elucidating the physiological and molecular characteristics of bacterial blight incitant Xanthomonas auxonopodis pv. punicae; a life threatening phytopathogen of pomegranate (Punica granatum. L) and assessment of H2O2 accumulation during host-pathogen interaction

Bacterial blight of pomegranate caused by Xanthomonas auxonopodis pv.punicae (Xap) threaten the existence of a group of farmers for the past few decades who rely on pomegranate cultivation for their livelihood since it will cause huge yield loss. The primary focus of this study was to conduct a thorough analysis of the characterization of this blight incitant Xap. Physiological, biochemical, and molecular characteristics of six phytopathogenic strains of Xap, designated as PBF1 (PBF: Pomegranate Blight Fruit), PBF2, PBF3, PBF4, PBF5, and PBF6, isolated from the infected fruits were examined. Bacterial colonies were featured as gram-negative, yellow-pigmented circular with a glistening appearance. An attempt to determine the best culture medium, favouring bacterial proliferation was successfully done with four distinct medium, Nutrient Glucose Agar (NGA), Nutrient sucrose Agar (NSA), Yeast Dextrose Calcium Carbonate Agar (YDCA) and Yeast Glucose Calcium Carbonate Agar (YGCA) and comparatively, significant growth was found in NGA (66.66%) followed by YDCA (33%). According to the antibiotic susceptibility results, both ampicillin and streptomycin were determined as potentially effective drugs in preventing the proliferation of Xap (P 0.05). The reactive oxygen species-mediated plant immune response during host-pathogen interaction was confirmed by accessing the presence of H2O2 accumulation in infected leaves via 3,3 - diaminobenzidine (DAB) -staining technique. Bacterial isolates from this study were confirmed by two universal constitutive genes such as gyrB and 16S rRNA. From the BLAST analysis, the isolates were identified as Xap with base pair lengths of 1408bp, 1180bp, and 1159bp, which correspond to PBF1, PBF2, and PBF3, respectively. A neighbor-joining phylogenetic tree study explaining a strong phylogenetic relationship between the query sequence and closely related bacterial species.

Assessment of genetic diversity among native Algerian rabbit populations using microsatellite markers.

Having higher adaptability against abiotic stress, which is characterized in rural areas in developing countries, local farm animal genetic resources (FAGRs) are increasingly precarious for random and unsystematic crossing with exotic breeds. In this study, 85 microsatellite loci were utilized to assess genetic diversity among native Algerian rabbits (NARs) sampled from an area of 753 km (from north to south) and 919 km (from east to west). Those distances covered 25 significant geographical points in seven rural areas (El Taref, Mostaganem, Sidi Bel Abbès, M'Sila, Dar Chioukh, Faidh El Botma, and Laghouat). A total of 558 alleles were observed in this study. The highest genetic diversity was registered in the southern direction among NAR populations. The mean number of alleles per locus (MNa) and the inbreeding coefficient () were highest in Laghouat (4.482 and 0.232), while they were lowest in El Taref (4.000 and 0.149). In the current study, the number of private alleles (Pa) ranged from 9 to 23. In addition, the average of observed heterozygosity (0.427) was lower than the expected value (0.524) due to high levels of inbreeding. The discriminant analysis of principal components (DAPC), the neighbor-joining tree (NJ), and the analysis of STRUCTURE software confirmed the classification of populations according to geographical zones into four main groups (east, west, south, and middle). The results of the current study are useful for breeding improvement and conservation plan research in relation to local animal genetic resources in Algeria.

Barcoding of ornamental freshwater shrimp, Neocaridina denticulata (De Haan, 1844) from the aquatic ornamental market in Purbalingga, Central Java, Indonesia

Abstract. Kusmintarsih ES, Mahmoud HHA, Sastranegara MH, Syakuri H,Nuryanto A, Ambarningrum TB. 2023. Barcoding of ornamental freshwater shrimp, Neocaridina denticulata (De Haan, 1844) from the aquatic ornamental market in Purbalingga, Central Java, Indonesia. Biodiversitas 24: 3601-3608. Indonesia is one of the world’s leading aquatic ornamental shrimps producers and exports. One of the aquatic ornament shrimp species is a Neocaridina denticulate (De Haan, 1844). There is a wide range of colors including red, bright red, yellow, orange, green, blue, violet, black, and color combinations. It is a landlocked Atydiae family species comprising31 species and subspecies. Due to taxonomic difficulties, this species is continually under revision, and the validation of a few species is currently questionable and uncertain for the relationships among the various colors of N. denticulata. The Cytochrome Oxidase gene I (CO1) gene sequences of mitochondrial DNA were used for species DNA barcoding studies. This study aimed to validate the taxonomic status of different colors of N. denticulata species using the mitochondrial DNA or mtDNA Cytochrome oxidase (CO1) gene sequences. Neighbour Joining trees were constructed based on 545 bp of CO1 gene from white, black, red, yellow, blue colors, and their combination. Several sequences were derived from GenBank for relevant species from different countries and the outgroup. The result showed that all samples are homolog, even to N. denticulata from China NC_023823.1.

Detecting SNP markers discriminating horse breeds by deep learning

The assignment of an individual to the true population of origin using a low-panel of discriminant SNP markers is one of the most important applications of genomic data for practical use. The aim of this study was to evaluate the potential of different Artificial Neural Networks (ANNs) approaches consisting Deep Neural Networks (DNN), Garson and Olden methods for feature selection of informative SNP markers from high-throughput genotyping data, that would be able to trace the true breed of unknown samples. The total of 795 animals from 37 breeds, genotyped by using the Illumina SNP 50k Bead chip were used in the current study and principal component analysis (PCA), log-likelihood ratios (LLR) and Neighbor-Joining (NJ) were applied to assess the performance of different assignment methods. The results revealed that the DNN, Garson, and Olden methods are able to assign individuals to true populations with 4270, 4937, and 7999 SNP markers, respectively. The PCA was used to determine how the animals allocated to the groups using all genotyped markers available on 50k Bead chip and the subset of SNP markers identified with different methods. The results indicated that all SNP panels are able to assign individuals into their true breeds. The success percentage of genetic assignment for different methods assessed by different levels of LLR showed that the success rate of 70% in the analysis was obtained by three methods with the number of markers of 110, 208, and 178 tags for DNN, Garson, and Olden methods, respectively. Also the results showed that DNN performed better than other two approaches by achieving 93% accuracy at the most stringent threshold. Finally, the identified SNPs were successfully used in independent out-group breeds consisting 120 individuals from eight breeds and the results indicated that these markers are able to correctly allocate all unknown samples to true population of origin. Furthermore, the NJ tree of allele-sharing distances on the validation dataset showed that the DNN has a high potential for feature selection. In general, the results of this study indicated that the DNN technique represents an efficient strategy for selecting a reduced pool of highly discriminant markers for assigning individuals to the true population of origin.

Genetic variation and population structure of Fasciola hepatica: an in silico analysis.

Fasciola hepatica is a trematode leading to heavy economic setbacks to the livestock sector globally. The population's genetic information and intimate kinship level are frequently assessed using analysis of mitochondrial DNA. In this analysis, we retrieved cox1 (n = 247) and nad1 (n = 357) sequences of F. hepatica from the NCBI GenBank database and aligned the sequences with the respective reference sequences using MEGA software. The median joining network was drawn using PopArt software while neutrality and diversity indices were estimated with the help of DnaSp software. Neighbor-joining phylogenetic tree was constructed using the MEGA software package. A total of 46 and 98 distinctive haplotypes were observed for cox1 and nad1 genes, respectively. Diversity indices indicated high haplotype and nucleotide diversities in both genes. Positive Tajima's D and Fu's Fs values were found for the entire population of both the genes under study. The cox1 and nad1 gene segments in this study showed high Tajima's D values, suggesting a low likelihood of future population growth. The Tajima's D value of the nad1 gene sequence is lower (2.14910) than that of the cox1 gene sequence (3.40314), which suggests that the former is growing at a slower rate. However, the region-wise analysis revealed that both the cox1 and nad1 genes showed deviation from neutrality suggesting a recent population expansion as a result of an excess of low-frequency polymorphism. Furthermore, the overall host-wise analysis showed positive and significant Tajima's D values for the cox1 and nad1 gene sequences. To the best of our knowledge, this is the first attempt to provide insights into genetic variations and population structure of F. hepatica at a global scale using cox1 and nad1 genes. Our findings suggest the existence of specific variants of F. hepatica in different parts of the world and provide information on the molecular ecology of F. hepatica. The results of this study also mark a critical development in upcoming epidemiological investigations on F. hepatica and will also contribute to understanding the global molecular epidemiology and population structure of F. hepatica.

Comparison of the evolutionary patterns of DNA repeats in ancient and young invertebrate species flocks of Lake Baikal.

DNA repeat composition of low coverage (0.1-0.5) genomic libraries of four amphipods species endemic to Lake Baikal (East Siberia) and four endemic gastropod species of the fam. Baicaliidae have been compared to each other. In order to do so, a neighbor joining tree was inferred for each quartet of species (amphipods and mollusks) based on the ratio of repeat classes shared in each pair of species. The topology of this tree was compared to the phylogenies inferred for the same species from the concatenated protein-coding mitochondrial nucleotide sequences. In all species analyzed, the fraction of DNA repeats involved circa half of the genome. In relatively more ancient amphipods (most recent common ancestor, MRCA, existed approximately sixty millions years ago), the most abundant were species-specific repeats, while in much younger Baicaliidae (MRCA equal to ca. three millions years) most of the DNA repeats were shared among all four species. If the presence/absence of a repeat is regarded as a separate independent trait, and the ratio of shared to total numbers of repeats in a species pair is used as the measure of distance, the topology of the NJ tree is the same as the quartet phylogeny inferred for the mitogenomes protein coding nucleotide sequences. Meanwhile, in each group of species, a substantial number of repeats were detected pointing to the possibility of non-neutral evolution or a horizontal transfer between species occupying the same biotope. These repeats were shared by non-sister groups while being absent in the sister genomes. On the other hand, in such cases some traits of ecological significance were also shared.

Phylogeography of the Asian green mussel, Perna viridis: pronounced regional genetic differentiation is explained by major freshwater input into the Bay of Bengal

The Asian green mussel (AGM), Perna viridis, is a mussel of ecological and economic importance throughout much of the tropical and subtropical regions of Asia, from China and Korea in the east to Oman on the Arabian Peninsula in the west. We collated published DNA sequence data and then analysed 467 bp of cytochrome c oxidase I gene (COI) sequence variation from 649 mussels (576 from SE Asia and 73 from India) to test for regional differentiation. Analysis of molecular variation, a haplotype network and a neighbour-joining tree all revealed significant differentiation between mussels from India and those from SE Asia. We observed a greater number of segregating sites (haplotypes) and private haplotypes than expected for Indian mussels compared to SE Asian mussels, based on the respective sample sizes. Tests of neutrality revealed population expansion or a recent selective sweep for only the mussels from India. We suggest that the differentiation of the Indian from the SE Asian mussels is explained by the pronounced seasonal input of freshwater into the northern Bay of Bengal area, which acts as a (semi-permeable) barrier to gene flow between the two regions (i.e., east versus west of the Bay). This suggestion is based on the oceanography of the region and is consistent with the biogeography and reports of genetic breaks in a range of taxa in this region. Further targetted sampling of AGMs from the east coast of India, Bangladesh and Myanmar is required to test this hypothesis, and additional sampling of AGMs from west of India (e.g., Pakistan, Iran, the Arabian Peninsula) will also be informative. Finally, this study is based on the analysis of a single marker (COI) because this is all that is presently available from published sources but we note that the application of new molecular markers such as single nucleotide polymorphisms to newly collected mussel samples will greatly advance our understanding of the AGM genetic discontinuity and its age, and help test its geographical location and its nature (e.g., a steep/shallow cline or a stepped cline).