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Kohlrabi is an important swollen-stem cabbage variety belonging to the Brassicaceae family. However, few complete chloroplast genome sequences of this genus have been reported. Here, a complete chloroplast genome with a quadripartite cycle of 153,364 bp was obtained. A total of 132 genes were identified, including 87 protein-coding genes, 37 transfer RNA genes and eight ribosomal RNA genes. The base composition analysis showed that the overall GC content was 36.36% of the complete chloroplast genome sequence. Relative synonymous codon usage frequency (RSCU) analysis showed that most codons with values greater than 1 ended with A or U, while most codons with values less than 1 ended with C or G. Thirty-five scattered repeats were identified and most of them were distributed in the large single-copy (LSC) region. A total of 290 simple sequence repeats (SSRs) were found and 188 of them were distributed in the LSC region. Phylogenetic relationship analysis showed that five Brassica oleracea subspecies were clustered into one group and the kohlrabi chloroplast genome was closely related to that of B. oleracea var. botrytis. Our results provide a basis for understanding chloroplast-dependent metabolic studies and provide new insight for understanding the polyploidization of Brassicaceae species. [ABSTRACT FROM AUTHOR]

Coxsackievirus A6 (CV-A6) has emerged as the predominant causative agent of hand, foot, and mouth disease (HFMD) in young children. Since the declaration of coronavirus disease 2019 (COVID-19) as a global pandemic, the incidence of infectious diseases, including HFMD, has decreased markedly. When social mitigation was relaxed during the COVID-19 pandemic in 2022, the re-emergence of HFMD was observed in Gwangju, South Korea, and seasonal characteristics of the disease appeared to have changed. To investigate the molecular characteristics of enterovirus (EV) associated with HFMD during 2022, 277 specimens were collected. Children aged younger than 5 years accounted for the majority of affected individuals. EV detection and genotyping were performed using real-time RT-PCR and nested RT-PCR followed by sequence analysis. The EV detection rate was found to be 82.3%, and the main genotype identified was CV-A6. Sixteen CV-A6 samples were selected for whole genome sequencing. According to phylogenetic analysis, all CV-A6 strains from this study belonged to the sub-genotype D3 clade based on VP1 sequences. Analysis of 3D polymerase phylogeny showed that only the recombinant RF-A group was identified. In conclusion, circulating EV types should be continuously monitored to understand pathogen emergence and evolution during the post-pandemic era. [ABSTRACT FROM AUTHOR]

Simple Summary: Ammannia arenaria and A. multifloras, the most common broad-leaved weeds in rice paddy fields in China, are morphologically similar at the seedling stage. However, their degree of damage to rice may vary. Furthermore, the sensitivity of two species to the constantly emerging new herbicides is also unknown. This study conducted field investigations, indoor biological experiments, and chloroplast genome construction and analysis to clarify the differences in biological characteristics, herbicide sensitivity, and chloroplast genetics between A. arenaria and A. multifloras. Our research results may provide theoretical basis for weed occurrence prediction, selection of herbicides, and Ammannia classification and distinction. Furthermore, the results provided valuable biological information on cp genomes of Ammannia that will be useful to identify and classify Ammannia, and study their phylogenetic relationships and evolution. Ammannia arenaria and A. multifloras, morphologically similar at the seedling stage, are the most common broad-leaved weeds in paddy fields. Our study showed that A. arenaria occupied more space than A. multifloras when competing with rice. However, A. multifloras germination has lower temperature adaptability. No difference in sensitivity to common herbicides between two Ammannia species was observed. Chloroplast (cp) genomes could be conducive to clarify their genetic relationship. The complete cp genome sequences of A. arenaria (158,401 bp) and A. multiflora (157,900 bp) were assembled for the first time. In A. arenaria, there were 91 simple sequence repeats, 115 long repeats, and 86 protein-encoding genes, one, sixteen, and thirty more than those in A. multiflora. Inverted repeats regions expansion and contraction and the phylogenetic tree based on cp genomes demonstrated the closely relationship between the two species. However, in A. arenaria, 20 single nucleotide polymorphisms in the CDS region were detected compared to A. multiflora, which can be used to distinguish the two species. Moreover, there was one unique gene, infA, only in A. arenaria. This study provides reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure, and biodiversity of Ammannia species. [ABSTRACT FROM AUTHOR]

In this study, we determined the complete mitochondrial genome of the invasive insect species Melanoplus differentialis captured in Korea. The complete mitochondrial genome of M. differentialis is 15,625 bp long and comprises 13 protein‐coding genes, two ribosomal RNA genes, and 22 transfer RNAs, with a GC ratio of 25.2%. In total, 353 SNPs and 11 INDEL regions (total length 67 bp) were found against the previously sequenced M. differentialis mitochondrial genome recorded as public genome data. The number of interspecific variations was greater than the number of intraspecific variations in this insect. Phylogenetic tree analysis showed that the mitochondrial genome clustered the Melanoplus clade with two previously reported Melanoplus sequences. However, the sequences were not divided at the species‐level clade possibly as a consequence of misidentification caused by an error in the public database. Our results extend the molecular database status of Melanoplus by providing a novel complete mitochondrial genome sequence for M. differentialis that could serve as reference for further molecular studies. [ABSTRACT FROM AUTHOR]

Hibiscus mutabilis is native to China with a long cultivation history, and is an ancient garden tree species and medicinal plant. In this study, we selected three cultivars of H. mutabilis in a hybrid combination(H. mutabilis cv. Danbanbai, H. mutabilis cv. Jinqiusong, H. mutabilis cv. Mudanfen)to investigate evolutionary characteristics between the cultivars of H. mutabilis and its related species, and clarify the phylogenetic relationship between the cultivars of H. mutabilis and its related species, as well as explore the genetic model of chloroplast genome(cpDNA)of H. mutaibilis at the same time. We first sequenced the three cultivars of H. mutaibilis using Illumina NovaSeq. After assembly and annotation, three complete chloroplast genome sequences were obtained. The cpDNAs of the related species H. taiwanensis from our group, and H. syricus and H. rosa-sinensis from the gene bank. Then we carried out comparative analysis on composition and structure of cpDNAs of four species of Hibiscus and three cultivars of H. mutabilis, and completed its phylogenetic tree reconstruction. The results were as follows: (1)Total sizes of cpDNAs of H. mutabilis cv. Danbanbai, H. mutabilis cv. Jinqiusong, H. mutabilis cv. Mudanfen were 160 880, 160 879, 160 920 bp, respectively, and the total gene number was 130, including 85 protein-coding genes, eight ribosomal RNAs, and 37 transfer RNAs. (2) The comparative analyses showed that the cpDNAs of three cultivars of H. mutabilis and the related species H. taiwanensis were highly conserved, and the inverted repeat regions(IR)were all 26 300 bp; H. rosa-sinensis and H. syriacus shrank to at 25 745 and 25 598 bp, respectively.(3)The phylogenetic analysis revealed that the three cultivars were planted into a monophyletic branch, and then together with H. taiwanensis into a high support branch, indicating that H. mutabilis and H. taiwanensis had the closest relationship; Compared with H. syriacus and H. rosa-sinensis, H. mutabilis and H. taiwanensis were more closely related to H. hamabo, H. tiliaceum and H. canabinus.(4)Three cultivars of H. mutabilis could be distinguished by cpDNA sequence, the length of LSC/SSC of H. mutabilis cv. Danbanbai, H. mutabilis cv. Jinqiusong, H. mutabilis cv. Mudanfen were 89 355 bp/18 925 bp, 89 353 bp/18 926 bp, 89 400 bp/18 920 bp, respectively. And candidate molecular markers and DNA barcodes had been developed from repeat sequence and nucleotide diversity analyses, which could be used as a tool for cultivars identification.(5)The cpDNAs of H. mutabilis cv. Danbanbai and H. mutabilis cv. Jinqiusong showed a minimum difference and had the closest phylogenetic relationship. According to the relationship between their female and offspring, the maternal genetic characteristics of the cpDNAs of Hibiscus were proved. This study will help us to understand the evolutionary characteristics and phylogenetic relationship of cpDNAs of three cultivars of H. mutabilis and H. taiwanensis, and provide basic data on cpDNA for accurate identification of the cultivars of H. mutabilis and breeding of excellent cultivars. [ABSTRACT FROM AUTHOR]

Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, we assembled the complete cp genome sequences of Echinochloa crus-galli var. crus-galli (139,856 bp), E. crus-galli var. zelayensis (139,874 bp), and E. glabrescens (139,874 bp), which exhibited a typical circular tetramerous structure, large and small single-copy regions, and a pair of inverted repeats. In Echinochloa crus-galli var. crus-galli, there were 136 simple sequence (SSRs) and 62 long (LRs) repeats, and in the other two species, 139 SSRs and 68 LRs. Each cp genome contains 92 protein-encoding genes. In Echinochloa crus-galli var. crus-galli and E. glabrescens, 321 and 1 single-nucleotide polymorphisms were detected compared to Echinochloa crus-galli var. zelayensis. IR expansion and contraction revealed small differences between the three species. The phylogenetic tree based on cp genomes demonstrated the phylogenetic relationship between ten barnyard grass species and other common Gramineae plants, showing new genetic relationships of the genus Echinochloa. This study provides valuable information on cp genomes, useful for identifying and classifying the genus Echinochloa and studying its phylogenetic relationships and evolution. [ABSTRACT FROM AUTHOR]

Estimating the time scale of species evolution is an important part of life evolution study. It is found that there are significant differences in the evolution rates of different genes and species in recent years, which challenges the molecular clock hypothesis to a great extent. Therefore, new methods are needed to re-estimate the evolutionary event time. The whole genome sequence of angiosperms makes it possible to estimate the evolutionary time from the whole genome perspective. In order to re-estimate the evolution time of angiosperms, an evolution rate correction model based on genomic data is established according to the idea that shared polyploidy events or shared divergence events should have the same Ks peak. The results were as follows:(1)Three common ways to obtain Ks distribution were compared and analyzed, which showed that the best way was to extract the median of Ks values on collinear blocks.(2)The change process of Ks distribution was simulated with time accumulation coefficient(v)of Ks values. When v was assumed to obey the normal distribution, the Ks distribution had a long tail phenomenon.(3)The correction process was described in detail, which was conducive to the understanding and wide spread of this method. From the application of correction method in angiosperms, it was found that the Ks peak before correction was not linear with time, while the Ks peak after correction was directly proportional to time, indicating that it is very necessary to estimate the time of species evolution events after correcting the Ks peak. It was also found that although the evolution rate of angiosperms was significantly different, the evolution rate between different branches was still partially consistent. For example, Magnoliids had the slowest evolutionary rate, followed by Eudicots and Monocots. When the environment changed greatly, most species of different lineages of angiosperms had synchronous radial evolution and adaptive evolution. Finally, a relatively reliable angiosperm evolution time axis was establish, which helps to understand the evolution process and model, especially to understand the phylogenetic relationship and the causes of diversity and provides phylogenetic and evolutionary support for plant research. [ABSTRACT FROM AUTHOR]

The Porcine reproductive and respiratory syndrome virus (PRRSV), a single (+) RNA virus, is characterized by high genome variability and constant evolution. Owing to increasingly complex mutations, there is a growing difficulty in accessing the whole genome. Additionally, there is limited knowledge on PRRSV intra‐host nucleotide variants, which may reflect the complex viral‐host dynamics. Here, we performed next‐generation sequencing on four clinical lung tissues to reveal the genomic diversity and highlight virus‐host interactions. The complete genomes of the HN0713 and GDYJ1224 strains shared 90.7% and 91.3% homology with the lineage 1 strain NADC30, respectively, while the GDGZ0408 and GDHY0425 strains shared 92.0% and 91.6% homology with the JXA1 strain, respectively. Recombination analysis showed that the ORF5–7 genes of the GDGZ0408 and GDHY0425 strains, whose complete genomes belong to lineage 8.7 based on the phylogenetic tree, are both recombined with lineage 3 strains. Furthermore, nsp3, nsp10–12, ORF2 genes and a part of the 3′‐UTR of the GDHY0425 strain were provided by the lineage 5.1 strain. Two lineage 1 strains (GDYJ1224 and HN0713) were produced by a recombination of lineages 8.7 and 1. Additionally, the lineage 3 strain was associated with the recombinant HN0713 strain. We determined the intra‐host single nucleotide variant frequencies and found more than 200 sites at a frequency of >1% in all samples. GDGZ0408 with parts of the nsp9 and nsp10 genes of HP‐PRRSV lineage 8.7 presented more genetically diverse populations than others, indicating that lineage 8.7 might drive robust intra‐host single nucleotide variants (iSNVs). Moreover, in the iSNV pools, nsp2 and ORF2a presented the highest mutation dynamic. Overall, this study provided evidence for the alarmingly increasing recombination and ever‐changing evolutionary dynamics of PRRSV, and revealed the potential causes of vaccine escape, providing a novel insight into the nucleotide variant population in clinical samples. [ABSTRACT FROM AUTHOR]

Background: Bovine mastitis is an important cause of economic loss in dairy farms. Streptococcus uberis is among the most frequently isolated bacterial species isolated from cows with mastitis. The aim of this study was to perform an in-depth genetic assessment of S. uberis strains isolated from bovine clinical mastitis (CM) and to perform a phylogenetic analysis to represent the evolutionary relationship among S. uberis sequences. Results: A total of 159 isolates was genetically characterized using whole genome sequencing. According to the virulence determinants, all strains harbored the hasC, leuS, perR, purH, and purN virulence genes. Thirty-four resistance genes were identified in at least one strain. In terms of acquired genes, we observed that 152 (95.6 %) strains had a resistance gene to lincosamine (lnuD), 48 (30.2 %) to tetracycline (tetM), 4 (2.51 %) to tobramicine (ant6), and 1 to lincosamide (lsa(E)). MLST detected the Sequence Type (ST)797 (n = 23), while 85.5 % of the strains did not match to known STs. Conclusions: Then, eleven distinct ST were identified after we submitted the new alleles to assign new STs. The other prevalent STs observed were ST1215 (n = 58), ST1219 (n = 35), and ST1213 (n = 15). And it was not possible to identify the MLST of four strains. Phylogenetic lineages indicated a high genomic diversity of S. uberis in our collection, confirming that most strains isolated from bovine mastitis have different reservoirs, typical of environmental pathogens. [ABSTRACT FROM AUTHOR]

Decapod hepandensovirus 1 (DHPV) is a viral pathogen that causes growth retardation and decreased feed conversion efficiency in penaeid shrimp. The virus exhibits high genetic variation between different hosts and geographical locations. It has been primarily reported in cultured Penaeus monodon , P. chinensis , and P. merguiensis , and a new type of DHPV has recently been reported in P. vannamei cultured in Korea and Taiwan. In this study, the genome of a recently reported new type of DHPV was fully sequenced by conventional Sanger sequencing combined with a next-generation sequencing approach. Similar to the other types of DHPVs infecting several shrimp species other than P. vannamei , a new type of DHPV contained a linear, single-stranded DNA genome of 6173 bp comprising three major open reading frames. However, by detailed comparative genome and phylogenetic analysis, the virus was not clustered with the pre-existing genotypes, suggesting the emergence of a possible novel genotype of DHPV in cultured shrimps. This study is the first to report the complete genomic sequence of DHPV identified in P. vannamei. • A new genotype of Decapod hepandensovirus 1 (DHPV) is found in Penaeus vannamei. • Complete genome sequence of DHPV infecting Penaeus vannamei presented in the study. • The DNA genome is 6173 bp in size, comprising 3 major open reading frames (ORFs). • ORF 3 region of the new DHPV shows notably low similarity to 9 historic viruses. • The phylogenetic tree shows the new DHPV doesn't cluster with existing genotypes. [ABSTRACT FROM AUTHOR]

Leptospirosis, a major zoonotic disease caused by pathogenic Leptospira spp. is recognized globally as an emerging zoonotic disease. Whole-genome sequencing reveals hidden messages about Leptospira's pathogenesis. We used Single Molecule Real-Time (SMRT) sequencing to obtain complete genome sequences of twelve L. interrogans isolates from febrile patients from Sri Lanka for a comparative whole genome sequencing study. The sequence data generated 12 genomes with a coverage greater than X600 with sizes ranging from 4.62 Mb to 5.16 Mb, and a G + C content ranging from 35.00% to 35.42%. The total number of coding sequences predicted by the NCBI (National Center for Biotechnology Information) genome assembly platform ranged from 3845 to 4621 for the twelve strains. Leptospira serogroup with similar-sized LPS biosynthetic loci that belonged to the same clade had a close relationship in the phylogenetic analysis. Nonetheless, variations in the genes encoding sugar biosynthesis were found in the serovar determinant region (rfb locus). Type I and Type III CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems were found in all of the strains. Genome BLAST Distance Phylogeny of these sequences allowed for detailed genomic strain typing. These findings may help us better understand the pathogenesis, develop a tools for early diagnosis, comparative genomic analysis and evolution of Leptospira. • Complete whole genome sequences of 12 Leptospira interrogans strains. • LPS biosynthesis gene of same clonal group had close relationship. • Type I and Type III CRISPR systems were found in all of the strains. • Seven main types of IS elements were detected ISLin1/2, IS1500B, IS1500A, IS1501, IS1533, ISlbp3. [ABSTRACT FROM AUTHOR]

Many processes, such as growth, aging, and adaptation to abiotic stress, are regulated in plants by NAC transcription factors. In woody plants, NAC transcription factors acts as a primary switch that regulates secondary xylem development by activating various downstream transcription factors and modulating expression levels of genes involved in the synthesis of the secondary cell wall. Our team had previously sequenced the whole genome of the camphor tree (Cinnamomum camphora). Here, we performed a detailed analysis of the NAC gene family of C. camphora and examined its evolutionary history. The genomic sequences of 121 NAC genes of C. camphora were identified and classified into 20 subfamilies in 2 major classes based on the phylogenetic analysis and structural features. Expansion of the CcNAC gene family occurred mainly by fragment replication and was influenced by the purifying selection. By analyzing predicted interactions of the homologous AtNAC proteins, we identified five CcNACs that potentially regulate xylem development in C. camphora. RNA sequencing revealed distinct expression profiles of CcNACs in seven different plant tissues. Subcellular localization prediction revealed that 120, 3, and 2 CcNACs have biological functions in the nucleus, cytoplasm, and chloroplast, respectively. Furthermore, we verified expression patterns of five CcNACs (CcNAC012 , CcNAC028 , CcNAC055 , CcNAC080 , and CcNAC119) in various tissue types using qRT-PCR. Our results will facilitate further in-depth studies of the molecular mechanisms by which CcNAC transcription factors regulate wood formation and other processes in C. camphora. • We identified 121 genes encoding NAC transcription factors in Cinnamomum camphora. • camphora NAC genes were divided into two major classes and 20 subfamilies. • Expansion of the CcNAC gene family occurred mainly by fragment replication. • Five CcNAC genes were identified that likely regulated wood formation. [ABSTRACT FROM AUTHOR]

Kosta goat is one of the Indonesian local goats which had the potential to utilize, while their genetics was not yet characterized. Since, a high mutation of Mitochondria DNA (mtDNA), it is widely applied to understand species evolutionary, phylogenetic, and characterized population genetics. Whole genome sequencing of Mitochondria DNA has new insight to elucidate genetic characteristic of goat completely. Therefore, this study purposes to explore the whole mitochondrial DNA of the Kosta goat and its relationship with other breeds based on Whole Genome Sequensing (WGS). The Kosta goat mitochondria genome was collected from whole blood, which was enriched using REPLI-g Mitochondrial DNA Kit (Qiagen). Oxford Nanopore Technology was employed in the mtDNA sequencing. The assembled sequence was polished with Racon and Medaka , and was further determined using Quast. Furthermore, Annotation and Visualization were conducted using MitoZ and Mitos Webserver. The sequence mitochondria genome of the Kosta goat has 16,641 bp, consisting of 13 PCGs (Protein Coding Genes), 22 tRNA, 2 rRNA, D_loop region, as well as OL (origin loop) sequences. Also, it has a base composition of 33.57 % for Adenin (A), 27.31 % for Timin (T), 26.04 % for Cytosin (C), and 13.08 % for Guanin (G), with sequential percentages of A>T>C>G. The start codons of PGCs are primarily initiated by ATG, whereas for ND2, ND3, and ND5 by ATA. Specific genetic characteristic of mitogenome Kosta goat has 309 bp length of ND3. Kosta goat belongs to Lineage B, and this follows the study of other Indonesian goats. Complete mitochondrial DNA of Kosta goats can be used to characterize their genetic potential, genetic diversity, phylogenetic analysis to support their utilization and conservation. • Kosta goat is one of Indonesian local goats. • Complete Mitochondrial DNA sequencing is a new insight to elucidate genetic characteristic of Kosta goats. • Complete mitochondrial DNA of Kosta goat may help provide data for further analysis on the mtDNA sequence to support goat genetic research. [ABSTRACT FROM AUTHOR]

Background: Patients often ask oncologists how long a cancer has been present before causing symptoms or spreading to other organs. The evolutionary trajectory of cancers can be defined using phylogenetic approaches but lack of chronological references makes dating the exact onset of tumours very challenging. Patients and methods: Here, we describe the case of a colorectal cancer (CRC) patient presenting with synchronous lung metastasis and metachronous thyroid, chest wall and urinary tract metastases over the course of 5 years. The chest wall metastasis was caused by needle tract seeding, implying a known time of onset. Using whole genome sequencing data from primary and metastatic sites we inferred the complete chronology of the cancer by exploiting the time of needle tract seeding as an in vivo 'stopwatch'. This approach allowed us to follow the progression of the disease back in time, dating each ancestral node of the phylogenetic tree in the past history of the tumour. We used a Bayesian phylogenomic approach, which accounts for possible dynamic changes in mutational rate, to reconstruct the phylogenetic tree and effectively 'carbon date' the malignant progression. Results: The primary colon cancer emerged between 5 and 8 years before the clinical diagnosis. The primary tumour metastasized to the lung and the thyroid within a year from its onset. The thyroid lesion presented as a tumour-to-tumour deposit within a benign Hurthle adenoma. Despite rapid metastatic progression from the primary tumour, the patient showed an indolent disease course. Primary cancer and metastases were microsatellite stable and displayed low chromosomal instability. Neo-antigen analysis suggested minimal immunogenicity. Conclusion: Our data provide the first in vivo experimental evidence documenting the timing of metastatic progression in CRC and suggest that genomic instability might be more important than themetastatic potential of the primary cancer in dictating CRC fate. [ABSTRACT FROM AUTHOR]

As surges of the COVID-19 pandemic continue globally, including in Palestine, several new SARS-CoV-2 variants have been introduced. This expansion has impacted transmission, disease severity, virulence, diagnosis, therapy, and natural and vaccine-induced immunity. Here, 183 whole genome sequences (WGS) were analyzed, of which 129 were from Palestinian cases, 62 of which were collected in 11 Palestinian districts between October 2020 and April 2021 and sequenced completely. A dramatic shift from the wild type to the Alpha variant (B 1.1.7) was observed within a short period of time. Cluster mapping revealed statistically significant clades in two main Palestinian cities, Al-Khalil (Monte Carlo hypothesis test-Poisson model, P = 0.00000000012) and Nablus (Monte Carlo hypothesis test-Poisson model, P = 0.014 and 0.015). The phylogenetic tree showed three main clusters of SARS-CoV-2 with high bootstrap values (>90). However, population genetics analysis showed a genetically homogenous population supported by low Wright's F-statistic values (Fst <0.25), high gene flow (Nm > 3), and statistically insignificant Tajima's D values (Tajima's test, neutrality model prediction, P = 0.02). The Alpha variant, rapidly replaced the wild type, causing a major surge that peaked in April 2021, with an increased COVID-19 mortality rate, especially, in the Al-Khalil and Nablus districts. The source of introduction remains uncertain, despite the minimal genetic variation. The study substantiates the use of WGS for SARS-CoV-2 surveillance as an early warning system to track down new variants requiring effective control. • Within a short period of time, a dramatic shift from wild type to the alpha variant (B 1.1.7) was observed. • Cluster mapping revealed two statistically significant clusters in two main Palestinian cities, Al-Khalil and Nablus. • Phylogenetic analysis showed three main clusters of SARS-CoV-2. • Population genetics analysis showed a genetically homogenous population. • In spring 2021, the alpha variant, rapidly replaced the wild type. [ABSTRACT FROM AUTHOR]

• Provided accurate genome and annotation data of Russula griseocarnosa firstly. • Clarified that non-correlation between taxonomy and nutritional ecological type. • Screened out the specific carbohydrate enzymes in R. griseocarnosa. Russula griseocarnosa is a well-known ectomycorrhizal mushroom, which is mainly distributed in the Southern China. Although several scholars have attempted to isolate and cultivate fungal strains, no accurate method for culture of artificial fruiting bodies has been presented owing to difficulties associated with mycelium growth on artificial media. Herein, we sequenced R. griseocarnosa genome using the second- and third-generation sequencing technologies, followed by de novo assembly of high-throughput sequencing reads, and GeneMark-ES, BLAST, CAZy, and other databases were utilized for functional gene annotation. We also constructed a phylogenetic tree using different species of fungi, and also conducted comparative genomics analysis of R. griseocarnosa against its four representative species. In addition, we evaluated the accuracy of one already sequenced genome of R. griseocarnosa based on the internal transcribed spacer (ITS) sequencing of that type of species. The assembly process resulted in identification of 230 scaffolds with a total genome size of 50.67 Mbp. The gene prediction showed that R. griseocarnosa genome included 14,229 coding sequences (CDs). In addition, 470 RNAs were predicted with 155 transfer RNAs (tRNAs), 49 ribosomal RNAs (rRNAs), 41 small noncoding RNAs (sRNAs), 42 small nuclear RNAs (snRNAs), and 183 microRNAs (miRNAs). The predicted protein sequences of R. griseocarnosa were analyzed to indicate the existence of carbohydrate-active enzymes (CAZymes), and the results revealed that 153 genes encoded CAZymes, which were distributed in 58 CAZyme families. These enzymes included 78 glycoside hydrolases (GHs), 34 glycosyl transferases (GTs), 30 auxiliary activities (AAs), 2 carbohydrate esterases (CEs), 8 carbohydrate-binding modules (CBMs), and only one polysaccharide lyase (PL). Compared with other fungi, R. griseocarnosa had fewer CAZymes, and the number and distribution of CAZymes were similar to other mycorrhizal fungi, such as Tricholoma matsutake and Suillus luteus. Well-defined effector proteins that were associated with mycorrhiza-induced small-secreted proteins (MiSSPs) were not found in R. griseocarnosa , which indicated that there may be some special effector proteins to interact with host plants in R. griseocarnosa. The genome of R. griseocarnosa may provide new insights into the energy metabolism of ectomycorrhizal (ECM) fungi, a reference to study ecosystem and evolutionary diversification of R. griseocarnosa , as well as promoting the study of artificial domestication. [ABSTRACT FROM AUTHOR]

• Avian polyomavirus (APV) isolates collected from parrots in Taiwan were amplified via polymerase chain reaction, after which the whole genomes of these isolates were sequenced. • The APV-positive rate was 14.2%, and the full lengths of the APV Taiwan isolates varied from 4971 to 4982 bps. • The nucleotide identities of the VP1 and VP4 genes ranged from 98.8 to 100%, whereas the nucleotide sequence of the Large T-Ag gene had the highest identity. • APV Taiwan isolates could be classified into five independent groups in a phylogenetic tree based on the whole genome. • Two possible recombination events in the genomes of APV isolates were identified. Avian polyomavirus (APV) is a non-enveloped virus with a circular double-stranded DNA genome approximately 5000 bp in length. APV was first reported in fledgling budgerigars (Melopsittacus undulatus) as the causative agent of budgerigar fledgling disease, resulting in high parrot mortality rates in the 1980s. This disease has been observed worldwide, and APV has a wide host range including budgerigars, cockatoos, lorikeets, lovebirds, and macaws. Twenty APV isolates have been collected from healthy and symptomatic parrots in Taiwan from 2015 to 2019. These isolates were then amplified via polymerase chain reaction, after which the whole genomes of these isolates were sequenced. The overall APV-positive rate was 14.2%, and the full lengths of the APV Taiwan isolates varied from 4971 to 4982 bps. The APV genome contains an early region that encodes two regulatory proteins (the large tumor antigen (Large T-Ag) and the small tumor antigen (Small t-Ag)) and a late region which encodes the capsid proteins VP1, VP2, VP3, and VP4. The nucleotide identities of the VP1 and VP4 genes ranged from 98.7 to 100%, whereas the nucleotide sequence of the Large T-Ag gene had the highest identity (99.2–100%) relative to other APV isolates from the GenBank database. A phylogenetic tree based on the whole genome demonstrated that the APV Taiwan isolates were closely related to Japanese and Portuguese isolates. Recombination events were analyzed using the Recombination Detection Program version 4 and APV Taiwan isolate TW-3 was identified as a minor parent of the APV recombinants. In this study, we first reported the characterization of the whole genome sequences of APV Taiwan isolates and their phylogenetic relationships with all APV isolates available in the GenBank database. [ABSTRACT FROM AUTHOR]

[Display omitted] • First report of whole genome sequencing of genus Jacksonvillea sp. ISTCYN1 is reported. • Desertifilum sp. IPPAS B-1220 was closest genus by phylogenetic tree constructed. • Biofilm formation and biodegradation of polyethylene were shown by this strain. • WGA revealed the presence of selenoproteins and gene involved in biotin synthesis. • Gene prediction analysis showed presence of enzymes responsible for PE and PP degradation. Filamentous cyanobacteria, Jacksonvillea sp. ISTCYN1 was isolated from agriculture field and cultured in BG-11 medium. This study, report the genome sequence of cyanobacteria Jacksonvillea that to the best of our knowledge is the first genome sequence of this genus. The 5.7 MB draft genome sequence of this cyanobacterium contains 5134 protein-coding genes. The phylogenetic tree was constructed based on genome and Desertifilum sp. IPPAS B-1220 validated the closest relationship with Jacksonvillea sp. ISTCYN1. The growth of strain ISTCYN1 has been reported in the presence of different types of plastic when used as a sole carbon source. SEM analysis revealed biofilm formation by cyanobacterial strain ISTCYN1 on the surface of high and low-density polyethylene and polypropylene. In the presence of these plastics, EPS production has also been reported by this strain. Whole genome sequence analysis reveals the presence of many genes involved in biofilm formation. The presence of key enzymes responsible for plastic degradation laccase, esterase, lipase, thioesterase, and peroxidase have been predicted in the genome analysis. Genome analysis also provides insight into the genes involved in biotin biosynthetic pathways. Furthermore, the presence of many selenoproteins reveals the selenium acquisition by this cyanobacterium. [ABSTRACT FROM AUTHOR]