Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species.

BACKGROUND: Plant genome information is fundamental to plant research and development. Along with the increase in the number of published plant genomes, there is a need for an efficient system to retrieve various kinds of genome-related information from many plant species across plant kingdoms. Various plant databases have been developed, but no public database covers both genomic and genetic resources over a wide range of plant species. MAIN BODY: We have developed a plant genome portal site, Plant GARDEN (Genome And Resource Database Entry: https://plantgarden.jp/en/index ), to provide diverse information related to plant genomics and genetics in divergent plant species. Elasticsearch is used as a search engine, and cross-keyword search across species is available. Web-based user interfaces (WUI) for PCs and tablet computers were independently developed to make data searches more convenient. Several types of data are stored in Plant GARDEN: reference genomes, gene sequences, PCR-based DNA markers, trait-linked DNA markers identified in genetic studies, SNPs, and in/dels on publicly available sequence read archives (SRAs). The data registered in Plant GARDEN as of March 2023 included 304 assembled genome sequences, 11,331,614 gene sequences, 419,132 DNA markers, 8,225 QTLs, and 5,934 SNP lists (gvcf files). In addition, we have re-annotated all the genes registered in Plant GARDEN by using a functional annotation tool, Hayai-Annotation, to compare the orthologous relationships among genes. CONCLUSION: The aim of Plant GARDEN is to provide plant genome information for use in the fields of plant science as well as for plant-based industries, education, and other relevant areas. Therefore, we have designed a WUI that allows a diverse range of users to access such information in an easy-to-understand manner. Plant GARDEN will eventually include a wide range of plant species for which genome sequences are assembled, and thus the number of plant species in the database will continue to expand. We anticipate that Plant GARDEN will promote the understanding of genomes and gene diversity by facilitating comparisons of the registered sequences.

An improved reference genome for Trifolium subterraneum L. provides insight into molecular diversity and intra-specific phylogeny.

Subterranean clover (Trifolium subterraneum L., Ts) is a geocarpic, self-fertile annual forage legume with a compact diploid genome (n = x = 8, 544 Mb/1C). Its resilience and climate adaptivity have made it an economically important species in Mediterranean and temperate zones. Using the cultivar Daliak, we generated higher resolution sequence data, created a new genome assembly TSUd_3.0, and conducted molecular diversity analysis for copy number variant (CNV) and single-nucleotide polymorphism (SNP) among 36 cultivars. TSUd_3.0 substantively improves prior genome assemblies with new Hi-C and long-read sequence data, covering 531 Mb, containing 41,979 annotated genes and generating a 94.4% BUSCO score. Comparative genomic analysis among select members of the tribe Trifolieae indicated TSUd 3.0 corrects six assembly-error inversion/duplications and confirmed phylogenetic relationships. Its synteny with T. pratense, T. repens, Medicago truncatula and Lotus japonicus genomes were assessed, with the more distantly related T. repens and M. truncatula showing higher levels of co-linearity with Ts than between Ts and its close relative T. pratense. Resequencing of 36 cultivars discovered 7,789,537 SNPs subsequently used for genomic diversity assessment and sequence-based clustering. Heterozygosity estimates ranged from 1% to 21% within the 36 cultivars and may be influenced by admixture. Phylogenetic analysis supported subspecific genetic structure, although it indicates four or five groups, rather than the three recognized subspecies. Furthermore, there were incidences where cultivars characterized as belonging to a particular subspecies clustered with another subspecies when using genomic data. These outcomes suggest that further investigation of Ts sub-specific classification using molecular and morpho-physiological data is needed to clarify these relationships. This upgraded reference genome, complemented with comprehensive sequence diversity analysis of 36 cultivars, provides a platform for future gene functional analysis of key traits, and genome-based breeding strategies for climate adaptation and agronomic performance. Pangenome analysis, more in-depth intra-specific phylogenomic analysis using the Ts core collection, and functional genetic and genomic studies are needed to further augment knowledge of Trifolium genomes.

Chromosome-scale genome assembly of Eustoma grandiflorum, the first complete genome sequence in the genus Eustoma.

Eustoma grandiflorum (Raf.) Shinn. is an annual herbaceous plant native to the southern United States, Mexico, and the Greater Antilles. It has a large flower with a variety of colors and is an important flower crop. In this study, we established a chromosome-scale de novo assembly of E. grandiflorum genome sequences by integrating four genomic and genetic approaches: (1) Pacific Biosciences (PacBio) Sequel deep sequencing, (2) error correction of the assembly by Illumina short reads, (3) scaffolding by chromatin conformation capture sequencing (Hi-C), and (4) genetic linkage maps derived from an F2 mapping population. Thirty-six pseudomolecules and 64 unplaced scaffolds were created, with a total length of 1,324.8 Mb. A total of 36,619 genes were predicted on the genome as high-confidence genes. A comparison of genome structure between E. grandiflorum and C. canephora or O. pumila suggested whole-genome duplication after the divergence between the families Gentianaceae and Rubiaceae. Phylogenetic analysis with single-copy genes suggested that the divergence time between Gentianaceae and Rubiaceae was 74.94 MYA. Genetic diversity analysis was performed for nine commercial E. grandiflorum varieties bred in Japan, from which 254,205 variants were identified. This first report on the construction of a reference genome sequence in the genus Eustoma is expected to contribute to genetic and genomic studies in this genus and in the family Gentianaceae.

De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'.

The first genome sequence of an interspecific grape hybrid (Vitis labruscana × Vitis vinifera), 'Shine Muscat', an elite table grape cultivar bred in Japan, is presented. The resultant genome assemblies included two types of sequences: a haplotype-phased sequence of the highly heterozygous genomes and an unphased sequence representing a 'pseudo-haploid' genome. The unphased sequences, assembled to the chromosome level with Hi-C reads, spanned 488.97 Mb in length, 99.1% of the estimated genome size, with 4,595 scaffold sequences and a 23.9-Mb N50 length. The phased sequences had 15,650 scaffolds spanning 1.0 Gb and a 4.2-Mb N50 length. 32,827 high-confidence genes were predicted on the unphased genomes. Clustering analysis of the 'Shine Muscat' gene sequences with three other Vitis species and Arabidopsis indicated that 11,279 orthologous gene clusters were common to Vitis spp. and Arabidopsis, 4,385 were Vitis specific, and 234 were 'Shine Muscat' specific. Whole-genome resequencing was also performed for the parental lines of 'Shine Muscat', Akitsu-21 and 'Hakunan', and parental-specific copy number variations were identified. The obtained genome resources provide new insights that could assist in cultivation and breeding strategies to produce high-quality table grapes.

Genome features of common vetch (Vicia sativa) in natural habitats.

Wild plants are often tolerant to biotic and abiotic stresses in their natural environments, whereas domesticated plants such as crops frequently lack such resilience. This difference is thought to be due to the high levels of genome heterozygosity in wild plant populations and the low levels of heterozygosity in domesticated crop species. In this study, common vetch (Vicia sativa) was used as a model to examine this hypothesis. The common vetch genome (2n = 14) was estimated as 1.8 Gb in size. Genome sequencing produced a reference assembly that spanned 1.5 Gb, from which 31,146 genes were predicted. Using this sequence as a reference, 24,118 single nucleotide polymorphisms were discovered in 1243 plants from 12 natural common vetch populations in Japan. Common vetch genomes exhibited high heterozygosity at the population level, with lower levels of heterozygosity observed at specific genome regions. Such patterns of heterozygosity are thought to be essential for adaptation to different environments. The resources generated in this study will provide insights into de novo domestication of wild plants and agricultural enhancement.

Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype.

Owing to its high ornamental value, the double flower phenotype of hydrangea (Hydrangea macrophylla) is one of its most important traits. In this study, genome sequence information was obtained to explore effective DNA markers and the causative genes for double flower production in hydrangea. Single-molecule real-time sequencing data followed by a Hi-C analysis were employed. Two haplotype-phased sequences were obtained from the heterozygous genome of hydrangea. One assembly consisted of 3,779 scaffolds (2.256 Gb in length and N50 of 1.5 Mb), the other also contained 3,779 scaffolds (2.227 Gb in length, and N50 of 1.4 Mb). A total of 36,930 genes were predicted in the sequences, of which 32,205 and 32,222 were found in each haplotype. A pair of 18 pseudomolecules was constructed along with a high-density single-nucleotide polymorphism (SNP) genetic linkage map. Using the genome sequence data, and two F2 populations, the SNPs linked to double flower loci (djo and dsu) were discovered. DNA markers linked to djo and dsu were developed, and these could distinguish the recessive double flower allele for each locus, respectively. The LEAFY gene is a very likely candidate as the causative gene for dsu, since frameshift was specifically observed in the double flower accession with dsu.

Phased genome sequence of an interspecific hybrid flowering cherry, 'Somei-Yoshino' (Cerasus × yedoensis).

We report the phased genome sequence of an interspecific hybrid, the flowering cherry 'Somei-Yoshino' (Cerasus × yedoensis). The sequence data were obtained by single-molecule real-time sequencing technology, split into two subsets based on genome information of the two probable ancestors, and assembled to obtain two haplotype phased genome sequences of the interspecific hybrid. The resultant genome assembly consisting of the two haplotype sequences spanned 690.1 Mb with 4,552 contigs and an N50 length of 1.0 Mb. We predicted 95,076 high-confidence genes, including 94.9% of the core eukaryotic genes. Based on a high-density genetic map, we established a pair of eight pseudomolecule sequences, with highly conserved structures between the two haplotype sequences with 2.4 million sequence variants. A whole genome resequencing analysis of flowering cherries suggested that 'Somei-Yoshino' might be derived from a cross between C. spachiana and either C. speciosa or its relatives. A time-course transcriptome analysis of floral buds and flowers suggested comprehensive changes in gene expression in floral bud development towards flowering. These genome and transcriptome data are expected to provide insights into the evolution and cultivation of flowering cherry and the molecular mechanism underlying flowering.

Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants.

SUMMARY: Hayai-Annotation Plants is a browser-based interface for an ultra-fast and accurate functional gene annotation system for plant species using R. The pipeline combines the sequence-similarity searches, using USEARCH against UniProtKB (taxonomy Embryophyta), with a functional annotation step. Hayai-Annotation Plants provides five layers of annotation: i) protein name; ii) gene ontology terms consisting of its three main domains (Biological Process, Molecular Function and Cellular Component); iii) enzyme commission number; iv) protein existence level; and v) evidence type. It implements a new algorithm that gives priority to protein existence level to propagate GO and EC information and annotated Arabidopsis thaliana representative peptide sequences (Araport11) within 5 min at the PC level. AVAILABILITY AND IMPLEMENTATION: The software is implemented in R and runs on Macintosh and Linux systems. It is freely available at https://github.com/kdri-genomics/Hayai-Annotation-Plants under the GPLv3 license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Comparison of the Tinetti and Short Physical Performance Battery test specificities for detecting neuromotor pathologies / Comparativo da especificidade das escalas de Tinetti e Short Physical Performance Battery na detecção de patologias neuromotoras

Introduction: Increasing elderly populations require specific and accurate health assessment tools. Purpose: To compare the specificities of the short physical performance battery (SPPB) and the Tinetti Index validated in Brazil in patients with and without neuromotor dysfunctions. Materials and methods: Thirty-nine individuals (19 healthy and 20 with neuromotor changes) of both sexes aged 60­75 years, living in Coari (Amazonas state in Brazil), underwent SPPB and Tinetti scale assessments on alternate dates. Results and discussion: We observed significant differences between the scales, where the distribution was very concentrated after the Tinetti assessment and more dispersed after the SPPB in healthy individuals. This demonstrated that SPPB can detect minimal differences in gait and balance between healthy individuals, while the Tinetti scale is better at discriminating between healthy and those affected by mobility disorders. Conclusion: SPPB was more specific than the Tinetti Index in detecting changes in gait and balance.

Introdução: o aumento do público idoso nos serviços de saúde requer instrumentos de avaliação cada vez mais específicos e precisos no diagnóstico deles. Objetivo: comparar a especificidade da SPPB e Índice de Tinetti validadas no Brasil em pacientes com e sem disfunções neuromotoras. Materiais e Métodos: 39 sujeitos (19 saudáveis e 20 com alterações neuromotoras) de ambos os sexos com idade entre 60 e 75 anos, residentes em Coari ­ AM, realizaram em datas alternadas avaliação pelas escalas SPPB e Tinetti. Resultados e discussão: foi observada diferença significativa entre as escalas, onde a distribuição mostrou-se muito concentrada em Tinetti e mais dispersa na SPPB para o grupo saudável, demonstrando que a SPPB conseguiu detectar as mínimas diferenças em marcha e equilíbrio entre indivíduos saudáveis; enquanto a escala de Tinetti discriminou melhor os indivíduos saudáveis dos patológicos. Conclusão: a SPPB mostrou-se mais específica que Tinetti, sendo capaz de detectar melhor alterações em marcha e equilíbrio.

Triportheus albus Cope, 1872 in the Blackwater, Clearwater, and Whitewater of the Amazon: A Case of Phenotypic Plasticity?

The Amazon basin includes 1000s of bodies of water, that are sorted according to their color in three types: blackwater, clearwater, and whitewater, which significantly differ in terms of their physicochemical parameters. More than 3,000 species of fish live in the rivers of the Amazon, among them, the sardine, Triportheus albus, which is one of the few species that inhabit all three types of water. The purpose of our study was to analyze if the gene expression of T. albus is determined by the different types of water, that is, if the species presents phenotypic plasticity to live in blackwater, clearwater, and whitewater. Gills of T. albus were collected at well-characterized sites for each type of water. Nine cDNA libraries were constructed, three biological replicates of each condition and the RNA was sequenced (RNA-Seq) on the MiSeq® Platform (Illumina®). A total of 51.6 million of paired-end reads, and 285,456 transcripts were assembled. Considering the FDR ≤ 0.05 and fold change ≥ 2, 13,754 differentially expressed genes were detected in the three water types. Two mechanisms related to homeostasis were detected in T. albus that live in blackwater, when compared to the ones in clearwater and whitewater. The acidic blackwater is a challenging environment for many types of aquatic organisms. The first mechanism is related to the decrease in cellular permeability, highlighting the genes coding for claudin proteins, actn4, itgb3b, DSP, Gap junction protein, and Ca2+-ATPase. The second with ionic and acid-base regulation [rhcg1, slc9a6a (NHE), ATP6V0A2, Na+/K+-ATPase, slc26a4 (pedrin) and slc4a4b]. We suggest T. albus is a good species of fish for future studies involving the ionic and acid-base regulation of Amazonian species. We also concluded that, T. albus, shows well defined phenotypic plasticity for each water type in the Amazon basin.

Biodegradation of the fungicide carbendazim by bacteria from Coriandrum sativum L rhizosphere / Biodegradação do agrotóxico carbendazim por bactérias da rizosfera de Coriandrum sativum L

The biocidal agrochemicals commonly used in agriculture can remain in the soil, affecting the environmental conditions and causing serious risks to health. Knowing that soil microorganisms, especially those from the rhizosphere, can degrade environmental xenobiotics, it was evaluated the potential of bacteria isolated from Coriandrum sativum L. rhizosphere to biodegrade carbendazim (MBC), a fungicide extensively used by agriculturists from rural farming communities in Manaus, Amazonas. Cultures carried out in medium containing carbendazim as a sole carbon source enabled the isolation of 80 bacteria, in the established conditions. Assays to determine degradation potential allowed the selection of the two elite isolates identified as Stenotrophomonas sp. and Ochrobactrum sp. Quantitative assays with each strain individually or in consortium, were carried out using minimal salt medium added with carbendazim (250 µg mL-1) and incubated at 30°C, under agitation (125 rpm) for 21 days. Samples used in the biodegradation test were HPLC analyzed for final fungicide quantitation. The Stenotrophomonas sp. strain was more efficient (68.9%) to degrade carbendazim and showed no toxicity in tests with Artemia salina.

Agrotóxicos são comumente utilizados na produção agrícola, podendo persistir no solo, afetar a qualidade do ambiente e causar sérios riscos à saúde. Sabendo-se que micro-organismos do solo, principalmente aqueles da rizosfera, podem degradar produtos xenobióticos avaliou-se o potencial de bactérias isoladas da rizosfera de Coriandrum sativum L. em degradar carbendazim, um fungicida usado extensivamente em comunidades de agricultores rurais em Manaus, Amazonas. Procedimentos de cultivo em meio, contendo carbendazim como única fonte de carbono, mostraram que 80 bactérias cresceram nas condições estabelecidas. Ensaios de eficiência de degradação permitiram a seleção dos dois melhores isolados que foram identificados como Stenotrophomonas sp. e Ochrobactrum sp. Os ensaios quantitativos, com cada cepa individualmente e com as duas em consórcio, foram conduzidos em meio mínimo contendo sais, acrescido de carbendazim (250 µg mL-1) e incubados a 30°C, 125 rpm, por 21 dias. A quantificação final do fungicida nas amostras do ensaio de biodegradação foi realizada em HPLC. A linhagem Stenotrophomonas sp. apresentou maior eficiência, degradando 68,9% do total de carbendazim e não apresentou toxicidade nos testes realizados com Artemia salina.

Functional categorization of transcriptome in the species Symphysodon aequifasciatus Pellegrin 1904 (Perciformes: Cichlidae) exposed to benzo[a]pyrene and phenanthrene.

This study aims to evaluate the transcriptome alterations, through cDNA libraries, associated with the combined effects of two PAHs, benzo[a]pyrene (0.5 µg/L) and phenanthrene (50 µg/L), present in crude oil, on specimens of Symphysodon aequifasciatus (discus fish) after 48 h of exposure. The cDNA libraries were constructed according to the SOLiD™ SAGE™ protocol for sequencing in the SOLiD v.3 Plus sequencer. The results were analyzed by bioinformatics and differentially expressed genes were categorized using the gene ontology program. The functional categories (terms) found in the gene ontology and the gene network generated using STRING software were used to predict the adverse effects of benzo[a]pyrene and phenanthrene in the liver. In the present study, 27,127 genes (compared to Danio rerio database) were identified. Considering only those genes with a p-value less than or equal to 0.05 and greater than or equal to two-fold change in expression across libraries, we found 804 genes, 438 down-regulated (54%) and 366 up-regulated (46%), in the experimental group compared to the control. Out of this total, 327 genes were successfully categorized, 174 down-regulated and 153 up-regulated, using gene ontology. Using String, the gene network was composed by 199 nodes, 124 of them resulting in 274 interactions. The results showed that even an acute exposure of 48 h caused metabolic change in response to environmental contaminants, resulting in changes of cell integrity, in oxidation-reduction processes, in the immune response and disturbances of intracellular signaling of discus fish. Also the gene network has showed no central interplay cluster, exhibiting instead interconnected clusters interactions and connected sub-networks. These findings highlight that even an acute sublethal exposure of PAHs can cause metabolism changes that may affect survival of discus. Our findings using SOLiD coupled with SAGE-method resulted in a powerful and reliable means for gene expression analysis in discus, a non-model Amazonian fish.

Percepção de sedentarismo e fatores associados em adolescentes grávidas no Município de Coari, Estado do Amazonas, Brasil / Perception of physical inactivity and associated factors in pregnant adolescents in the City of Coari, Amazonas State, Brazil

Na adolescência, hábitos sedentários são fatores preocupantes, pois além de constituírem fator de risco para várias doenças, predispõem na fase adulta a ocorrência de doenças crônicas. Em se tratando do desenvolvimento de patologias, a gravidez na adolescência é fator determinante de vulnerabilidade quando associada ao sedentarismo. Este estudo teve como objetivo verificar a percepção de sedentarismo entre adolescentes grávidas atendidas nas Unidades Básicas de Saúde do Município de Coari, Estado do Amazonas, Brasil, e levantar os fatores associados a esta questão por meio de um estudo transversal, quantitativo, com adolescentes grávidas residentes na zona urbana da Cidade de Coari. Os dados foram coletados por meio da utilização de questionário semiestruturado, constituído por perguntas abertas e fechadas referentes ao nível de atividade física e sedentarismo aplicado durante o mês de setembro de 2010, Os resultados revelaram que 69 por cento das adolescentes grávidas tinham idade entre 17 e 18 anos, 44 por cento eram solteiras, e 56 por cento haviam cursado, sem concluir, o ensino fundamental. Entre as entrevistadas, 97 por cento alegaram não praticar exercício durante a gravidez. Depois de tomarem conhecimento do conceito de sedentarismo, 75 por cento referiram-se sedentárias e somente 25 por cento classificaram-se como ativas. Desta forma, infere-se que a percepção de sedentarismo entre adolescentes grávidas revelou-se um fator preocupante, sendo o padrão de atividade das entrevistadas baixo e inadequado desde o início da gravidez. Conclui-se que fatores comportamentais, biológicos e culturais participam na determinação do sedentarismo, demonstrando a ausência de incentivo à prática de atividade física durante a gestação e suscitando uma atenção especial dos agentes públicos de saúde.

Sedentary habits are an issue of concern during adolescence because they are a risk factor for several diseases and predispose adolescents to chronic diseases in adulthood. When associated with a sedentary lifestyle, pregnancy during adolescence is a determining factor for becoming vulnerable to developing disease. This study aimed to assess the perception of sedentary behavior by pregnant adolescents treated in Basic Health Care Units in the Municipality of Coari, Amazonas State, Brazil. The study also aimed to survey for associated factors through a cross-sectional, quantitative investigation of pregnant adolescents living in the urban area of the Municipality of Coari. Data were collected in September 2010 through the use of a semi-structured questionnaire with open- and closed-ended items covering the level of physical activity and sedentary behavior. The results show that 69 per cent of the pregnant adolescents were 17 or 18 years old, 44 per cent were single, and 56 per cent had started but not concluded primary education. Among the interviewees, 97 per cent stated that they did not exercise during pregnancy; 75 per cent considered themselves sedentary after acknowledging the meaning of a sedentary lifestyle, and only 25 per cen considered themselves physically active. Thus, the perception of sedentary behavior by pregnant adolescents proved to be worrisome, and the pattern of activity on the part of the interviewees was classified as low and inadequate after the beginning of pregnancy. We conclude that behavioral, biological and cultural factors influence the determination of sedentary behavior. We also show a lack of stimulus for physical activities during pregnancy and illustrate the need for special attention from public health servants.