Labor- and cost-effective long-read amplicon sequencing using a plasmid analysis service: Application to transposon-inserted alleles in Japanese morning glory.

The sequencing of PCR fragments amplified from specific regions of genomes is a fundamental technique in molecular genetics. Sanger sequencing is commonly used for this analysis; however, amplicon sequencing utilizing next-generation sequencing has become widespread. In addition, long-read amplicon sequencing, using Nanopore or PacBio sequencers to analyze long PCR fragments, has emerged, although it is often more expensive than Sanger sequencing.

Advanced Fungal Biotechnologies in Accomplishing Sustainable Development Goals (SDGs): What Do We Know and What Comes Next?

The present era has witnessed an unprecedented scenario with extreme climate changes, depleting natural resources and rising global food demands and its widespread societal impact. From providing bio-based resources to fulfilling socio-economic necessities, tackling environmental challenges, and ecosystem restoration, microbes exist as integral members of the ecosystem and influence human lives. Microbes demonstrate remarkable potential to adapt and thrive in climatic variations and extreme niches and promote environmental sustainability.

Plant-Microbe Interactions under the Extreme Habitats and Their Potential Applications.

Plant-microbe associations define a key interaction and have significant ecological and biotechnological perspectives. In recent times, plant-associated microbes from extreme environments have been extensively explored for their multifaceted benefits to plants and the environment, thereby gaining momentum in global research. Plant-associated extremophiles highlight ubiquitous occurrences, inhabiting extreme habitats and exhibiting enormous diversity.

Tomato seeds pretreated with Antifreeze protein type I (AFP I) promotes the germination under cold stress by regulating the genes involved in germination process.

This study was conducted to investigate the involvement of antifreeze proteins (AFPs; type I and III) in the germination mechanism of tomato seeds under low temperature stress. Germination of the seeds grown at a room temperature (25°C) was observed on 5 days after sowing (DAS), while all seeds exposed to a low temperature started to germinate at 16 days after sowing (DAS). However, in comparison with control seeds (0 µg/l), seeds treated with AFP I (100, 300, or 500 µg/l) germinated earlier and at a higher percentage until 20 DAS, and seeds treated with 100 µg/l AFP I showed the highest percentage of germination.

Silencing of the phytoene desaturase () gene affects the expression of fruit-ripening genes in tomatoes.

Background: Past research has shown that virus-induced phytoene desaturase () gene silencing via agroinjection in the attached and detached fruit of tomato plants results in a pale-yellow fruit phenotype. Although the gene is often used as a marker for gene silencing in tomatoes, little is known about the role of in fruit ripening. In this study, we investigated whether the pepper gene silenced endogenous genes in the fruit of two tomato cultivars, Dotaerang Plus and Legend Summer.

The role of antifreeze proteins in the regulation of genes involved in the response of to cold.

Cold temperatures are a major source of stress for plants and negatively impact crop yield. A possible way to protect plants is to treat them with antifreeze proteins (AFPs). Here, we investigated whether fish AFPs can shield the rare ornamental species from low-temperature stress.

Anthocyanin mutants of Japanese and common morning glories exhibit normal proanthocyanidin accumulation in seed coats.

Anthocyanin and proanthocyanidin biosynthesis pathways are believed to overlap. This study examined proanthocyanidin accumulation in seed coats of morning glories ( and ) carrying mutations in , , and genes encoding chalcone synthase, chalcone isomerase, and anthocyanidin synthase, respectively. Chemical staining revealed that mutants accumulate proanthocyanidin normally.

Differential expression of anthocyanin structural genes and transcription factors determines coloration patterns in gerbera flowers.

We investigated the expression of anthocyanin structural genes and transcription factors (TFs) associated with varying anthocyanin content during different developmental stages (S1-S4) of the gerbera cultivars 'Nathasha' and 'Rosalin'. Accumulation of anthocyanin started at S1 and reached a maximum at S3 in both cultivars. Enhancement of anthocyanin content in 'Nathasha' was associated with upregulation of and MYB10, whereas in 'Rosalin', upregulation was associated with , MYB10, and MYC1.

Hymenobacter jeollabukensis sp. nov., isolated from soil.

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterial strain, designated 1-3-3-8, was isolated from soil and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 1-3-3-8 belongs to the family Cytophagaceae of phylum Bacteroidetes and is most closely related to Hymenobacter paludis KBP-30 (96.8% similarity), Hymenobacter ocellatus Myx2105 (96.

Hymenobacter terrigena sp. nov., isolated from soil.

A Gram-stain-negative, non-motile, non-spore-forming, rodshaped, aerobic bacterial strain, designated S1-2-2-5, was isolated from the Jeollabuk-do province, Republic of Korea, and was characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain S1-2-2-5 belonged to the family Cytophagaceae in phylum Bacteroidetes, and was most closely related to Hymenobacter terrae DG7A (98.2%), Hymenobacter rubidus DG7B (98.

Transcriptional control of anthocyanin biosynthesis genes and transcription factors associated with flower coloration patterns in .

We analyzed the expression of anthocyanin biosynthesis genes and transcription factors (TFs) in the cultivars 'Bintang' and 'Alliance' that exhibit different coloration patterns. Differential expression of biosynthesis genes and TFs was associated with variable anthocyanin content at different flower developmental stages (S1-S3) in both cultivars; higher anthocyanin content was correlated with higher levels of gene expression. Exposure to different temperatures (6 and 22 °C) also resulted in different anthocyanin content levels: the lower temperature (6 °C) enhanced anthocyanin content compared to the higher temperature (22 °C).

Larkinella roseus sp. nov., a species of the family Cytophagaceae isolated from beach soil.

The taxonomic position of bacterial strain, designated 15J16-1T3A, recovered from a soil sample was established using a polyphasic approach. Phylogenic analysis based on the 16S rRNA gene sequence showed that strain 15J16-1T3A belonged to the family Cytophagaceae, phylum Bacteroidetes, and was most closely related to 'Larkinella harenae' 15J9-9 (95.9% similarity), Larkinella ripae 15J11-11 (95.

Overexpression of snapdragon Delila (Del) gene in tobacco enhances anthocyanin accumulation and abiotic stress tolerance.

Background: Rosea1 (Ros1) and Delila (Del) co-expression controls anthocyanin accumulation in snapdragon flowers, while their overexpression in tomato strongly induces anthocyanin accumulation. However, little data exist on how Del expression alone influences anthocyanin accumulation.

Results: In tobacco (Nicotiana tabacum 'Xanthi'), Del expression enhanced leaf and flower anthocyanin production through regulating NtCHS, NtCHI, NtF3H, NtDFR, and NtANS transcript levels.

Genome sequence and analysis of the Japanese morning glory Ipomoea nil.

Ipomoea is the largest genus in the family Convolvulaceae. Ipomoea nil (Japanese morning glory) has been utilized as a model plant to study the genetic basis of floricultural traits, with over 1,500 mutant lines. In the present study, we have utilized second- and third-generation-sequencing platforms, and have reported a draft genome of I.

Activation and epigenetic regulation of DNA transposon nDart1 in rice.

A large part of the rice genome is composed of transposons. Since active excision/reintegration of these mobile elements may result in harmful genetic changes, many transposons are maintained in a genetically or epigenetically inactivated state. However, some non-autonomous DNA transposons of the nDart1-3 subgroup, including nDart1-0, actively transpose in specific rice lines, such as pyl-v which carries an active autonomous element, aDart1-27, on chromosome 6.

A WD40-repeat protein controls proanthocyanidin and phytomelanin pigmentation in the seed coats of the Japanese morning glory.

The protein complex composed of the transcriptional regulators containing R2R3-MYB domains, bHLH domains, and WDR in plants controls various epidermal traits, including anthocyanin and proanthocyanidin pigmentation, trichome and root hair formation, and vacuolar pH. In the Japanese morning glory (Ipomoea nil), InMYB1 having R2R3-MYB domains and InWDR1 containing WDR were shown to regulate anthocyanin pigmentation in flowers, and InWDR1 was reported to control dark-brown pigmentation and trichome formation on seed coats. Here, we report that the seed pigments of I.

Identification of r mutations conferring white flowers in the Japanese morning glory (Ipomoea nil).

The wild-type Japanese morning glory [Ipomoea nil (L.) Roth.] exhibits blue flowers with red stems, and spontaneous r mutants display white flowers with green stems.

A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthesis in flowers, proanthocyanidin and phytomelanin pigmentation in seeds, and seed trichome formation.

The transcriptional regulators for anthocyanin pigmentation include proteins containing R2R3-MYB domains, bHLH domains and conserved WD40 repeats, and their interactions determine the set of genes to be expressed. Spontaneous ivory seed (ivs) mutants of Ipomoea purpurea displaying pale pigmented flowers and ivory seeds are caused by insertions of DNA transposons into the bHLH2 gene that encodes a bHLH transcriptional regulator. A partial reduction in the expression of all structural genes encoding enzymes for anthocyanin biosynthesis was observed in the young flower buds of these ivs mutants.

Spontaneous mutations caused by a Helitron transposon, Hel-It1, in morning glory, Ipomoea tricolor.

Helitrons are newcomers among eukaryotic DNA transposons and have originally been identified by computational analysis in the genomes of Arabidopsis, rice and nematode. They are distinguished from other transposons in their structural features, and their proposed transposition mechanisms are involved in rolling circle replication. Computer-predicted autonomous Helitrons with conserved terminal sequences 5'-TC and CTRR-3' are presumed to encode a putative transposase, Rep/Hel-TPase, which contains a characteristic nuclease/ligase domain for the replication-initiation protein (Rep) and a DNA helicase domain (Hel).

Genetics and epigenetics in flower pigmentation associated with transposable elements in morning glories.

Among the genus Ipomoea, three morning glories, I. nil (the Japanese morning glory), I. purpurea (the common morning glory), and I.

Genetics and epigenetics in flower pigmentation associated with transposable elements in morning glories.

Among the genus Ipomoea, three morning glories, I. nil the Japanese morning glory), I. purpurea (the common morning glory), and I.

An intragenic tandem duplication in a transcriptional regulatory gene for anthocyanin biosynthesis confers pale-colored flowers and seeds with fine spots in Ipomoea tricolor.

While the wild-type morning glory (Ipomoea tricolor) displays bright-blue flowers and dark-brown seeds, its spontaneous mutant, Blue Star, carrying the mutable ivory seed-variegated (ivs-v) allele, exhibits pale-blue flowers with a few fine blue spots and ivory seeds with tiny dark-brown spots. The mutable allele is caused by an intragenic tandem duplication of 3.3 kbp within a gene for transcriptional activator containing a basic helix-loop-helix (bHLH) DNA-binding motif.