Function Annotation of an SBP-box Gene in Arabidopsis Based on Analysis of Co-expression Networks and Promoters

The SQUAMOSA PROMOTER BINDING PROTEIN–LIKE (SPL) gene family is an SBP-box transcription family in Arabidopsis. While several physiological responses to SPL genes have been reported, their biological role remains elusive. Here, we use a combined analysis of expression correlation, the interactome, and promoter content to infer the biological role of the SPL genes in Arabidopsis thaliana. Analysis of the SPL-correlated gene network reveals multiple functions for SPL genes. Network analysis shows that SPL genes function by controlling other transcription factor families and have relatives with membrane protein transport activity. The interactome analysis of the correlation genes suggests that SPL genes also take part in metabolism of glucose, inorganic salts, and ATP production. Furthermore, the promoters of the correlated genes contain a core binding cis-element (GTAC). All of these analyses suggest that SPL genes have varied functions in Arabidopsis

SBP-domain transcription factors as possible effectors of cryptochrome-mediated blue light signalling in the moss Physcomitrella patens

Cryptochromes are blue light absorbing photoreceptors found in many organisms and involved in numerous developmental processes. At least two highly similar cryptochromes are known to affect branching during gametophytic development in the moss Physcomitrella patens. We uncovered a relationship between these cryptochromes and the expression of particular members of the SBP-box genes, a plant specific transcription factor family. Transcript levels of the respective moss SBP-box genes, all belonging to the LG1-subfamily, were found to be dependent, albeit not exclusively, on blue light. Moreover, disruptant lines generated for two moss representatives of this SBP-box gene subfamily, both showed enhanced caulonema side branch formation, a phenotype opposite to that of the ppcry1a/1b double disruptant line. In this report we show that PpCRY1a and PpCRY1b act negatively on the transcript levels of several related moss SBP-box genes and that at least PpSBP1 and PpSBP4 act as negative regulators of side branch formation

The MOBIOS+: A FAIR (Findable, Accessible, Interoperable and Reusable) database for Mindanao's terrestrial biodiversity

Due to its complex geological history and the emergence of various biogeographic regions, the Philippines boasts an extraordinary array of flora and fauna. This unique combination has contributed to the country’s exceptional density of terrestrial species, making it amongst the highest in the world. Mindanao, in the southern part of the Philippines, is the second largest group of islands and supports high levels of endemism and proportion of threatened species. However, consolidated biodiversity records and information remain unavailable for the region. The primary goal of the Mindanao Open Biodiversity Information (MOBIOS+) database is to address these substantial data deficiencies by compiling contemporary biodiversity information from the 21st century. This initiative seeks to enhance our comprehension of biodiversity trends in Mindanao over temporal and spatial dimensions, while also creating an openly-accessible database. The database we present here is the first of its kind and currently the most comprehensive attempt to establish the largest consolidated database for Mindanao biodiversity, based on publicly available literature. With its vast collection of biodiversity data, this database will prove to be a valuable resource for advancing biodiversity research and analysis. It will further facilitate the identification of species and areas that require immediate conservation prioritisation and action, addressing the urgent challenges posed by our rapidly changing planet.The MOBIOS+ database is the first attempt to create a massive FAIR database aiming to collate biodiversity records from published literature in the Mindanao faunal region, south of the Philippines. The database currently includes 12,813 georeferenced specimen occurrences representing 1,907 unique taxa across 10 animal classes inhabiting the terrestrial and freshwater environments of Mindanao faunal region. We made all georeferenced specimen occurrences available in the Global Biodiversity Information Facility (GBIF) platform

Genome-wide Identifcation and Characterization of SPL Transcription Factor Family and Their Evolution and Expression Profiling Analysis in Cotton

Abstract Plant specific transcription factors, SQUAMOSA promoter-binding protein-like (SPL), are involved in many biological processes. However, no systematical study has been reported in cotton. In this study, a total of 177 SPL genes were identified, including 29, 30, 59 and 59 SPLs in Gossypium arboreum, G. raimondii, G. barbadense, and G. hirsutum, respectively. These SPL genes were classified into eight phylogenetical groups. The gene structure, conserved motif, and clustering were highly conserved within each orthologs. Two zinc finger-like structures (Cys3His and Cys2HisCys) and NLS segments were existed in all GrSPLs. Segmental duplications play important roles in SPL family expansion, with 20 genes involved in segmental duplications and 2 in tandem duplications, and ten ortholog pairs in syntenic regions between G. raimondii and A. thaliana. Several putative cis-elements, involved in light, stresses and phytohormones response, were found in the promoter regions of GhSPLs, suggesting that plant responses to those environmental changes may be induced through targeting SPL transcription factors. RNA-seq analysis shows that SPL genes were differentially expressed in cotton; some were highly expressed during fiber initiation and early development. Comparing with other plants, SPL genes show subfunctionalization, lost and/or gain functions in cotton during long-term domestication and evolution