Integrative gene duplication and genome-wide analysis as an approach to facilitate wheat reverse genetics: An example in the TaCIPK family

Genus-Wide Pan-Genome Analysis of Oryza Calcium-Dependent Protein Kinase Genes and Their Related Kinases Highlights the Complexity of Protein Domain Architectures and Expression Dynamics

The Oryza genus serves not only as a gene pool for rice improvement but also as a model system for plant evolutionary research. Calcium-dependent protein kinases (CPKs) function as both effectors and sensors in calcium signaling and play versatile roles in plant development and stress responses. Four kinase families, namely CPK-related kinases (CRKs), phosphoenolpyruvate carboxylase kinases (PPCKs), PPCK-related kinases (PEPRKs), and calcium- and calmodulin-dependent kinases (CCaMKs), are frequently called CPK-related kinases. This study utilized evolutionary genomics approaches and provided the pan-genome repertoires of CPKs and their related kinases in 34 Oryza genomes by leveraging the rich genomics resources of the Orzya genus. Gene duplication analysis revealed that distinct duplication types contributed to expanding CPKs and their related kinases in wild rice. We depicted the protein domain architectures of CPKs and their related kinases, highlighting the complexity of EF-hand motifs in CPKs and CCaMKs. Transcriptome analysis determined that alternative splicing was a mechanism contributing to the diversity in the domain architectures of CPKs and CCaMKs. We also generated the expression atlas of CPKs and their related kinases in multiple species of Oryza genus, emphasizing divergent homoeolog expression patterns across tissues and species in allotetraploid wild rice. Collectively, our Oryza-wide analysis of CPKs and their related kinases revealed their evolutionary trajectories and highlighted their diversified domain architectures and expression dynamics, providing gene resources of wild relatives for rice improvement.

Genome wide identification of LcC2DPs gene family in Lotus corniculatus provides insights into regulatory network in response to abiotic stresses

Low temperatures and drought reduce forage yield and quality, with protein kinases crucial for plant stress response. This study examines the LcC2DPs protein kinase family in Lotus corniculatus, identifying 90 members, with some tandemly distributed on chromosomes 2-6, and grouped into 5 subfamilies (I-V). 34 homologous gene pairs were found in Arabidopsis thaliana. LcC2DP genes promoters contain hormone and stress response elements. GO analysis highlights enrichment in hormone response and kinase activity. Transcriptomic analysis links 78 genes to environmental response and stress growth, with 10 validated by qRT-PCR after treatment with 100 μM ABA and IAA, 20% PEG6000, and 4 °C. Protein interaction analysis identifies 5 core proteins (LcC2DP5, 11, 15, 38, and 58) activated by drought and cold stress. Gene analysis revealed that only LcC2DP5 and LcC2DP15 share co-expression transcription factors, with bZIP, bHLH, WRKY, NAC, MYB-related, MYB, C3H, and C2H2 being prominent. These proteins are expressed under drought and cold conditions, highlighting LcC2DP5 and LcC2DP15 activity. NAC and C2H2 are vital for drought response, while bZIP and MYB-related are important for cold response. This suggests that various LcC2DPs in Lotus corniculatus respond to hormones and stress via a TF regulatory network.

Genome-wide analysis of CBL and CIPK gene families in bermudagrass reveals the CdCIPK29-A1 as a stem growth angle regulator

KEY MESSAGE

Genome-wide analysis of CBL and CIPK gene family was conducted in bermudagrass while a functional role in stem growth angle regulation was established for CdCIPK29-A1 via the generation of molecularly modified Arabidopsis plants. Calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) are plant-specific Ca2+ sensors and effectors which mediate diverse Ca2+ signaling transduction pathways in plant growth, development, and stress responses. However, the functions of CBLs and CIPKs in bermudagrass (Cynodon dactylon L.), a widely planted warm-season turfgrass species with great economic value, remain poorly understood. In this study, a total of 33 CdCBL and 81 CdCIPK genes were identified in the bermudagrass genome, and were clustered in three and five groups according to their phylogenetic relationships, respectively. In line with their sequence divergence, different groups of CdCBL and CdCIPK genes exhibited different gene structures and expression patterns. Systematic yeast two-hybrid screening indicated that 27 CdCBL-CdCIPK complexes could be formed from 290 putative CdCBL and CdCIPK protein pairs. Among the CdCIPK proteins, CdCIPK29-A1 was found to interact with up to four CdCBL proteins. The CdCIPK29-A1 gene was preferentially expressed in the stolon internode of bermudagrass plants and the CdCIPK29-A1 protein was located to the cytoplasm. The expression of CdCIPK29-A1 in molecularly modified Arabidopsis thaliana (Arabidopsis) plants further indicated that CdCIPK29-A1 could regulate the stem growth angle and gravitropism possibly through modulating the starch metabolism in stem endodermal cells. These results not only established a solid foundation to explore the Ca2+ signaling transduction pathways in bermudagrass but also provided new insight into the function of CBL-CIPK complex in plant gravitropic response and stem growth angle regulation.

Characterization and Transcriptomic Analysis of Sorghum EIN/EIL Family and Identification of Their Roles in Internode Maturation

Ethylene-insensitive 3/Ethylene-insensitive3-like proteins (EIN3/EIL) represent a group of transcription factors critical for the ethylene signaling transduction that manipulate downstream ethylene-responsive genes, thereby regulating plant growth, development, and stress responses. However, the identification, evolution, and divergence of the EIL family remain to be studied in Sorghum bicolor. Here, we identified eight SbEILs, which were expanded due to whole-genome-duplication (WGD) events. Characterization of the protein sequences and expression atlas demonstrates that the WGD-duplicated SbEILs could become divergent due to the differential expression patterns, rather than domain and motif architectures. Comparative expression analysis was performed between the RNA-seq data sets of internodes from several sorghum cultivars to understand the potential roles of SbEIL members in internode elongation and maturation. Our results identified SbEIL3 and 7 (the latter as a homolog of OsEIL7/OsEIL1) to be the highly expressed SbEIL genes in sorghum internodes and revealed a potential functional link between SbEIL7 and internode maturation. The co-expression analysis and comparative expression analysis with ethylene-regulated gene sets found that SbEIL7 was co-regulated with a set of ubiquitin-related protein degradation genes, suggesting possible involvement of SbEIL7 in protein degradation and processing during the post-anthesis stages. Altogether, our findings lay a foundation for future functional studies of ethylene signaling-mediated gene regulation and improvement of sorghum internode development.

Potential Roles of the GRF Transcription Factors in Sorghum Internodes during Post-Reproductive Stages

Growth-regulating factor (GRF) is a plant-specific family of transcription factors crucial for meristem development and plant growth. Sorghum (Sorghum bicolor L. Moench) is a cereal species widely used for food, feed and fuel. While sorghum stems are important biomass components, the regulation of stem development and the carbohydrate composition of the stem tissues remain largely unknown. Here, we identified 11 SbGRF-encoding genes and found the SbGRF expansion driven by whole-genome duplication events. By comparative analyses of GRFs between rice and sorghum, we demonstrated the divergence of whole-genome duplication (WGD)-derived OsGRFs and SbGRFs. A comparison of SbGRFs' expression profiles supports that the WGD-duplicated OsGRFs and SbGRFs experienced distinct evolutionary trajectories, possibly leading to diverged functions. RNA-seq analysis of the internode tissues identified several SbGRFs involved in internode elongation, maturation and cell wall metabolism. We constructed co-expression networks with the RNA-seq data of sorghum internodes. Network analysis discovered that SbGRF1, 5 and 7 could be involved in the down-regulation of the biosynthesis of cell wall components, while SbGRF4, 6, 8 and 9 could be associated with the regulation of cell wall loosening, reassembly and/or starch biosynthesis. In summary, our genome-wide analysis of SbGRFs reveals the distinct evolutionary trajectories of WGD-derived SbGRF pairs. Importantly, expression analyses highlight previously unknown functions of several SbGRFs in internode elongation, maturation and the potential involvement in the metabolism of the cell wall and starch during post-anthesis stages.

Functional Differentiation of the Duplicated Gene BrrCIPK9 in Turnip (Brassica rapa var. rapa)

Gene duplication is a key biological process in the evolutionary history of plants and an important driving force for the diversification of genomic and genetic systems. Interactions between the calcium sensor calcineurin B-like protein (CBL) and its target, CBL-interacting protein kinase (CIPK), play important roles in the plant's response to various environmental stresses. As a food crop with important economic and research value, turnip (Brassica rapa var. rapa) has been well adapted to the environment of the Tibetan Plateau and become a traditional crop in the region. The BrrCIPK9 gene in turnip has not been characterized. In this study, two duplicated genes, BrrCIPK9.1 and BrrCIPK9.2, were screened from the turnip genome. Based on the phylogenetic analysis, BrrCIPK9.1 and BrrCIPK9.2 were found located in different sub-branches on the phylogenetic tree. Real-time fluorescence quantitative PCR analyses revealed their differential expression levels between the leaves and roots and in response to various stress treatments. The differences in their interactions with BrrCBLs were also revealed by yeast two-hybrid analyses. The results indicate that BrrCIPK9.1 and BrrCIPK9.2 have undergone Asparagine-alanine-phenylalanine (NAF) site divergence during turnip evolution, which has resulted in functional differences between them. Furthermore, BrrCIPK9.1 responded to high-pH (pH 8.5) stress, while BrrCIPK9.2 retained its ancestral function (low K+), thus providing further evidence of their functional divergence. These functional divergence genes facilitate turnip's good adaptation to the extreme environment of the Tibetan Plateau. In summary, the results of this study reveal the characteristics of the duplicated BrrCIPK9 genes and provide a basis for further functional studies of BrrCBLs-BrrCIPKs in turnip.