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Introduction: Reverse genetic studies conducted in the plant with a complex or polyploidy genome enriched with large gene families (like wheat) often meet challenges in identifying the key candidate genes related to important traits and prioritizing the genes for functional experiments. Objective: To overcome the above-mentioned challenges of reverse genetics, this work aims to establish an efficient multi-species strategy for genome-wide gene identification and prioritization of the key candidate genes. Methods: We established the integrative gene duplication and genome-wide analysis (iGG analysis) as a strategy for pinpointing key candidate genes deserving functional research. The iGG captures the evolution, and the expansion/contraction of large gene families across phylogeny-related species and integrates spatial–temporal expression information for gene function inference. Transgenic approaches were also employed to functional validation. Results: As a proof-of-concept for the iGG analysis, we took the wheat calcineurin B-like protein-interacting protein kinases (CIPKs) family as an example. We identified CIPKs from seven monocot species, established the orthologous relationship of CIPKs between rice and wheat, and characterized Triticeae-specific CIPK duplicates (e.g., CIPK4 and CIPK17). Integrated with our analysis of CBLs and CBL-CIPK interaction, we revealed that divergent expressions of TaCBLs and TaCIPKs could play an important role in keeping the stoichiometric balance of CBL-CIPK. Furthermore, we validated the function of TaCIPK17-A2 in the regulation of drought tolerance by using transgenic approaches. Overexpression of TaCIPK17 enhanced antioxidant capacity and improved drought tolerance in wheat. Conclusion: The iGG analysis leverages evolutionary and comparative genomics of crops with large genomes to rapidly highlight the duplicated genes potentially associated with speciation, domestication and/or particular traits that deserve reverse-genetic functional studies. Through the identification of Triticeae-specific TaCIPK17 duplicates and functional validation, we demonstrated the effectiveness of the iGG analysis and provided a new target gene for improving drought tolerance in wheat.

[Display omitted] • The iGG analysis has been proposed to utilize evolutionary information between the crop and several its relatives. • The evolution of CIPK and CBL genes have been characterized in seven species to prove the iGG method. • The divergent expression is important for keeping the stoichiometric balance of TaCBL-TaCIPK. • Our iGG analysis reveals a Triticeae-specific TaCIPK duplicate responding to drought. • Transgenic plants of TaCIPK17 -OE in tobacco and wheat showed higher resistance to drought. Reverse genetic studies conducted in the plant with a complex or polyploidy genome enriched with large gene families (like wheat) often meet challenges in identifying the key candidate genes related to important traits and prioritizing the genes for functional experiments. To overcome the above-mentioned challenges of reverse genetics, this work aims to establish an efficient multi-species strategy for genome-wide gene identification and prioritization of the key candidate genes. We established the integrative gene duplication and genome-wide analysis (iGG analysis) as a strategy for pinpointing key candidate genes deserving functional research. The iGG captures the evolution, and the expansion/contraction of large gene families across phylogeny-related species and integrates spatial–temporal expression information for gene function inference. Transgenic approaches were also employed to functional validation. As a proof-of-concept for the iGG analysis, we took the wheat calcineurin B-like protein-interacting protein kinases (CIPKs) family as an example. We identified CIPK s from seven monocot species, established the orthologous relationship of CIPK s between rice and wheat, and characterized Triticeae-specific CIPK duplicates (e.g. , CIPK4 and CIPK17). Integrated with our analysis of CBLs and CBL-CIPK interaction, we revealed that divergent expressions of TaCBL s and TaCIPK s could play an important role in keeping the stoichiometric balance of CBL-CIPK. Furthermore, we validated the function of TaCIPK17-A2 in the regulation of drought tolerance by using transgenic approaches. Overexpression of TaCIPK17 enhanced antioxidant capacity and improved drought tolerance in wheat. The iGG analysis leverages evolutionary and comparative genomics of crops with large genomes to rapidly highlight the duplicated genes potentially associated with speciation, domestication and/or particular traits that deserve reverse-genetic functional studies. Through the identification of Triticeae-specific TaCIPK17 duplicates and functional validation, we demonstrated the effectiveness of the iGG analysis and provided a new target gene for improving drought tolerance in wheat. [ABSTRACT FROM AUTHOR]

SUMMARY: The sugar transporter (ST) family is considered to be the most important gene family for sugar accumulation, but limited information about the ST family in the important sugar‐yielding crop Saccharum is available due to its complex genetic background. Here, 105 ST genes were identified and clustered into eight subfamilies in Saccharum spontaneum. Comparative genomics revealed that tandem duplication events contributed to ST gene expansions of two subfamilies, PLT and STP, in S. spontaneum, indicating an early evolutionary step towards high sugar content in Saccharum. The analyses of expression patterns were based on four large datasets with a total of 226 RNA sequencing samples from S. spontaneum and Saccharum officinarum. The results clearly demonstrated 50 ST genes had different spatiotemporal expression patterns in leaf tissues, 10 STs were specifically expressed in the stem, and 10 STs responded to the diurnal rhythm. Heterologous expression experiments in the defective yeast strain EBY.VW4000 indicated STP13, pGlcT2, VGT3, and TMT4 are the STs with most affinity for glucose/fructose and SUT1_T1 has the highest affinity to sucrose. Furthermore, metabolomics analysis suggested STP7 is a sugar starvation‐induced gene and STP13 has a function in retrieving sugar in senescent tissues. PLT11, PLT11_T1, TMT3, and TMT4 contributed to breaking the limitations of the storage sink. SUT1, SUT1_T1, PLT11, TMT4, pGlcT2, and VGT3 responded for different functions in these two Saccharum species. This study demonstrated the evolutionary expansion and functional divergence of the ST gene family and will enable the further investigation of the molecular mechanism of sugar metabolism in Saccharum. Significance Statement: An early evolutionary step towards high sugar content in Saccharum was indicated to be caused by recent tandem duplication events in Saccharum spontaneum, and functional divergence of the ST family between S. spontaneum and Saccharum officinarum was further unveiled based on heterologous expression experiments, a large set of transcriptome data, and metabolomics analysis. This study will enable the further investigation of the molecular mechanism of sugar metabolism in Saccharum. [ABSTRACT FROM AUTHOR]

Valine-glutamine motif-containing (VQ) proteins are transcriptional cofactors widely involved in plant growth, development, and response to various stresses. Although the VQ family has been genome-wide identified in some species, but the knowledge regarding duplication-driven functionalization of VQ genes among evolutionarily related species is still lacking. Here, 952 VQ genes have been identified from 16 species, emphasizing seven Triticeae species including the bread wheat. Comprehensive phylogenetic and syntenic analyses allow us to establish the orthologous relationship of VQ genes from rice (Oryza sativa) to bread wheat (Triticum aestivum). The evolutionary analysis revealed that whole-genome duplication (WGD) drives the expansion of OsVQ s, while TaVQ s expansion is associated with a recent burst of gene duplication (RBGD). We also analyzed the motif composition and molecular properties of TaVQ proteins, enriched biological functions, and expression patterns of TaVQ s. We demonstrate that WGD-derived TaVQ s have become divergent in both protein motif composition and expression pattern, while RBGD-derived TaVQ s tend to adopt specific expression patterns, suggesting their functionalization in certain biological processes or in response to specific stresses. Furthermore, some RBGD-derived TaVQ s are found to be associated with salt tolerance. Several of the identified salt-related TaVQ proteins were located in the cytoplasm and nucleus and their salt-responsive expression patterns were validated by qPCR analysis. Yeast-based functional experiments confirmed that TaVQ27 may be a new regulator to salt response and regulation. Overall, this study lays the foundation for further functional validation of VQ family members within the Triticeae species. • With our integrative framework, we genome-wide identified VQ proteins from 16 species. • TaVQ s are expanded by recent duplication events by comparing VQ genes among the Triticeae species. • RBGD-derived TaVQ genes likely become functionally divergent to the OsVQ orthologs. • Homoeolog expression bias in wheat contributes to the regulation and divergence of TaVQ s. • Several TaVQ s linked with salt tolerance may be regulated via the ABRE element. [ABSTRACT FROM AUTHOR]

The asymmetry of the cerebral sulcal morphology is particularly obvious in higher primates. The sulcal asymmetry in macaque monkeys, a genus of the Old World monkeys, in our previous studies and others is summarized, and its evolutionary significance is speculated. Cynomolgus macaques displayed fetal sulcation and gyration symmetrically, and the sulcal asymmetry appeared after adolescence. Population-level rightward asymmetry was revealed in the length of arcuate sulcus (ars) and the surface area of superior temporal sulcus (sts) in adult macaques. When compared to other nonhuman primates, the superior postcentral sulcus (spcs) was left-lateralized in chimpanzees, opposite of the direction of asymmetry in the ars, anatomically-identical to the spcs, in macaques. This may be associated with handedness: either right-handedness in chimpanzees or left-handedness/ambidexterity in macaques. The rightward asymmetry in the sts surface area was seen in macaques, and it was similar to humans. However, no left/right side differences were identified in the sts morphology among great apes, which suggests the evolutionary discontinuity of the sts asymmetry. The diversity of the cortical lateralization among primate species suggests that the sulcal asymmetry reflects the species-related specialization of the cortical morphology and function, which is facilitated by evolutionary expansion in higher primates. [ABSTRACT FROM AUTHOR]

The subventricular zone (SVZ) of the developing cerebral cortex appears transiently during cortical neurogenesis and is known as the second proliferative zone that contains intermediate progenitor cells and self-renewable neuronal stem cells-the so-called basal radial glia (bRG). The present study attempted to track the differentiation and migration dynamics of SVZ progenitors undergoing multiple cell divisions at the late stage of neurogenesis in a course of sulcogyrogenesis in the ferret, a gyrencephalic mammal. Ferret pups were given a 5-ethynyl-2'-deoxyuridine (EdU) injection on postnatal day (PD) 5 followed by a 5-bromo-2'-deoxyuridine (BrdU) injection on PD 7. The 48 h interval between EdU and BrdU injections covered the minimum times for the first and second S-phase of self-renewing bRG. Two h after BrdU injection, EdU/BrdU-double labeled cells were found in the inner or outer SVZ (iSVZ and oSVZ), more than 80% of which were Sox2-positive. Furthermore, 95.8% of EdU/BrdU-double labeled Sox2-positive progenitors in the iSVZ and 84.2% in the oSVZ were also Pax6-positive, defining these progenitors as bRG. On PD 20, all EdU/BrdU-double labeled cells were NeuN-immunopositive, and more than 60% of these were parvalbumin-immunopositive. EdU/BrdU-double labeled neurons were distributed densely in the superficial portion of the outer cortical stratum. Cluster analysis divided the gyral and sulcal regions into higher and lower density groups, respectively, based on the diversity of the cortical density of EdU/BrdU-double labeled neurons. The higher density group included the gyral and sulcal regions of the prefrontal, parietooccipital and/or cingulate cortex, corresponding to cortical regions associated with evolutionary expansion. Although a limited population of neurons within a narrow time window of cortical neurogenesis was tracked, the present findings suggest that neurons derived from bRG at the late stage of neurogenesis express parvalbumin during corticohistogenesis. Due to the diversity of sulcogyral distributions, neurons derived from bRG may be implicated in evolutionary cortical expansion.