Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame (Sesamum indicum L.)

Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions

ENSO-related East Asian climate transition at ~ 3600 B.P. and its implications for the rise of pastoralism in North China

A transition from cereal-based agriculture to pastoralism in North China occurred around 3600 cal yr B.P., and corresponded to Northern Hemisphere cooling and the onset of an arid climate over North China. In this paper, we investigate the mechanisms for the ~3600 cal yr B.P. climate transition that may have triggered this change in Chinese civilization based on a compilation of 33 high-resolution paleoclimate records spanning the 4000–3000 cal yr B.P. interval. Results show that North and South China experienced a meridional dipole pattern of the climate change. From 4000 to 3600 cal yr B.P., the region north of 30°N was wet and the region south of 30°N was dry, then from 3600 to 3000 cal yr B.P., the pattern reversed with a drier north and a wetter south. We found that this climate transition was related to the onset of a more El Niño-like state in the tropical Pacific Ocean after ~3600 cal yr B.P., which resulted in more precipitation in South China but less precipitation in North China. Climate in the marginal monsoon areas of North China deteriorated, becoming more cold and arid, and pastoralism replaced cereal agriculture as the dominant mode of subsistence. Our study highlights the important role of the paleo-El Niño-Southern Oscillation (paleo-ENSO) for the evolution of civilization in China

Spatial differences in East Asian climate transition at ∼260 ka and their links to ENSO

The East Asian summer precipitation exhibits significant spatial differences from inter-annual to sub-orbital timescales, which has been associated with El Niño-Southern Oscillation (ENSO). However, studies on spatial patterns of climate and their mechanisms on orbital and tectonic timescales are still scarce, impeding a better understanding of Asian monsoon dynamics on long timescales. Here, we present a loess section spanning the past 430 ka in the Menyuan (MY) basin from the Northeastern Tibetan Plateau (NETP), and compare it with records from other sites in East Asia in order to explore the spatial patterns of climate changes and their mechanisms. Our results reveal a distinct climate transition at ∼260 ka in various records, which is characterized a transition from a “wet–dry–wet” to a “dry–wet–dry” pattern in the north-south direction and a transition from a “dry–wet” to “wet–dry” pattern in the west-east direction. This climate transition coincides with a significant weakening of the equatorial Pacific zonal (east–west) thermal gradient which indicates a shift to a more El Niño-like state, suggesting that the climate transition in East Asia at ∼260 ka could be related to paleo-ENSO variation. A more El Niño-like state could force an intensification and southwestward extension of the Western Pacific Subtropical High (WPSH) which could in turn move the rainfall front westward with the maximum rainfall belt over central China, resulting in the persistence of the observed climate patterns in East Asia. Our model results suggest that the change of the paleo-ENSO condition at ∼260 ka could be related to the eccentricity-modulated insolation and the ice shelve changes in northern high latitudes. Our study highlights the important role of paleo-ENSO in regulating the long-term climate changes in different sub-regions in East Asia

Periodic variations of alpine glaciation and desertification of the NE Tibetan Plateau: Evidence from the loess-paleosol sequences in the Menyuan Basin

The NE Tibetan Plateau (NETP) is one of the most ecologically vulnerable areas, with large expansion and retreat of desert area since the Last Glacial Maximum. However, the long-term history of desertification in this area and its mechanisms are still unknown due to lack of long-term and well-dated records. Here we present the results of sand particle content (a proxy of local materials) and detrital-zircon ages from a high-resolved loess-paleosol section spanning the past 420 ka in the Menyuan (MY) Basin lying in the NETP. Our results show that the provenance of loess units (formed in glacial periods) was strongly influenced by local desertified materials that were mainly produced by alpine glaciers surrounding the basin, which was significantly different from the paleosol units (formed in interglacial periods). The strong signals of ∼100 kyr and ∼ 20 kyr cycles in the content of local materials suggest that the desertification of the MY Basin was controlled by both the late Quaternary ∼100-kyr ice age and the ∼20-kyr precession cycles, which is obviously different from the periodicities of the classic Luochuan loess section in the mainland of the Chinese Loess Plateau (CLP). The strong ∼20-kyr cycle in the MY Basin suggest that the alpine glaciation activities in the NETP were driven by local summer insolation. These results allow us to characterize the long-term natural variability of desertification in the NETP, as well as the mechanisms for the spatial and glacial-interglacial variations of loess provenance on the CLP

Table_6_Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame (Sesamum indicum L.).xlsx

Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions.</p

Table_7_Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame (Sesamum indicum L.).xlsx

Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions.</p

Table_4_Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame (Sesamum indicum L.).xlsx

Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions.</p

Table_2_Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame (Sesamum indicum L.).xlsx

Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions.</p

Table_3_Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame (Sesamum indicum L.).xlsx

Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions.</p