Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays.

Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.This work is part of the ‘‘SpatioTemporal Omics Consortium’’ (STOC) paper package. A list of STOC members is available at: http://sto-consortium.org. We would like to thank the MOTIC China Group, Rongqin Ke (Huaqiao University, Xiamen, China), Jiazuan Ni (Shenzhen University, Shenzhen, China), Wei Huang (Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China), and Jonathan S. Weissman (Whitehead Institute, Boston, USA) for their help. This work was supported by the grant of Top Ten Foundamental Research Institutes of Shenzhen, the Shenzhen Key Laboratory of Single-Cell Omics (ZDSYS20190902093613831), and the Guangdong Provincial Key Laboratory of Genome Read and Write (2017B030301011); Longqi Liu was supported by the National Natural Science Foundation of China (31900466) and Miguel A. Esteban’s laboratory at the Guangzhou Institutes of Biomedicine and Health by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA16030502), National Natural Science Foundation of China (92068106), and the Guangdong Basic and Applied Basic Research Foundation (2021B1515120075).S

Long-term responses of riparian plants' composition to water level fluctuation in China's Three Gorges Reservoir.

The water level fluctuation zone (WLFZ) has experienced a novel hydrological regime due to the anti-seasonal operation of China's Three Gorges Reservoir. Overall, hydrological change can significantly influence the riparian environment and shift the riparian vegetation. Although numerous studies have investigated the short-term responses of riparian plants to water level fluctuation in this zone, few have addressed long-term effects. In this study, four permanent plots in the WLFZ of the canyon landform area were chosen to evaluate the long-term responses of riparian plants to water level fluctuation from 2008 to 2015 and to screen candidate plants for ecological restoration. We recorded 146 species in 2008, 110 species in 2009, 68 species in 2012 and 69 species in 2015, indicating a conspicuous loss in riparian plants. Most of the remnant plants were annual and perennial herbs. Of the native species present in 2008, 82, 22 and 8 had disappeared in 2009, 2012 and 2015, respectively. Simultaneously, 45, 15 and 11 non-native species were first found, respectively. Additionally, over half of the native and the non-native species were not found after being subjected to a water level fluctuation. From 2008 to 2015, only 27 native species always presented; however, not all of them were chosen as candidates for ecological restoration because of their decreased importance values. In contrast, the importance value of Cynodon dactylon increased over time, suggesting its high tolerance to long-term winter flooding. We concluded that riparian plants' composition of the canyon landform area dramatically declined after long-term water level fluctuation and their presence was determined by the novel hydrological condition. Our results also suggested that Cynodon dactylon or its combination with other species (i.e. Digitaria chrysoblephara, Setaria glauca, Setaria viridis) is a better candidate for ecological restoration in the WLFZ

Effect of off-season flooding on growth, photosynthesis, carbohydrate partitioning, and nutrient uptake in Distylium chinense.

Distylium chinense is an evergreen shrub used for the vegetation recovery of floodplain and riparian areas in Three Gorges Reservoir Region. To clarify the morphological and physiological responses and tolerance of Distylium chinense to off-season flooding, a simulation flooding experiment was conducted during autumn and winter. Results indicated that the survival rate of seedlings was 100%, and that plant height and stem diameter were not significantly affected by flooding. Adventitious roots and hypertrophic lenticels were observed in flooded seedlings after 30 days of flooding. Flooding significantly reduced the plant biomass of roots, net photosynthetic rate (Pn), stomatal conductance (gs), transpiration rate (Tr), maximum photochemical efficiency (Fv/Fm), photochemical quenching (qP), and electron transport rate (ETR) in leaves, and also affected the allocation and transport of carbohydrate and nutrients. However, D. chinense was able to maintain stable levels of Pn, Fv/Fm, qP, ETR, and nutrient content (N and P) in leaves and to store a certain amount of carbohydrate in roots over prolonged durations of flooding. Based on these results, we conclude that there is a high flooding tolerance in D. chinense, and the high survival rate of D. chinense may be attributable to a combination of morphological and physiological responses to flooding

Maxent modeling for predicting impacts of climate change on the potential distribution of Thuja sutchuenensis Franch., an extremely endangered conifer from southwestern China

Objectives Detailed and reliable information about the spatial distribution of species provides important information for species conservation management, especially in the case of rare species of conservation interest. We aimed to study the consequences of climate change on geographical distributions of the tertiary rare tree species Thuja sutchuenensis Franch. (Cupressaceae) to provide reference for conservation management of this species, including priority area selection for introduction and cultivation of the species. We expect that this approach could be promising in predicting the potential distribution of other rare tree species, and as such can be an effective tool in rare tree species restoration and conservation planning, especially species with narrow distribution or raw presence-only occurrence data. Methods 107 records covering the whole distribution range of T. sutchuenensis in the Daba Mountains were obtained during a 3-year field survey. The principle of maximum entropy (Maxent) was used to model the species' potential distribution area under paleoclimate, current and future climate background. Results The Maxent model was highly accurate with a statistically significant AUC value of 0.998, which is higher than 0.5 of a null model; The location of the potential distribution for the last interglacial period is in southeastern China, with the largest optimal habitat area being only 1666 km(2). In other periods, the central location of the potential distribution is accordant with the real present distribution, but the model's predicted optimal habitat area is outside the current distribution. Conclusions Our findings can be applied in various ways such as the identification of additional localities where T. sutchuenensis may already exist, but has not yet been detected; the recognition of localities where it is likely to spread to; the priority selection area for introduction and cultivation and the conservation management of such rare tree species. (C) 2017 The Authors. Published by Elsevier B.V

Soluble sugar and starch content (means ± S.E., n = 3) of <i>D.chinense</i> seedlings under non-flooded and flooded conditions.

<p>*,**: significant differences (P<0.05 and P<0.01, respectively) based on a t-test.</p><p>Soluble sugar and starch content (means ± S.E., n = 3) of <i>D.chinense</i> seedlings under non-flooded and flooded conditions.</p

The effect of flooding on Fv/Fm, qP, qN, and ETR in leaves of <i>D.chinense</i>.

<p>Means and standard errors based on three replicates are shown. Significant difference induced by flooding is indicated by asterisk: * P<0.05 and ** P<0.01.</p

Biomass characteristics (means ± S.E., n = 5) of <i>D.chinense</i> seedlings under non-flooded and flooded conditions.

<p>*, **: significant differences (P<0.05 and P<0.01, respectively) based on a t-test.</p><p>Biomass characteristics (means ± S.E., n = 5) of <i>D.chinense</i> seedlings under non-flooded and flooded conditions.</p

Maxent modeling for predicting impacts of climate change on the potential distribution of Thuja sutchuenensis Franch., an extremely endangered conifer from southwestern China

Objectives: Detailed and reliable information about the spatial distribution of species provides important information for species conservation management, especially in the case of rare species of conservation interest. We aimed to study the consequences of climate change on geographical distributions of the tertiary rare tree species Thuja sutchuenensis Franch. (Cupressaceae) to provide reference for conservation management of this species, including priority area selection for introduction and cultivation of the species. We expect that this approach could be promising in predicting the potential distribution of other rare tree species, and as such can be an effective tool in rare tree species restoration and conservation planning, especially species with narrow distribution or raw presence-only occurrence data. Methods: 107 records covering the whole distribution range of T. sutchuenensis in the Daba Mountains were obtained during a 3-year field survey. The principle of maximum entropy (Maxent) was used to model the species’ potential distribution area under paleoclimate, current and future climate background. Results: The Maxent model was highly accurate with a statistically significant AUC value of 0.998, which is higher than 0.5 of a null model; The location of the potential distribution for the last interglacial period is in southeastern China, with the largest optimal habitat area being only 1666 km2. In other periods, the central location of the potential distribution is accordant with the real present distribution, but the model’s predicted optimal habitat area is outside the current distribution. Conclusions: Our findings can be applied in various ways such as the identification of additional localities where T. sutchuenensis may already exist, but has not yet been detected; the recognition of localities where it is likely to spread to; the priority selection area for introduction and cultivation and the conservation management of such rare tree species

<i>P</i>_n, <i>g</i>_s, <i>C</i>_i, <i>T</i>_r, and <i>L</i>_s in leaves of <i>D.chinense</i> in response to flooding.

<p>Means and standard errors based on three replicates are shown. Significant difference induced by flooding is indicated by asterisk: * P<0.05 and ** P<0.01.</p

Morphological characteristics of <i>D.chinense</i> seedlings after 60 days of flooding (means ± S.E., n = 5).

<p>Morphological characteristics of <i>D.chinense</i> seedlings after 60 days of flooding (means ± S.E., n = 5).</p