The genome sequence of the wisent (Bison bonasus)

This work was supported by the Youth Science and Technology Innovation Team of Sichuan Province (2014TD003), Shenzhen Industrial Designation Services Cloud Platform (GGJS20150429172906635), International Collaboration 111 Projects of China, Fundamental Research Funds for the Central Universities, 985 and 211 Projects of Sichuan University.The wisent, also known as the European bison, was rescued from extinction approximately 80 years ago through the conservation of 12 individuals. Here, we present the draft genome sequence of a male wisent individual descended from this founding stock. A total of 366 billion base pairs (Gb) of raw reads from whole-genome sequencing of this wisent were generated using the Illumina HiSeq2000 platform. The final genome assembly (2.58 Gb) is composed of 29,074 scaffolds with an N50 of 4.7 Mb. 47.3% of the genome is composed of repetitive elements. We identified 21,542 genes and 58,385 non-coding RNAs. A phylogenetic tree based on nuclear genomes indicated sister relationships between bison and wisent and between the wisent-bison clade and yak. For 75 genes we obtained evidence of positive evolution in the wisent lineage. We provide the first genome sequence and gene annotation for the wisent. The availability of these resources will be of value for the future conservation of this endangered large mammal and for reconstructing the evolutionary history of the Bovini tribe.Publisher PDFPeer reviewe

The genome evolution and domestication of tropical fruit mango

Background: Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. Results: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. Conclusions: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces

The genome evolution and domestication of tropical fruit mango

Background: Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. Results: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. Conclusions: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces

Response of Wetland Evapotranspiration to Land Use/Cover Change and Climate Change in Liaohe River Delta, China

This study aims to investigate the effects of land use/cover change (LUCC) and climate change on wetland evapotranspiration (ET), and to identify the importance of the main effect factors in the spatiotemporal dynamics of ET. In the wetland of Liaohe River Delta, China, the ET of eight growing seasons during 1985−2017 was estimated using the surface energy balance algorithm for land (SEBAL) model with Landsat and meteorological data. Results show that the average relative error of regional ET estimated by the SEBAL model is 9.01%, and the correlation coefficient between measured and estimated values is 0.61, which indicates that the estimated values are reliable. This study observed significant spatial and temporal variations in ET across the region of interest. The distribution of the average and relative change rate of daily ET in the study area showed bimodal characteristics, that is, the lowest trough occurred in 2005, whereas crests occurred in 1989 and 2014. Simultaneously, the daily ET varied with the land use/cover area. Regional daily ET displays highly heterogeneous spatial distribution, that is, the ET of different land uses/cover types in descending order is as follows: water body, wetland vegetation, non-wetland vegetation, and non-vegetation (except water area). Therefore, the spatial pattern of ET is relevant to the land use/cover types to some extent. In addition, the temporal variation of wetland ET is closely related to landscape transformation and meteorological factor change. A strong correlation was found between ET and the weighted values of meteorological factors, with a correlation coefficient of 0.69. Meanwhile, the annual fluctuations of daily ET and the weighted values were relatively similar. Therefore, the findings highlight the importance of using cheap and readily available remote sensing data for estimating and mapping the variations in ET in coastal wetland

Parameterizing Anthropogenic Heat Flux with an Energy-Consumption Inventory and Multi-Source Remote Sensing Data

Anthropogenic heat (AH) generated by human activities is an important factor affecting the urban climate. Thus, refined AH parameterization of a large area can provide data support for regional meteorological research. In this study, we developed a refined anthropogenic heat flux (RAHF) parameterization scheme to estimate the gridded anthropogenic heat flux (AHF). Firstly, the annual total AH emissions and annual mean AHF of Beijing municipality in the year 2015 were estimated using a top-down, energy-consumption inventory method, which was derived based on socioeconomic statistics and energy consumption data. The heat released from industry, transportation, buildings (including both commercial and residential buildings), and human metabolism were taken into account. Then, the county-scale AHF estimation model was constructed based on multi-source remote sensing data, such as Suomi national polar-orbiting partnership (Suomi-NPP) visible infrared imaging radiometer suite (VIIRS) nighttime light (NTL) data and moderate resolution imaging spectroradiometer (MODIS) data. This model was applied to estimate the annual mean AHF of the counties in the Beijing–Tianjin–Hebei region. Finally, the gridded AHF data with 500-m resolution was obtained using a RAHF parameterization scheme. The results indicate that the annual total AH emissions of Beijing municipality in the year 2015 was approximately 1.704 × 1018 J. Of this, the buildings contribute about 34.5%, followed by transportation and industry with about 30.5% and 30.1%, respectively, and human metabolism with only about 4.9%. The annual mean AHF value of the Beijing–Tianjin–Hebei region is about 6.07 W·m−2, and the AHF in urban areas is about in the range of 20 W·m−2 and 130 W·m−2. The maximum AHF value is approximately 130.84 W·m−2, mostly in airports, railway stations, central business districts, and other densely-populated areas. The error analysis of the county-scale AHF results showed that the residual between the model estimation and energy consumption statistics is less than 1%. In addition, the spatial distribution of RAHF results is generally centered on urban area and gradually decreases towards suburbs. The spatial pattern of the RAHF results within urban areas corresponds well to the distribution of population density, building density, and the industrial district. The spatial heterogeneity of AHF within urban areas is well-reflected through the RAHF results. The RAHF results can be used in meteorological and environmental modeling for the Beijing–Tianjin–Hebei region. The results of this study also highlight the superiority of Suomi-NPP VIIRS NTL data for AHF estimation

A Partition Modeling for Anthropogenic Heat Flux Mapping in China

Anthropogenic heat (AH) generated by human activities has a major impact on urban and regional climate. Accurately estimating anthropogenic heat is of great significance for studies on urban thermal environment and climate change. In this study, a gridded anthropogenic heat flux (AHF) estimation scheme was constructed based on socio-economic data, energy-consumption data, and multi-source remote sensing data using a partition modeling method, which takes into account the regional characteristics of AH emission caused by the differences in regional development levels. The refined AHF mapping in China was realized with a high resolution of 500 m. The results show that the spatial distribution of AHF has obvious regional characteristics in China. Compared with the AHF in provinces, the AHF in Shanghai is the highest which reaches 12.56 W·m−2, followed by Tianjin, Beijing, and Jiangsu. The AHF values are 5.92 W·m−2, 3.35 W·m−2, and 3.10 W·m−2, respectively. As can be seen from the mapping results of refined AHF, the high-value AHF aggregation areas are mainly distributed in north China, east China, and south China. The high-value AHF in urban areas is concentrated in 50–200 W·m−2, and maximum AHF in Shenzhen urban center reaches 267 W·m−2. Further, compared with other high resolution AHF products, it can be found that the AHF results in this study have higher spatial heterogeneity, which can better characterize the emission characteristics of AHF in the region. The spatial pattern of the AHF estimation results correspond to the distribution of building density, population, and industry zone. The high-value AHF areas are mainly distributed in airports, railway stations, industry areas, and commercial centers. It can thus be seen that the AHF estimation models constructed by the partition modeling method can well realize the estimation of large-scale AHF and the results can effectively express the detailed spatial distribution of AHF in local areas. These results can provide technical ideas and data support for studies on surface energy balance and urban climate change