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Comparative transcriptomics revealed enhanced light responses, energy transport and storage in domestication

Zhiqiang XIA,Xin CHEN,Cheng LU,Meiling ZOU,Shujuan WANG,Yang ZHANG,Kun PAN,Xincheng ZHOU,Haiyan WANG,Wenquan WANG

《农业科学与工程前沿（英文）》 2016年 第3卷 第4期   页码 295-307 doi: 10.15302/J-FASE-2016126

摘要： Cassava is a staple food, feed and bioenergy crop important to the world especially in the tropics. Domesticated cassava is characterized by powerful carbohydrate accumulation but its wild progenitor is not. Here, we investigated the transcriptional differences of eight cDNA libraries derived from developing leaf, stem and storage root of cassava cv. Arg7 and an ancestor line, W14, using next generation sequencing system. A total of 41302 assembled transcripts were obtained and from these, 25961 transcripts with FPKM≥3 in at least one library were named the expressed genes. A total of 2117, 1963 and 3584 transcripts were found to be differentially expressed in leaf, stem and storage root (150 d after planting), respectively, between Arg7 and W14 and ascribed to 103, 93 and 119 important pathways in leaf, stem and storage root, respectively. The highlight of this work is that the genes involved in light response, such as those for photosystem I (PSA) and photosystem II (PSB), other genes involved in light harvesting, and some of the genes in the Calvin cycle of carbon fixation were specially upregulated in leaf. Genes for transport and also for key rate-limiting enzymes (PFK, PGK and PK, GAPDH) coupling ATP consumption in glycolysis pathway were predominantly expressed in stem, and genes for sucrose degradation (INVs), amylose synthesis (GBSS) and hydrolysis (RCP1, AMYs), the three key steps of starch metabolism, and transport associated with energy translocation (ABC, AVPs and ATPase) and their upstream transcription factors had enhanced expression in storage root in domesticated cassava. Co-expression networks among the pathways in each organs revealed the relationship of the genes involved, and uncovered some of the important hub genes and transcription factors targeting genes for photosynthesis, transportation and starch biosynthesis.

关键词： cassava     comparative transcriptomics     energy transport     photosynthesis     starch synthesis    

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A brief history of wheat utilization in China

Minxia LU, Liang CHEN, Jinxiu WANG, Ruiliang LIU, Yang YANG, Meng WEI, Guanghui DONG

《农业科学与工程前沿（英文）》 2019年 第6卷 第3期   页码 288-295 doi: 10.15302/J-FASE-2019266

摘要：

Wheat is one of the most important crops in both China and the world, and its domestication can be traced back to ~10000 years ago. However, the history of its origin and utilization in China remains highly ambiguous. Drawing upon the most recent results of taxonomic, genetic, archeological and textual studies focused on the wheat in prehistory, this paper argues that wheat was not domesticated but introduced into China in the late fifth millennium BP. In the subsequent centuries, this exotic crop was quickly utilized as a staple food in northwest China. In contrast, it was not adopted as a staple in Central Plains until the Han Dynasty (202 BCE–220 CE), which was mainly as a consequence of the living environment, population and innovations in food processing technology.

关键词： multidisciplinary evidence     prehistoric food globalization     wheat consumption     wheat domestication    

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Genome-wide analysis reveals selection for Chinese Rongchang pigs

Lei CHEN, Shilin TIAN, Long JIN, Zongyi GUO, Dan ZHU, Lan JING, Tiandong CHE, Qianzi TANG, Siqing CHEN, Liang ZHANG, Tinghuan ZHANG, Zuohua LIU, Jinyong WANG, Mingzhou LI

《农业科学与工程前沿（英文）》 2017年 第4卷 第3期   页码 319-326 doi: 10.15302/J-FASE-2017161

摘要： Livestock have undergone domestication and consequently strong selective pressure on genes or genomic regions that control desirable traits. To identify selection signatures in the genome of Chinese Rongchang pigs, we generated a total of about 170 Gb of DNA sequence data with about 6.4-fold coverage for each of six female individuals. By combining these data with the publically available genome data of 10 Asian wild boars, we identified 449 protein-coding genes with selection signatures in Rongchang pigs, which are mainly involved in growth and hormone binding, nervous system development, and drug metabolism. The accelerated evolution of these genes may contribute to the dramatic phenotypic differences between Rongchang pigs and Chinese wild boars. This study illustrated how domestication and subsequent artificial selection have shaped patterns of genetic variation in Rongchang pigs and provides valuable genetic resources that can enhance the use of pigs in agricultural production and biomedical studies.

关键词： domestication     genome     pig     re-sequencing     selection    

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氯霉素及其产物降解菌群在长期驯化过程中的微生物群落和关键基因演替模式

张家禹, 周开颜, 郭芳亮, 雷华新, 赵仁鑫, 林琳, 李晓岩, 李炳

《工程（英文）》 2023年 第31卷 第12期   页码 59-69 doi: 10.1016/j.eng.2023.07.009

摘要：

氯霉素（CAP）作为一种广泛存在的新污染物，对水环境中的生态群落产生了负面影响。生物处理广泛应用于水体污染物的去除，而功能微生物的性能决定了其效果。本研究从活性污泥中驯化了一个具有强大CAP降解能力的菌群。对硝基苯甲酸（PNB）和2,2-二氯乙酸（DCA）是CAP生物和化学处理过程中产生的主要产物，它们也分别作为菌群的唯一底物进行长期驯化。宏基因组分析揭示了2.5年驯化过程中微生物群落和关键功能基因的演替模式。经过长期驯化，Sphingomonas、Caballeronia和Cupriavidus分别成为CAP、PNB和DCA降解菌群中的优势菌属，并且它们分别是CAP、PNB和DCA的关键降解菌，它们之间的协同合作实现了CAP的高度矿化。PNB转化为原儿茶酸（PCA），然后通过间位和邻位裂解途径被矿化。通过长期驯化，参与CAP、PNB和DCA代谢的关键功能基因，包括CAP乙酰转移酶、CAP氧化还原酶、卤代酸脱卤酶和原儿茶酸双加氧酶，在菌群中显著富集。本研究还发现pH和碳源对CAP的生物降解效率有显著影响。本研究驯化的菌群和分离的菌株可用作加强CAP、PNB和DCA污染环境生物修复的微生物资源。

关键词： 抗生素     生物降解     代谢作用     微生物群落演替     宏基因组    

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标题 作者 时间 类型 操作

Comparative transcriptomics revealed enhanced light responses, energy transport and storage in domestication

Zhiqiang XIA,Xin CHEN,Cheng LU,Meiling ZOU,Shujuan WANG,Yang ZHANG,Kun PAN,Xincheng ZHOU,Haiyan WANG,Wenquan WANG

期刊论文

A brief history of wheat utilization in China

Minxia LU, Liang CHEN, Jinxiu WANG, Ruiliang LIU, Yang YANG, Meng WEI, Guanghui DONG

期刊论文

Genome-wide analysis reveals selection for Chinese Rongchang pigs

Lei CHEN, Shilin TIAN, Long JIN, Zongyi GUO, Dan ZHU, Lan JING, Tiandong CHE, Qianzi TANG, Siqing CHEN, Liang ZHANG, Tinghuan ZHANG, Zuohua LIU, Jinyong WANG, Mingzhou LI

期刊论文

氯霉素及其产物降解菌群在长期驯化过程中的微生物群落和关键基因演替模式

张家禹, 周开颜, 郭芳亮, 雷华新, 赵仁鑫, 林琳, 李晓岩, 李炳

期刊论文