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Genomics and genetic breeding in aquatic animals: progress and prospects

Wenteng XU, Songlin CHEN

《农业科学与工程前沿（英文）》 2017年第4卷第3期页码 305-318 doi: 10.15302/J-FASE-2017154

摘要： Genomics focuses on dissection of genome structure and function to provide a molecular basis for understanding the genetic background. In a pivotal step, the expense of whole genome sequencing has been largely eliminated by the rapid updating of sequencing technology, leading to increasing numbers of decoded genomes of aquatic organisms, driving the aquaculture industry into the genomic era. Multiple aquatic areas have been influenced by these findings, such as accelerated generation shift in the seed industry and the process of breeding improved lines. In this article, we have summarized the latest domestic and international progress of aquatic animals in nine aspects, including WGS and fine mapping, construction of high density genetic/physical maps, trait-related marker/genes screening, as well as sex control, genome editing, and other molecular breeding technologies. Finally, the existing problems in this field have been discussed and five future counter measures have been proposed accordingly.

关键词： aquaculture genomics genetic breeding progress

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Sepsis biomarkers: an omics perspective

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《医学前沿（英文）》 2014年第8卷第1期页码 58-67 doi: 10.1007/s11684-014-0318-2

摘要：

Sepsis is a common cause of death in hospitalized patients worldwide. The early detection of sepsis remains a great challenge for clinicians, and delayed diagnosis frequently undermines treatment efforts, thereby contributing to high mortality. Omics technologies allow high-throughput screening of sepsis biomarkers. This review describes currently available and novel sepsis biomarkers in the context of genomics, transcriptomics, proteomics, and metabolomics. The combination of these technologies can help refine the diagnosis of sepsis. This review paper serves as a reference for future studies that employ an integrated, multi-omics approach to disease identification.

关键词： sepsis biomarker genomics transcriptomics proteomics metabolomics

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An introduction to the medicinal plant genome project

Shilin Chen, Li Xiang, Xu Guo, Qiushi Li

《医学前沿（英文）》 2011年第5卷第2期页码 178-184 doi: 10.1007/s11684-011-0131-0

摘要： In recent years, genomics has developed rapidly with the application of next-generation sequencing technology. However, very few studies have been carried out on genomics for medicinal plants. This paper introduces the genome research of medicinal plants, including genome sequencing, assembly, annotation, and functional genomics, to set up the foundation for the development of natural medicines and the selection of cultivars with good agricultural traits. This study places the study on traditional Chinese medicine into the frontier field of life science.

关键词： genomics medicinal plant sequencing application

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Do not let precision medicine be kidnapped

null

《医学前沿（英文）》 2015年第9卷第4期页码 512-513 doi: 10.1007/s11684-015-0425-8

摘要：

Obama’s precision medicine initiative made the medical community boil over after the initiative’s release. Precision medicine has been advocated by the majority of scientists and doctors. However, some experts have questioned this concept. This article does not oppose precision medicine. However, the incentive of vigorously promoting precision medicine at present is a concern.

关键词： precision medicine personalized medicine genomics

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Genomic and pharmacogenetic studies of childhood acute lymphoblastic leukemia

null

《医学前沿（英文）》 2015年第9卷第1期页码 1-9 doi: 10.1007/s11684-015-0381-3

摘要：

With the cure rate of childhood acute lymphoblastic leukemia (ALL) approaching 90%, further improvement in the treatment outcome and quality of life of patients will require better understanding of the mechanisms of drug resistance, identifying new leukemic cell genetic lesions that are amendable to available target therapy, and optimizing treatment based on host pharmacodynamics and pharmacogenomics. Deeper characterization of leukemic cell genetic abnormalities has discovered new subtypes of leukemia such as early T-cell precursor ALL and Philadelphia chromosome-like ALL, and identified many genomic alterations that have diagnostic, prognostic, or therapeutic implications. In this regard, several novel fusion transcripts are responsive to ABL tyrosine kinase inhibitors and potentially to JAK inhibitors. Genome-wide analyses have also unraveled the role of inherited cancer predisposing genes and small nucleotide polymorphisms of several genes in the development of childhood ALL. These advances promise to lead to more sophisticated personalized treatment strategies in the near future.

关键词： pharmacogenomics acute lymphoblastic leukemia genomics pharmacogenetics

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Genomics approaches to unlock the high yield potential of cassava, a tropical model plant

Shengkui ZHANG,Ping’an MA,Haiyan WANG,Cheng LU,Xin CHEN,Zhiqiang XIA,Meiling ZOU,Xinchen ZHOU,Wenquan WANG

《农业科学与工程前沿（英文）》 2014年第1卷第4期页码 259-266 doi: 10.15302/J-FASE-2014043

摘要： Cassava, a tropical food, feed and biofuel crop, has great capacity for biomass accumulation and an extraordinary efficiency in water use and mineral nutrition, which makes it highly suitable as a model plant for tropical crops. However, the understanding of the metabolism and genomics of this important crop is limited. The recent breakthroughs in the genomics of cassava, including whole-genome sequencing and transcriptome analysis, as well as advances in the biology of photosynthesis, starch biosynthesis, adaptation to drought and high temperature, and resistance to virus and bacterial diseases, are reviewed here. Many of the new developments have come from comparative analyses between a wild ancestor and existing cultivars. Finally, the current challenges and future potential of cassava as a model plant are discussed.

关键词： cassava genomics yield potential adaptability tropical model

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Recent advances in fruit crop genomics

Qiang XU,Chaoyang LIU,Manosh Kumar BISWAS,Zhiyong PAN,Xiuxin DENG

《农业科学与工程前沿（英文）》 2014年第1卷第1期页码 21-27 doi: 10.15302/J-FASE-2014002

摘要： In recent years, dramatic progress has been made in the genomics of fruit crops. The publication of a dozen fruit crop genomes represents a milestone for both functional genomics and breeding programs in fruit crops. Rapid advances in high-throughput sequencing technology have revolutionized the manner and scale of genomics in fruit crops. Research on fruit crops is encompassing a wide range of biological questions which are unique and cannot be addressed in a model plant such as . This review summarizes recent achievements of research on the genome, transcriptome, proteome, miRNAs and epigenome of fruit crops.

关键词： fruit crops fruit biology gene function genomics

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深古菌门的核心代谢功能和热环境起源 Article

冯晓远, 王寅炤, Rahul Zubi, 王风平

《工程（英文）》 2019年第5卷第3期页码 498-504 doi: 10.1016/j.eng.2019.01.011

摘要：

深古菌门具有复杂的亚群分类，是地球上丰度最高的微生物之一。然而，深古菌的代谢特征和演化历史仍然有待进一步研究。本研究对来自10个不同亚群的15个新获得和36个已经发表的深古菌基因组进行了比较基因组分析，揭示了深古菌门的核心代谢特征，即蛋白质、脂质、芳香族化合物降解，糖酵解途径和Wood–Ljungdahl (WL) 途径。上述核心代谢特征表明深古菌使用乙酰辅酶A作为重要的代谢中间物。此外，部分深古菌亚群还具有不完整的柠檬酸循环、产乙酸途径和硫化物相关的代谢潜能，表明不同亚群具有多样的代谢能力和生态功能。亚群Bathy-21和Bathy-22位于深古菌系统发育树根部，是目前已知最古老的两个深古菌亚群。它们广泛分布于热液（泉）环境中，并编码超嗜热适应性特征的标记基因逆促旋酶（reverse gyrase, rgy）。综上，本研究对深古菌门的核心代谢能力进行了系统性研究和总结，并揭示了深古菌热环境起源的演化历史。

关键词：深古菌宏基因组比较基因组超嗜热适应性

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10x Genomics单细胞转录组测序及多组学数据挖掘技术

会议日期： 2019年08月02日

会议地点：北京海淀区

主办单位：北京市计算中心

近十二年人类蛋白质N-糖基化的全基因组关联研究综述 Review

Anna Timoshchuk, Sodbo Sharapov, Yurii S. Aulchenko

《工程（英文）》 2023年第26卷第7期页码 17-31 doi: 10.1016/j.eng.2023.03.013

摘要：

人类分泌的以及膜结合的大多数蛋白质都有共价连接的寡糖链或聚糖。糖基化影响着蛋白质的物理和化学性质及其生物功能。不难理解，蛋白质糖基化的改变与越来越多的人类疾病有关，而聚糖也越来越多地被视为潜在的治疗靶点、治疗药物的重要组成部分和生物标志物。尽管糖基化途径在生化方面被研究得很透彻，但人们对指导人类体内这些生化反应的细胞和组织特异性调节的基因网络知之甚少。由于缺乏对糖组变化的调控机制以及糖组与人类健康和疾病之间联系的详细了解，人类糖生物学的临床应用进展缓慢。人类遗传学和基因组学是用于提供人类体内糖生物学知识的两种亟待开发的工具，它们为剖析复杂性状的生物学特性提供了一种强大的数据驱动型不可知方法。本文总结了人类群体糖原组学的现状。在第1节中，简要概述了N-聚糖的结构组织；在第2节中，介绍了主要的血浆糖蛋白。接下来，在第3节中，总结、分类并归纳了当前N-糖基化全基因组关联研究（GWAS）的结果，这些研究提供了有关糖基化群体变异遗传调控的新知识。迄今为止，此类研究仅限于分析人体血浆N-糖组以及免疫球蛋白G和转铁蛋白的N-糖基化。虽然与不同组织和糖蛋白的大量糖组相比，这三种糖组只构成了相当有限的集合，但这三种糖组的研究确实可以提供有力的分析和归纳。然后，在第4节中讨论已确定位点中的基因，并在第5节中特别关注具有强支持作用的基因。最后，在第6节和第7节中介绍新发现的特殊案例，重点关注与人类蛋白质N-糖基化有关的基因变异的潜在作用机制和生物靶标。

关键词：糖组学聚糖 N-糖基化基因组学遗传学全基因组关联研究

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新孢子虫病——分子流行病学及发病机制综述 Review

Asis Khan, Jahangheer S. Shaik, Patricia Sikorski, Jitender P. Dubey, Michael E. Grigg

《工程（英文）》 2020年第6卷第1期页码 10-19 doi: 10.1016/j.eng.2019.02.010

摘要：

犬新孢子虫（Neospora caninum）是一种囊肿形成的原生动物寄生虫，它是世界范围内牛的流产和新生儿死亡的主要原因。犬新孢子虫具有广泛的中间宿主范围，其有性繁殖只在犬科动物中发生。另一种新孢子虫——休斯新孢子虫也已经被发现，它能导致马的脑髓炎。虽然分子流行病学研究尚处于起步阶段，但核糖体小亚单位RNA（small subunit ribosomal RNA, ssuRNA）和犬新孢子虫物种特异性DNA探针（pNc5）中的18S rRNA和ITS1区域已被广泛应用于区分新孢子虫和其他密切相关的顶复门寄生虫。虽然这些重复区域比管家或抗原基因具有更高的敏感性和特异性，但它们具有较低的区分能力，无法捕捉物种内部的多样性。同样，尽管多个小卫星或微卫星标记研究显示了新孢子虫体内清晰的地理亚结构，但由于不同等位基因的大小在微卫星位点上趋同（称为同形质），虫株往往被错误分类。只有一株名为N. caninum Liverpool（Nc-Liv）的虫株被进行基因组测序，并与其近亲弓形虫（Toxoplasma gondii）进行了比较。因此，需要基于全世界多个虫株的全基因组序列进行详细的群体基因组学研究，以便更好地了解新孢子虫目前的种群遗传结构，最终
确定能够更有效对抗牛新孢子虫病的疫苗候选者。本文的目的是概述我们目前对新孢子虫的分子流行病学和基因组学的理解，并将其与密切相关的顶复门寄生虫哈蒙球虫和弓形虫结合起来。

关键词：新孢子虫病，分子流行病学，群体遗传学，基因组学，宿主反应，疫苗

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