扁蓿豆叶绿体基因组密码子偏好性分析

为阐明扁蓿豆（Medicago ruthenica）叶绿体基因组密码子使用模式，以其50条蛋白编码序列（CDS）为对象，利用软件CodonW 1.4.2、Excel以及在线程序对其ENC，RSCU，GC含量、中性绘图、PR2-plot、最优密码子等进行分析得到以下结果：基因组平均GC含量为40.58%，其中GC1>GC2>GC3；ENC的取值介于35.77～56.62之间，表明密码子使用偏好性较弱；基因组中共有30个密码子RSCU>1，其中29个以A/U结尾；ENC-plot绘图分析结果中多数基因分布于标准曲线下方，22个基因ENC比值在—0.05～0.05之间，密码子偏好性主要受选择影响；PR2-plot分析表明碱基T的使用频率大于A，G大于C，说明密码子偏好性还受其他因素影响；该基因组中共有UUU，UUA，ACU等11个最优密码子并均以A/U结尾。以上研究结果可为扁蓿豆叶绿体基因组优良基因利用提供理论与基础。     

Two-year surveillance of tilapia lake virus (TiLV) reveals its wide circulation in tilapia farms and hatcheries from multiple districts of Bangladesh

Tilapia lake virus (TiLV) is an emerging pathogen in aquaculture, reportedly affecting farmed tilapia in 16 countries across multiple continents. Following an early warning in 2017 that TiLV might be widespread, we executed a surveillance programme on tilapia grow-out farms and hatcheries from 10 districts of Bangladesh in 2017 and 2019. Among farms experiencing unusual mortality, eight out of 11 farms tested positive for TiLV in 2017, and two out of seven tested positive in 2019. Investigation of asymptomatic broodstock collected from 16 tilapia hatcheries revealed that six hatcheries tested positive for TiLV. Representative samples subjected to histopathology confirmed pathognomonic lesions of syncytial hepatitis. We recovered three complete genomes of TiLV from infected fish, one from 2017 and two from 2019. Phylogenetic analyses based on both the concatenated coding sequences of 10 segments and only segment 1 consistently revealed that Bangladeshi TiLV isolates formed a unique cluster within Thai clade, suggesting a close genetic relation. In summary, this study revealed the circulation of TiLV in 10 farms and six hatcheries located in eight districts of Bangladesh. We recommend continuing TiLV-targeted surveillance efforts to identify contaminated sources to minimize the countrywide spread and severity of TiLV infection.     

Genome-wide detection of selective signatures in a Jinhua pig population

The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig genome. These results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production traits. In the present study, we performed extended haplotype homozygosity(EHH) tests to identify significant core regions in 202 Jinhua pigs. A total of 26 161 core regions spanning 636.42 Mb were identified, which occupied approximately 28% of the genome across all autosomes, and 1 158 significant(P0.01) core haplotypes were selected. Genes in these regions were related to several economically important traits, including meat quality, reproduction, immune responses and exterior traits. A panel of genes including ssc-mir-365-2, KDM8, RABEP2, GSG1L, RHEB, RPH3AL and a signal pathway of PI3K-Akt were detected with the most extreme P-values. The findings in our study could draw a comparatively genome-wide map of selection signature in the pig genome, and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.     

淅川乌骨鸡全基因组转座子的鉴定与分析

【目的】 通过分析淅川乌骨鸡全基因组重测序数据,获取淅川乌骨鸡转座子的基本信息和特征分布,探究转座子相关基因参与的通路。不仅对研究淅川乌骨鸡转座子的生物学功能具有重要的意义,而且为探索基因组扩增、基因组功能及进化研究提供重要基础数据。 【方法】 对淅川乌骨鸡血液DNA进行全基因组重测序,采用双末端短序列比对基因组,运用RepeatModeler、TEclass、RepeatMasker等使用流程对转座子进行鉴定、构建、校正、分类和注释,获得淅川乌骨鸡整个基因组所有的转座子,对转座子的特征、分布及和基因的关系等方面进行分析。并对转座子插入的所有基因进行GO和KEGG数据库富集,分别结合GO和KEGG注释结果对功能进行描述。 【结果】 经鉴定、分类和注释,淅川乌骨鸡共鉴定到370 252个转座子序列,分为19个超家族,主要为CR1、TcMar-Mariner、ERVL、ERV1等超家族,进一步说明淅川乌骨鸡转座子类型主要是逆转录转座子;转座子的数目和染色体长度有关,染色体越长,转座子数目越多。在基因组中转座子和基因的密度成反比,基因密集的区域中转座子密度较低;基因组内转座子的插入并非随机的,LTR/ERVL、LTR/ERV1、DNA/PIF-Harbinger、DNA/Hat-Charlie、RC/Helitron等转座子倾向于插入基因外部。GO富集分析表明,在生物过程条目中鉴定出的转座子富集相对较多的是细胞过程、单生物过程、代谢过程、生物调节、刺激反应等;分子功能条目中鉴定出的转座子富集相对较多的是结合、催化活性等;细胞组分条目中鉴定出的转座子富集相对较多的是细胞部分、细胞器、膜等。KEGG富集分析表明,鉴定出的转座子主要在甘油酯代谢、PPAR信号通路、PI3K-Akt信号通路、胰岛素抵抗、Jak-STAT信号通路等通路。着重关注了与淅川乌骨鸡特性相关的通路,如和色素沉积有关的酪氨酸代谢、和肉品质有关的脂代谢、脂肪酸的合成、PI3K-Akt信号通路等。 【结论】 转座子含量与基因组大小,具有一定的正相关性,而且淅川乌骨鸡转座子在基因组的分布存在一定偏好性。转座子相关基因在色素相关通路中富集,其可能与淅川乌骨鸡的种质特性有关,具体的调控机制还有待进一步研究。     

林麝肺源ST1249型铜绿假单胞菌的分离鉴定及其全基因组序列分析

【目的】对分离自林麝化脓肺脏的1株疑似铜绿假单胞菌(PA)进行鉴定,并分析其致病和耐药机制,为林麝PA感染化脓性疾病的防控奠定基础。【方法】将病原菌分离纯化后,依次进行生化试验、16S rRNA序列分析、药敏试验和小鼠致病性试验,并通过全基因组测序,对分离菌株进行群体进化和物种分型分析以及基因功能注释。【结果】分离自林麝化脓肺脏的1株疑似铜绿假单胞菌经鉴定与PA相符,命名为FMDP001。药敏试验显示其对阿莫西林、头孢曲松、氨曲南、多粘菌素B和林可霉素耐药;对小鼠半数致死量为9.4×10~5 CFU/mL。全基因组序列分析显示该菌基因组大小为6 955 100 bp,序列类型为ST1249,与B136-33株同源性最高,且两菌株基因组平均核苷酸一致性(ANI)值达98.93%;全基因组中共有357个序列编码FMDP001与致病性相关的基因,根据功能分为黏附、铁摄取、胞外毒性蛋白和调控系统;84个序列编码耐药基因,其中多药耐药外排泵为主要成分。【结论】从林麝化脓肺脏中分离到1株致病性较强的PA,并获得ST1249型林麝源PA的全基因组序列,序列显示该菌携带大量药物外排泵及生物膜形成相关基因,决定其具有多重耐药特性,哌拉西林等可作为该类型PA感染的临床用药。     

Embryo-mediated genome editing for accelerated genetic improvement of livestock

Selecting beneficial DNA variants is the main goal of animal breeding. However, this process is inherently inefficient because each animal only carries a fraction of all desirable variants. Genome editing technology with its ability to directly introduce beneficial sequence variants offers new opportunities to modernize animal breeding by overcoming this biological limitation and accelerating genetic gains. To realize rapid genetic gain, precise edits need to be introduced into genomically-selected embryos, which minimizes the genetic lag. However, embryo-mediated precision editing by homology-directed repair (HDR) mechanisms is currently an inefficient process that often produces mosaic embryos and greatly limits the numbers of available edited embryos. This review provides a summary of genome editing in bovine embryos and proposes an embryo-mediated accelerated breeding scheme that overcomes the present efficiency limitations of HDR editing in bovine embryos. It integrates embryo-based genomic selection with precise multi-editing and uses embryonic cloning with elite edited blastomeres or embryonic pluripotent stem cells to resolve mosaicism, enable multiplex editing and multiply rare elite genotypes. Such a breeding strategy would enable a more targeted, accelerated approach for livestock improvement that allows stacking of beneficial variants, even including novel traits from outside the breeding population, in the most recent elite genetic background, essentially within a single generation.     

Genome-edited crops: how to move them from laboratory to market

Recent breakthroughs in CRISPR technology allow specific genome manipulation of almost all crops and have initiated a revolution in precision crop breeding. Rationally-based regulation and widespread public acceptance are needed to propel genome-edited crops from laboratory to market and to translate this innovative technology into agricultural productivity.     

基于流式细胞术的桫椤基因组大小测定

以买麻藤(Gnetum montanum)为内参,测定5种常用裂解液(Tris·MgCl_2、LB01、WPB、Otto’s、Galbraith’s)对桫椤(Alsophila spinulosa)细胞核的裂解效果,并通过比较桫椤和买麻藤流式细胞仪测定的荧光峰值,计算出桫椤的基因组大小。结果表明:5种裂解液中,WPB为桫椤最佳裂解液;桫椤基因组大小为6 003.25Mb,即2C DNA含量为6.138 pg。