Here, we report a draft genome sequence of endophytic fungus Nemania diffusa YAFEF818, isolated from Artemisia argyi. Oxford Nanopore Technologies PromethION and Illumina NovaSeq sequence reads were assembled using NECAT and polished using pilon to yield a 55.63 Mb genome.

Ultra performance liquid chromatography-high resolution mass spectrometry (UPLC-MS/MS) were used to target quantitative determination anthocyanins and flavonoids in the fresh leaves (purple and green) of Eleutherococcus senticosus. The results showed that the content of total anthocyanins was 99.68 μg/g (Fresh Weight, FW) in purple leaves and 29.12 μg/g in green leaves. Cyanidin-3-O-galactoside and delphinidin were the main anthocyanins compound in purple and green leaves, and the content of the both declined sharply in green leaves. The content of cyanidin-3-O-galactoside reached 616.23 ng/100 mg in purple leaves and was only fifth in green leaves. The total flavonoids content was 4.90 mg/g in purple leaves and 2.23 mg/g in green leaves. Quercetin-3-β-D-glucoside (236.96 ng/mg) and kaempferol-3-O-glucoside (145.27 ng/mg) were the main flavonoids compound in purple leaves. Besides the two main flavonoids, large quantities of rutin (269.11 ng/mg) was detected in green leaves of E. senticosus.

ObjectiveThe comparison of the codon usage patterns in the transcriptomes of Pinus kesiya and P. yunnanensis provided a basis for the codon modification of hetero-expression of P. kesiya genes.MethodsIn the present study, the codon base composition and other relative parameters of the transcriptomes of P. kesiya and P. yunnanensis were analyzed and calculated using Codon W 1.4.2, and the optimal codon was deduced and compared with the codon usage frequency of other fungus and plants.ResultsThe base composition of the transcriptome of P. yunnanensis was GC12 (0.50) > GC3s (0.47), and the composition of the P. kesiya transcriptome was GC12 (0.51) > GC3s (0.32). In terms of the base composition of the transcriptomes of different tissues, the high-resin bark was in the order of GC12 (0.49) > GC3s (0.45), and the low-resin bark was in the order of GC12 (0.50) > GC3s (0.41), which illustrated that their codons all preferred AU at the third base of the transcriptome of different tissues of P. yunnanensis and P. kesiya. All their CAI values were relatively lower than those of angiosperms, indicating the transcriptome codon preference of different tissues of P. yunnanensis and P. kesiy. The neutrality plot and ENC-plot analysis indicated that their usage patterns were mainly affected by selection pressures. The optimal codons had a small difference between the transcriptome of different tissues of P. kesiya and P. yunnanensis. The codon usage frequency of P. kesiya, P. yunnanensis, Arabidopsis thaliana, Populus trichocarpa, Aspergillus nidulans and Saccharomyces prombe was compared, and the results revealed that the codon preferences of P. kesiya and P. yunnanensis were pretty similar, which were relatively close to those of A. niger and A. thaliana, illustrating that the eukaryotic expression system of A. nidulans was more suitable for the heterologous expression of the P. kesiya genes.ConclusionThe codon usage bias of the transcriptome coding sequences of P. yunnanensis and P. kesiya was mainly affected by selection and the joint action of many factors, and A. nidulans was the optimal heterologous expression receptor for P. kesiya genes. The present study has provided some scientific background and a theoretical basis for the transgenic breeding and hybridization breeding, heterologous expression of specific genes of P. kesiya and the improvement of the expression efficiency of exogenous genes.

为了解真菌红汁乳菇(Lactarius hatsudake)萜类合成酶(TPS)基因的功能,从红汁乳菇全基因组中分离获得TPS基因,并对其进行生物信息学分析,系统发育树构建,对它们在不同碳源和氮源培养条件下的表达情况进行分析.结果显示:在红汁乳菇基因组中共分离出16个LhTPS基因,LhTPS10、LhTPS13、LhTPS14仅具有萜烯合酶的DXXD保守结构域,其余蛋白均具有DXXD和NSE保守结构域,因此把16个萜类合成酶分成两类.系统发育树将16个LhTPS分为4个大分支,第Ⅰ、Ⅱ分支为倍半萜合成酶,第Ⅲ分支为倍半萜及二萜合成酶,第Ⅳ分支为倍半萜和三萜合成酶,LhTPS6、LhTPS8、LhTPS11、LhTPS16主要生成A-6 protoilludene的相似物或者衍生物,LhTPS7主要生成γ-cadinene的相似物或者衍生物;LhTPS 10主要生成δ-cadinene的类似物或者衍生物.表达分析表明,不同氮源的培养基培养条件下的表达情况整体上要优于不同碳源的培养基培养条件下的表达情况.在不同碳源及质量浓度培养基中,以10.0g·L-1山梨醇培养基为最优,在不同氮源培养基中以番茄培养基为最优.基因簇分析显示7个编码基因所在重叠群有基因簇的存在.

The first complete chloroplast genome (cpDNA) sequence of Brachypodium sylvaticum was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 136,392 bp in length, contains a large single-copy region (LSC) of 80,854 bp and a small single-copy region (SSC) of 12,765 bp, which were separated by a pair of inverted repeats (IR) regions of 21,383 bp. The genome contains 130 genes, including 84 protein-coding genes, 8 ribosomal RNA genes, and 38 transfer RNA genes. Further phylogenomic analysis showed that B. sylvaticum and B. distachyon clustered in a unique clade in Brachypodium genus.

为研究西南桦(Betula alnoides)中木质素生物合成途径的关键酶4-香豆酸:辅酶A连接酶的调控机制,本研究采用RT-PCR技术从西南桦中克隆得到一个具有完整开放阅读框的4-香豆酸:辅酶A连接酶基因(Ba4CL,NCBI登录号为MK959316),该基因全长1 629 bp,共编码542个氨基酸.西南桦Ba4CL与光皮桦(Betula luminifera,ACJ38668.1)4CL 的蛋白序列同源性为99.63％,与白桦(Betula platyphylla,AAV65114.1)4CL同源性为99.45％;Ba4CL基因拥有4CL基因家族的保守域及具有保守序列SSGTTGLPKGV和GEICIRG,Ba4CL与桦木属植物白桦和光皮桦聚在一起.Ba4CL基因在西南桦的根、小枝、树皮和叶片中均有表达,且在小枝中表达量最高,树皮次之.本研究为培育西南桦优良用材品种提供参考.

为了解高等药用真菌桑黄的萜类合成酶(TPS)基因的功能,从桑黄全基因组中分离获得TPS基因,并对其进行生物信息学分析、系统发育树构建,分析其在不同碳源和氮源培养条件下的表达情况.结果表明:在桑黄基因组中分离出9个SsTPS基因,除SsTPS2蛋白质没有特征基序外,其余SsTPS蛋白质均具有TPS的典型特征基序;二级结构以α-螺旋和无规则卷曲为主.9个SsTPS聚为2个支系,初步推测SsTPS1为倍半萜合成酶,且可以催化合成α-muurolene;SsTPS3、SsTPS4、SsTPS5、SsTPS9属于倍半萜合成酶,SsTPS3和SsTPS5合成δ-cadinene的类似物或衍生物,SsTPS4和SsTPS9分别合成β-copaene、α-muurolene的类似物或衍生物;SsTPS2为三萜合成酶.SsTPS1、SsTPS4、SsTPS6基因在所有培养基中均不表达,其余基因呈现差异化表达,SsTPS7仅在添加肌醇为碳源、大豆蛋白粉为氮源的培养基中低量表达;SsTPS2、SsTPS3、SsTPS5、SsTPS8、SsTPS9分别在添加果糖为碳源、大豆蛋白粉为氮源、牛肉浸粉为氮源、酵母粉为氮源、香蕉粉为氮源的培养基中表达量最高.基因簇分析显示,SsTPS1和SsTPS4编码基因所在contig有基因簇的存在.

膳食纤维具有多种生理活性和保健功能而被广泛的开发和利用,竹笋膳食纤维资源丰富.对国内竹笋(包括副产物笋头、笋壳等)膳食纤维提取方法、改性方法和应用现状进行综述,以期为竹笋副产物高效利用和竹笋膳食纤维工业化开发利用提供参考.

The first complete chloroplast genome (cpDNA) sequence of Beckmannia syzigachne was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 136,181 bp in length, contains a large single-copy region (LSC) of 80,345 bp and a small single-copy region (SSC) of 12,810 bp, which were separated by a pair of inverted repeats (IR) regions of 21,513 bp. The genome contains 132 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 39 transfer RNA genes. Further phylogenomic analysis showed that B. syzigachne clustered in a unique clade in the Pooideae subfamily.

为了解降香黄檀叶绿体基因组密码子使用模式,该文利用Codon W 1.4.2和在线软件CUSP对降香黄檀叶绿体基因组中的52条基因编码序列密码子进行中性绘图、ENC-plot和PR2-plot分析.结果表明:降香黄檀叶绿体基因组密码子的3个位置上GC含量依次为GC1(46.01％)>GC2(38.98％)>GC3(27.80％).有效密码子数(ENC)范围为37.66～54.43,及ENC值>45的有37个;RSCU>1的密码子有29个,其中16个以U结尾、12个以A结尾.这些说明其偏好以A和U结尾,且偏性较弱.中性绘图分析显示GC12与GC3的相关系数为0.250,相关性不显著,回归系数为0.394;ENC-plot分析显示ENC比值位于-0.05～0.05区间外的基因有38个;PR2-plot分析说明在碱基的使用频率方面,U>A、G>C,说明降香黄檀叶绿体基因组密码子偏好性主要受选择的影响;19个密码子被确定为最优密码子.该研究为降香黄檀叶绿体基因工程、遗传多样性分析等研究提供了科学参考依据.

为研究环阿屯醇合成酶（cycloartenol synthase）基因在滇牡丹生物合成中的作用机制,该文采用RTPCR技术首次从滇牡丹（Paeonia delavayi）中克隆得到一个具完整开放阅读框的环阿屯醇合成酶基因（PdCAS）,该基因全长2 274 bp,共编码757个氨基酸,PdCAS蛋白序列与桃（Prunus persica）、日本裸樱（Prunus yedoensis var. nudiflora）、葡萄（Vitis vinifera）蛋白序列相似性在86%以上。序列比对分析显示PdCAS具有氧化鲨烯环化酶超家族典型的DCTAE结构域和三萜合成酶的标志性序列DGSWYGSWGVCFTYG。滇牡丹PdCAS蛋白与蔷薇科植物苹果（Malus domestica XP 008391430.1）、白梨（Pyrus bretschneideri XP 009370034.1）、月季（Rosa chinensis XP 024193310.1）、日本裸樱（Prunus yedoensis var. nudiflora PQQ11009.1）、桃（Prunus persica XP007225240.1）的CAS蛋白聚为一类。PdCAS基因在滇牡丹各组织中均有表达,但是在花瓣中表达量较高。该研究克隆的PdCAS基因与滇牡丹甾醇类化合物的合成密切相关。

为了解蒜头果叶绿体基因组密码子的使用偏性,利用Codon W 1.4.2和CUSP软件对蒜头果叶绿体基因组中33个基因的密码子进行中性绘图,应用ENC-plot、PR2-plot绘图分析并确定了其最优密码子.结果 表明:蒜头果叶绿体基因组密码子的第3位碱基GC含量为28.43％,远低于第1位(47.74％)和第2位(41.05％),RSCU值大于1的密码子有30个,其中12个以A结尾,16个以U结尾,说明蒜头果叶绿体基因组的编码基因偏好以A和U结尾.GC12和GC3的相关系数为0.1646,相关性不显著,回归系数为0.0004;有效密码子数(ENC)范围为40.39～54.86,大于45的有25个,ENC比值主要分布在-0.05～0.05之外.蒜头果叶绿体基因组中的大部分基因分布在PR2平面图的下半部或右下半部,说明蒜头果叶绿体基因组密码子偏好性更多地受选择的影响,同时亦受其他因素的影响.蒜头果叶绿体基因组的最优密码子确定为UUU、UUA、GUA等18个.

The first complete chloroplast genome (cpDNA) sequence ofElaeocarpus braceanuswas determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 158,225 bp in length, contains a large single-copy region (LSC) of 85,731 bp and a small single-copy region (SSC) of 17,654 bp, which were separated by a pair of inverted repeats (IR) regions of 27,420 bp. The genome contains 133 genes, including 88 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Further phylogenomic analysis showed thatE. braceanusclustered in a clade in Celastrales order.

以黄花滇牡丹为试材,克隆得到2条查尔酮异构酶基因(PdCHI1和PdCHI2)的cDNA全长,以生物信息学手段预测其功能,并检测这2条基因在花不同发育时期的表达量,以期了解滇牡丹花色的形成原因.结果表明:PdCHI1基因长654 bp,编码217个氨基酸;PdCHI2基因长666 bp,编码221个氨基酸;PdCHIl与圆叶牵牛(Ipomoea purpurea, AAB86474)、脐橙(Citrussinensis,BAA36552)、大豆(Glycine max, AAT94360)和百脉根(Lotusjaponicus,BAC53984)等高等植物的Ⅰ型CHI蛋白聚为一支;PdCHI2与玉米(Zea mays, NP_001151452)、大豆(Glycine max AAT94362)和葡萄(Vitisvinifera ,XP_002280158)的I型CHI蛋白聚为一支.PdCHI1基因的表达量花蕾期最高,初花期和盛花期急剧降低,末花期的表达微量提升;而PdCHI2基因的表达量随着花的不断发育呈现逐渐降低的趋势.

法尼基焦磷酸合酶(famesyl pyrophosphate synthase,FPS)是萜类化合物生物合成过程中的关键酶和限速酶,影响后续支路产物的代谢.为探究牛樟芝中Ac FPS基因与萜类化合物生物合成间的关系,本研究从牛樟芝基因组中分离并克隆得到AcFPS基因,并对其蛋白进行生物信息学分析,比较AcFPS基因在含不同碳、氮源添加物培养基上的表达量.结果 表明,AcFPS基因含5个外显子、4个内含子,其外显子拼接总长1 095 bp,编码364个氨基酸;AcFPS是一种位于细胞质中无信号肽和跨膜结构的蛋白,该蛋白含有4个保守序列,分别为DomainⅠ(GGKLNRG LSVVD)、DomainⅡ(DDMMD)、DomainⅢ(KFSLQKHXLIVIXKT)、DomainⅣ(DDFLD);牛樟芝AcFPS与污叉丝孔菌(XP_007371273)、白腐菌(XP_008044628)、绣球菌(XP_027616692)、根纤维孔菌(XP_012183648)和绵腐卧孔菌(XP_024343411)等多孔菌目真菌的FPS蛋白聚为一支;以果糖为碳源、以番茄浸粉为氮源能有效诱导AcFPS基因的表达.本研究为深入解析牛樟芝萜类化合物合成分子机制及其异源表达提供了依据.

为研究3-羟基-3-甲基戊二酰辅酶A合酶基因(HMGS)在思茅松二萜类生物合成中的作用机制,采用RT-PCR技术从思茅松中获得3-羟基-3-甲基戊二酰辅酶A合酶基因的cDNA序列.序列分析显示,该基因全长1425 bp,编码474个氨基酸,属于HMGS基因家族.序列比对分析显示PkHMGS基因所编码的氨基酸序列拥有HMGS家族蛋白特有的保守序列GNTEIEGVDSTNACYGGTA,与樟子松HMGS的蛋白序列同源性为99.79％.系统进化分析显示,思茅松与裸子植物的HMGS聚为1支,与樟子松的亲缘关系最近.荧光定量PCR分析表明,在思茅松的树皮中HMGS基因的表达明显受到割脂物理伤害的诱导,在高产脂思茅松松针表达量最高.结果 为揭示思茅松高产脂的分子机理提供理论依据.

为了探讨印度紫檀(Pterocarpusindicus)萜类化合物的生物合成,本研究通过对合成萜类物质的MEP途径的第一个限速酶(1-脱氧-D-木酮糖-5-磷酸合酶,DXS)基因进行克隆,获得了印度紫檀DXS的全长cDNA PiDXS基因(NCBI登录号:MK959226),并对其进行生物信息学和组织表达特异性分析.结果显示:PiDXS基因cDNA开放阅读框长2 025 bp,编码674个氨基酸,Blast比对发现,PiDXS具有一个二磷酸硫胺结合位点和一个转酮醇酶结构域;系统进化分析显示,PiDXS基因与大豆DXS和狭叶羽扇豆DXS聚为一类;组织表达特异分析结果显示PiDXS在茎、叶、树皮和根中均能表达,主要在幼嫩的组织中表达.研究结果为确定印度紫檀中DXS的基因功能以及揭示印度紫檀萜类化合物的生物合成提供了基础.

为研究肉桂酰辅酶A还原酶基因(CCR)在西南桦木质素合成中的作用机制,采用RT-PCR技术从西南桦中克隆得到1个具完整开放阅读框的肉桂酰CoA还原酶基因(BaCCR),该基因全长975 bp,编码324个氨基酸.序列比对分析显示西南桦CCR蛋白序列与胡桃、欧洲栓皮栎、梅、甜樱桃的蛋白序列相似性均在80％以上.BaCCR拥有CCR蛋白的NADP结合域和底物结合域KNWYCYGK.进化分析表明,BaCCR与梅、甜樱桃、亚洲棉、葡萄聚为一个枝系.转录模式分析表明,BaCCR基因在根和小枝中高量表达.

The first complete chloroplast genome (cpDNA) sequence of Fosbergia shweliensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 154,717 bp in length, contains a large single-copy region (LSC) of 84,747 bp and a small single-copy region (SSC) of 18,230 bp, which were separated by a pair of inverted repeats (IR) regions of 25,870 bp. The genome contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 36 transfer RNA genes. Further phylogenomic analysis showed that F. shweliensis was close to Coffea genus in the family Rubiaceae.

The first complete chloroplast genome (cpDNA) sequence of Litsea cubeba was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 152,725 bp in length, contains a large single-copy region (LSC) of 93,673 bp, and a small single-copy region (SSC) of 18,924 bp, which were separated by a pair of inverted repeats (IR) regions of 20,064 bp, each. The genome contains 126 genes, including 82 protein-coding genes, 8 ribosomal RNA genes, and 36 transfer RNA genes. The further phylogenomic analysis showed that L. cubeba and Litsea garrettii clustered in a clade in Lauraceae family.