Direct organogenesis and plantlet regeneration from mature zygotic embryos of masson pine (Pinus massoniana L.)

Mature zygotic embryos of masson pine were cultured as initial explants to investigate the process of direct organogenesis. Adventitious buds were initiated on DCR medium (Douglas-fir cotyledon revised medium) supplemented with 0.5 mg l⁻¹ N⁶-benzyladenine (BA) and 0.05 mg l⁻¹ indolebutyric acid (IBA) or α-naphthaleneacetic acid (NAA). The highest induction frequency of adventitious buds was 99.3%. Subsequent transfer of buds to medium with lower concentrations of plant growth regulators in time was necessary for differentation of high quality adventitious buds. After culturing on elongating medium, in which the proportion of cytokinins to auxins was reduced, shoots higher than 2 cm were transferred for root induction to GD medium with half of the concentration of macro-salts (½ GD) and with 2 mg l⁻¹ IBA and 0.05 mg l⁻¹ BA. The average root frequency was over 70%. After adventitious roots had appeared, the shoots were transferred to ½ GD medium with a lower concentration of IBA (0.2 mg l⁻¹) for further root development.     

投加石灰石和菱镁矿对酸化土壤上马尾松(Pinus massoniana)林的影响

为了确定酸化森林生态系统的修复效果,在重庆铁山坪的马尾松林内设立了6个10m×10m的样地,其中2个作为对照样地,另外4个分别在土壤表面施撒石灰石和菱镁矿粉末,各有2个重复。在处理前和处理1a后的生长季末各进行了一次植被观测,协方差分析和多重比较的结果显示投加修复剂对马尾松生长的影响已经初步显现,马尾松的胸径增量和针叶平均长度都有显著的增加,而针叶中Ca、Mg元素含量也表现出显著的差别。另外,立木更新的变化、细根生物量的增加和物种多度的变化也较明显,总体来说生态系统有恢复的趋势。土壤上层细根的增加较快,这与在土壤表面施撒修复剂,上层土壤的化学变化较显著是一致的。而两种修复剂对生态系统的影响也表现出明显的差异,相对而言,施撒菱镁矿的效果可能会更好。由于土壤修复的效果是长期的,其影响观测还将继续下去。     

Characterization of masson pine (Pinus massoniana Lamb.) microsatellite DNA by 454 genome shotgun sequencing

Microsatellites (simple sequence repeats, SSRs) are important genetic markers in tree breeding and conservation. Here we utilized high-throughput 454 sequencing technology to mine microsatellites from masson pine (MP) genomic DNA. First, we analyzed the characteristics of SSRs in all nonredundant MP reads (genome survey sequences, GSSs) and compared them with loblolly pine (LP) GSSs and BACs (bacterial artificial chromosome clone sequences), and three other nonconiferous species GSSs. Second, a set of MP GSS–SSR primer pairs were designed. There were extremely low overall GSS–SSR densities (28 SSR/Mb) in MP when compared with LP (48 SSR/Mb) and the other species. AT, AAT, AAAT, and AAAAAT were the richest motifs in di-, tri-, tetra-, and hexanucleotides, respectively. Two hundred forty GSS–SSR primer pairs were designed in total, and 20 novel polymorphic markers were identified using three populations (two natural and one clonal seed orchard) as evaluating samples. These markers should be useful for future MP population genetics studies.     

植物LTR类反转录转座子序列分析识别方法

LTR类反转录转座子(Long terminal repeat retrotransponson)是真核生物中的一类重要转座元件,具有分布广泛、异质性高等特点,在真核生物基因组进化中起着重要作用,现广泛应用于植物的基因功能分析和遗传多样性研究等方面。LTR类反转录转座子的序列识别是其应用的前提条件,因此对LTR类反转录转座子的序列鉴定和分析方法的研究具有重要的理论意义和实际应用价值。LTR类反转录转座子序列的生物信息学分析软件按原理可大致分为序列比对分析和相关序列保守区域识别鉴定两类。比对软件如BLAST、DNAstar等,是一种序列相似性搜索程序,通过与已知的反转录转座子序列比对后的序列相似性来判断未知序列是否是反转录转座子序列,但这类软件不能直接获得具体的LTR等特征序列的相关信息,不能对反转录转座子序列的全长进行识别。识别鉴定软件按原理可分为从头算起法、比较基因组法、同源搜索法和结构基础法4种,如LTR-Finder等基于从头算起法的识别鉴定软件,可对LTR类反转录转座子全序列进行较准确地预测和注释,RepeatMasker等基于同源搜索法的软件,通过与数据库中的序列的相似性比对后发现可能存在的LTR类反转录转座子。文章对不同的LTR类反转录转座子预测方法进行了比较和分析,在此基础上归纳总结出一套分析LTR类反转录转座子序列的操作流程,旨在为LTR类反转录转座子序列的分析提供参考。     

Isolation and cell regeneration of protoplasts from sugar pine (Pinus lambertiana)

Protoplasts were isolated at high yields from actively growing callus and cell suspensions of cotyledons and needles of mature trees. The best protoplast growth response was obtained from cell suspensions of cotyledon and needle callus. Lower protoplast yields were obtained directly from young needles of flushing buds on explants from mature shoots (30-year-old trees) growing in vitro. In all cases, the first divisions, promoted by dimethyl sulfoxide, were observed in 10–45% of the protoplasts by 7–10 days. After 25–30 days, colonies of 8–10 cells were established. Browning of protoplast-derived cell cultures was observed within 40–45 days (cotyledons) and 20–25 days (mature tree sources).Abbreviations BA N⁶-Benzyladenine - DCR Douglas-fir cotyledon revised medium - 2,4-D 2,4-dichlorophenoxyacetic acid - DMSO dimethyl sulfoxide - FDA Fluorescein diacetate - Mes 2-(N-morpholino) ethanesulfonic acid - NAA -naphthaleneacetic acid     

马尾松中的抗氧化成分

从马尾松(Pinus massoniana)枝条中分离得到21个已知化合物,经波谱学方法将其结构鉴定为7,13,15-abietatrien-18-oic acid (1),12-methoxy-7,13-abietadien-18-oic acid (2),15-methoxy-7,13-abietadien-18-oic acid methyl ester(3),12-hydroxydehydroabietic acid(4),dehydroabietic acid(5),15-hydroxydehydroabietic acid methyl ester (6),3β-methoxyserrat-14-en-21-one (7),3β-methoxy-30-hydroxyserrat-14-en-21-one(8),β-sitosterol (9),(±)-pinoresinol(10),(±)-matairesinol(11),(-)-nortrachelogenin(12),balanophonin (13),cedrusin (14),pinocembin (15),5-methoxypinosylvin (16),pinosylvin (17),1,2-bis-(4-hydroxy-3-methoxyphenyl)-propane-l,3-diol(18),cleistophostaudin(19),lignoceryl ferulate(20)和coniferaldehyde (21).其中化合物12,14,18和21在DPPH抗氧化模型上显示一定的抗氧化活性,其EC50值分别为11.36,6.76,14.07和13.33 μg· mL-1.化合物2～4,6～8,10,11,13,15～21均是从该植物中首次分离得到.     

Isolation of 4-coumarate Co-A ligase gene promoter from loblolly pine (Pinus taeda) and characterization of tissue-specific activity in transgenic tobacco

We characterized promoter activity of a phenylpropanoid biosynthetic gene encoding 4-coumarate Co-A ligase (4CL), Pta4Clα, from Pinus taeda. Histochemical- and quantitative assays of GUS expression in the vascular tissue were performed using transgenic tobacco plants expressing promoter-GUS reporters. Deletion analysis of the Pta4Clα promoter showed that the region ?524 to ?252, which has two AC elements, controls the high expression levels in ray-parenchyma cells of older tobacco stems. High activity level of the promoter domain of Pta4CLα was also detected in the xylem cells under bending stress. DNA-protein complexes were detected in the reactions of the Pta4CLα promoter fragments with the nuclear proteins of xylem of P. taeda. The AC elements in the Pta4CLα promoter appeared to have individual roles during xylem development that are activated in a coordinated manner in response to stress in transgenic tobacco.     

Cloning, sequencing, and characterization of genomic subtracted sequences from Listeria monocytogenes

Individual sequences of a genomic subtracted, PCR-amplified, mixed-sequence probe (GS probe) were cloned and sequenced. The GS probe differentiated restriction fragment length polymorphism patterns for Listeria monocytogenes but did not hybridize with members of other bacterial genera. Sequence analysis identified several L. monocytogenes sequences already present in the GenBank database; the putative identities of other sequences were inferred from homology data, and still other sequences did not exhibit significant levels of homology with any GenBank sequences.     

Phylogeography of the Korean pine (Pinus koraiensis) in northeast Asia: inferences from organelle gene sequences

Range-wide genetic variation of Korean pine (Pinus koraiensis) was assessed using maternally inherited mtDNA and paternally inherited cpDNA for 16 natural populations throughout northeast Asia in order to study its phylogeographical history during the Quaternary. The cpDNA variation indicated that there was no difference between populations on the Asian continent and those in the Japanese archipelago. In contrast, the mtDNA variation indicated that there was significant difference between the populations from the two regions, with each region having a different lineage. The continental populations exhibited no diversity in the mtDNA examined despite the species’ current extensive range and large populations. Conversely, while the Korean pine is rare in Japan, the Japanese populations exhibited greater levels of mtDNA diversity (H _T?=?0.502). The higher mtDNA diversity and evidence from numerous Korean pine macrofossil remains dated to the Pleistocene and recovered various sites in Japan suggest that the Japanese archipelago once served as a refugium to a much larger Korean pine population with a more extensive range than is the case today. The presence of the single mtDNA haplotype across the Asian continent suggests that the present widespread populations could have expanded from a single refugium population after the last glacial periods.     

Isolation,identification and genomic characterization of the Asian lineage Zika virus imported to China

正Dear Editor,Zika virus(ZIKV)used to be an unknown mosquito-borne flavivirus,and maintained its limited sylvatic circulation in a few African and Asian countries(Enfissi et al.,2016).Based on available clinical data,the symptoms in human infections with ZIKV are supposed to be similar to other arbovirus infections such as dengue,and characterized by fever,skin rashes,conjunctivitis,muscle and joint pain,malaise,and headache(Duffy et al.,2009).However,its     

LTR retrotransposon dynamics in the evolution of the olive (Olea europaea) genome

Improved knowledge of genome composition, especially of its repetitive component, generates important information for both theoretical and applied research. The olive repetitive component is made up of two main classes of sequences: tandem repeats and retrotransposons (REs). In this study, we provide characterization of a sample of 254 unique full-length long terminal repeat (LTR) REs. In the sample, Ty1-Copia elements were more numerous than Ty3-Gypsy elements. Mapping a large set of Illumina whole-genome shotgun reads onto the identified retroelement set revealed that Gypsy elements are more redundant than Copia elements. The insertion time of intact retroelements was estimated based on sister LTR’s divergence. Although some elements inserted relatively recently, the mean insertion age of the isolated retroelements is around 18 million yrs. Gypsy and Copia retroelements showed different waves of transposition, with Gypsy elements especially active between 10 and 25 million yrs ago and nearly inactive in the last 7 million yrs. The occurrence of numerous solo-LTRs related to isolated full-length retroelements was ascertained for two Gypsy elements and one Copia element. Overall, the results reported in this study show that RE activity (both retrotransposition and DNA loss) has impacted the olive genome structure in more ancient times than in other angiosperms.     

Isolation, characterization and cross-species testing of microsatellites obtained from a sand smelt (Atherina boyeri) genomic library

This study reports the isolation and characterization of 11 polymorphic microsatellites from a sand smelt (Atherina boyeri) genomic library. Enrichment was performed with di-, tri- and tetranucleotide motifs following the FIASCO procedure (fast isolation by AFLP of sequences containing repeats). All loci were found to be in linkage and in Hardy-Weinberg equilibrium. This represents the first microsatellite isolation for the family Atherinidae and the isolated loci were accordingly tested on four additional species of the family: two recognized (A. presbyter and A. hepsetus) and two proposed ('punctata' and 'non-punctata' forms). Moreover their cross-species suitability on Menidia menidia, belonging to the same order but to the family Atherinopsidae, was also tested.