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Abstract
Liverwort Pellia borealis is an allopolyploid species that originated after the hybridization and chromosome doubling of two cryptic species; Pellia epiphylla species N and Pellia epiphylla species S. A sequence comparison of chloroplast tRNAUCCGly, tRNAUUULys gene introns, the mitochondrial tRNAGCUSer gene intron,
and the first intron of the coxIII gene in the case of three liverwort species studied revealed that the chloroplast and mitochondrial
sequences are identical in P. borealis and P. epiphylla species N but different from homologous P. epiphylla species S sequences. Both mitochondria and chloroplasts of P. borealis were thus inherited from one parent—P. epiphylla species N. Studies on 14 different populations of P. borealis gave the same result. These are the first data on organellar transmission in liverworts, the earliest land plants. Moreover,
we show that the intron sequences of some organellar genes, until now not used in any systematic studies, could be very good
markers in studying taxonomic relationships in closely related species and reconstructing historical events. 相似文献
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叶绿体遗传转人是近几年发展起来的新领域。本文主要介绍了叶绿体遗传转化的特点、基本原理和衣藻叶绿体遗传转化的方法与技术; 相似文献
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To investigate seasonal changes in the taxon richness and abundance of mobile invertebrates inhabiting holdfasts of the warm temperate annual kelp Ecklonia radicosa, five holdfasts were collected monthly at the central Pacific coast of Japan from April to November 2014. During the study period, there was little variation in holdfast height and diameter, which ranged from 5.9 to 8.5 cm and from 7.1 to 10.8 cm, respectively. In total 7087 animals were collected from 40 holdfasts (177.2 individuals inds./holdfast, on average). The number of mobile invertebrates gradually increased from May (15 ± 9.9 inds./holdfast) to August (346 ± 152.5 inds./holdfast), with over 300 inds./holdfast until October before rapidly decreasing in November (110 ± 85.6 inds./holdfast). Similarly, taxon richness increased gradually from April (4.3 ± 1.0 taxa/holdfast) to August (11.0 ± 3.7 taxa/holdfast), and decreased in November (8.6 ± 2.3 taxa/holdfast). Interestingly, hundreds of mobile invertebrates inhabited holdfasts of kelp plants that had shed their blade in October and November. Taxon composition from August to October and the number of invertebrates from July to November were comparable to data previously reported for perennial kelps. In this study, the importance of annual Ecklonian species as biogenic habitats was demonstrated for the first time. 相似文献
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《生物技术通报》2025,41(3)
目的 探究玄参科(Scrophulariaceae)叶绿体基因组(chloroplast DNA, cpDNA)的特征及其系统发育关系。 方法 对湖北玄参进行DNA测序;通过组装与注释获得了其叶绿体基因组序列;并从GenBank下载46条玄参科植物叶绿体基因组序列进行比较分析。 结果 玄参科叶绿体基因组长度在142 336-154 710 bp;GC含量为37.7%-38.1%;展现出典型的四分体结构;其中大单拷贝区长度为83 531-97 103 bp;小单拷贝区为17 375-18 600 bp;反向重复区为13 497-25 695 bp。通过对玄参科叶绿体基因组成的比较;揭示了在进化过程中获得与丢失的模式。此外;共线性分析发现;玄参科叶绿体基因组排列较为保守;但也存在基因组重排事件。长重复序列分析结果显示;玄参科叶绿体基因组大多数是正向重复和回文重复;而简单重复序列分析则鉴定了117-156个SSR位点;其中以A/T组成的单核苷酸重复次数最多;占比高达85.50%-91.50%。通过相对同义密码子使用度(RSCU)分析;筛选出25个最优密码子;绝大部分以A/U结尾。分化时间分析表明;玄参科的共同祖先与近缘物种大约在70.5百万年前(MYA)分开;并在约52.4 MYA形成了一个单系分支;绝大多数玄参科物种出现在近50 MYA。 结论 玄参科叶绿体基因组虽具有相似的结构特征;但在其进化历程中;基因的获得与丢失以及基因组的重排现象亦有所发生。基于叶绿体基因组;构建了更为精细的玄参科系统发育树。此外;分化时间的研究表明;玄参科物种的快速分化主要发生在大约50百万年前。 相似文献
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X. Xie Y. Yang Q. Ren X. Ding P. Bao B. Yan X. Yan J. Han P. Yan Q. Qiu 《Animal genetics》2018,49(5):384-392
Deleterious mutations play an important functional role, affecting trait phenotypes in ways that decrease the fitness of organisms. Estimating the frequency of occurrence and abundance has been a topic of much interest, especially in crops and livestock. The processes of domestication and breeding allow deleterious mutations to persist at high frequency, and identifying such deleterious mutations is particularly important for breed improvement. Here, we assessed genome‐wide patterns of deleterious variation in 59 domestic and 13 wild yaks using genome resequencing data. Based on the intersection of results given by three methods (provean , polyphen 2 and sift 4g ), we identified 3187 putative deleterious mutation sites affecting 2586 genes in domestic yaks and 2067 affecting 1701 genes in wild yaks. Multiple lines of evidence indicate a significant increase in the load of deleterious mutations in domesticated yaks compared to wild yaks. Private deleterious genes were found to be associated with the perception of smell and detection of chemical stimulus. We also identified 36 genes related to Mendelian genetic diseases involved in sensory perception, skeletal development and the nervous and immune systems. This study not only adds to the understanding of the genetic basis of yak domestication but also provides a rich catalog of variants that will facilitate future breeding‐related research on the yak genome and on other bovid species. 相似文献
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大粒香作为贵州重要的优质稻资源,推广种植面积大,并且在乡村振兴过程中为社会带来了较高的经济效益。然而,目前对大粒香基因组学的理论研究报道较少。为揭示大粒香水稻叶绿体基因组(cpDNA)特征及系统发育关系,该研究对大粒香叶绿体进行测序,并分析其基因组特征。结果表明:(1)大粒香水稻cpDNA全长134 563 bp,包括1个大单拷贝区(LSC,80 864 bp)、1个小单拷贝区(SSC,12 347 bp)和2个反向重复序列区(IRs,20 676 bp)。(2)注释到129个基因,可分为蛋白编码、tRNA和rRNA三类基因,数量分别为85个、36个和8个。(3)密码子偏好分析显示,大粒香cpDNA密码子偏好A碱基或U(T)碱基,亮氨酸密码子使用了1 944次,使用次数最多; 半胱氨酸的密码子仅使用198次,使用次数最少。(4)检测到129个SSR,其中有95个单核苷酸重复且大部分SSR序列由A/T碱基组成。(5)系统发育分析结果显示,大粒香与热带粳稻亲缘关系最近,聚为一类。该研究结果揭示了大粒香叶绿体基因组信息,并确定了大粒香系统发育所属分支。 相似文献
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【目的】为明确鲜黄小檗叶绿体基因组结构特征及其与同属类群的系统发育关系,对鲜黄小檗叶绿体基因组的结构特征进行解析和系统发育分析。【方法】用Illumina Hiseq X Ten技术测序,用CPGview、CodonW、MISA、Reputer、IRscope、mVISTA软件对鲜黄小檗叶绿体基因组特征进行分析,MEGA7软件中的ML法构建系统发育树。【结果】鲜黄小檗叶绿体基因组全长166 225 bp,呈典型的四分体结构,全基因组GC含量为38.07%;共注释得到144个基因,包括99个蛋白质编码基因、37个tRNA基因和8个rRNA基因,其中23个基因含有内含子,32个基因为双拷贝基因;偏好使用A/U结尾的密码子;共检测到98个SSR位点和150个散在重复序列,大部分SSR位点由A和T碱基组成;SSC和IR区的变异程度高于LSC区;系统发育分析发现鲜黄小檗与威宁小檗亲缘关系最近。【结论】鲜黄小檗叶绿体基因组特征与小檗属其他物种类似,为该属物种的分子鉴定、进化关系等提供了理论基础。 相似文献
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Brügger K Chen L Stark M Zibat A Redder P Ruepp A Awayez M She Q Garrett RA Klenk HP 《Archaea (Vancouver, B.C.)》2007,2(2):127-135
Hyperthermus butylicus, a hyperthermophilic neutrophile and anaerobe, is a member of the archaeal kingdom Crenarchaeota. Its genome consists of a single circular chromosome of 1,667,163 bp with a 53.7% G+C content. A total of 1672 genes were annotated, of which 1602 are protein-coding, and up to a third are specific to H. butylicus. In contrast to some other crenarchaeal genomes, a high level of GUG and UUG start codons are predicted. Two cdc6 genes are present, but neither could be linked unambiguously to an origin of replication. Many of the predicted metabolic gene products are associated with the fermentation of peptide mixtures including several peptidases with diverse specificities, and there are many encoded transporters. Most of the sulfur-reducing enzymes, hydrogenases and electron-transfer proteins were identified which are associated with energy production by reducing sulfur to H(2)S. Two large clusters of regularly interspaced repeats (CRISPRs) are present, one of which is associated with a crenarchaeal-type cas gene superoperon; none of the spacer sequences yielded good sequence matches with known archaeal chromosomal elements. The genome carries no detectable transposable or integrated elements, no inteins, and introns are exclusive to tRNA genes. This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment. 相似文献
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叶绿体基因组在系统发育学及基因工程领域的应用 总被引:6,自引:0,他引:6
介绍了叶绿体基因组在系统发育学和基因工程这两个领域的应用研究进展:1)叶绿体基因组的DNA序列比较为植物系统发育学研究提供了可靠数据基础;2)叶绿体基因工程是高水平表达外源基因的重要途径之一,在生产医用蛋白、改良作物农艺性状和环境保护等方面有着广阔的应用前景。 相似文献
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Robbens S Derelle E Ferraz C Wuyts J Moreau H Van de Peer Y 《Molecular biology and evolution》2007,24(4):956-968
The complete nucleotide sequence of the mt (mitochondrial) and cp (chloroplast) genomes of the unicellular green alga Ostreococcus tauri has been determined. The mt genome assembles as a circle of 44,237 bp and contains 65 genes. With an overall average length of only 42 bp for the intergenic regions, this is the most gene-dense mt genome of all Chlorophyta. Furthermore, it is characterized by a unique segmental duplication, encompassing 22 genes and covering 44% of the genome. Such a duplication has not been observed before in green algae, although it is also present in the mt genomes of higher plants. The quadripartite cp genome forms a circle of 71,666 bp, containing 86 genes divided over a larger and a smaller single-copy region, separated by 2 inverted repeat sequences. Based on genome size and number of genes, the Ostreococcus cp genome is the smallest known among the green algae. Phylogenetic analyses based on a concatenated alignment of cp, mt, and nuclear genes confirm the position of O. tauri within the Prasinophyceae, an early branch of the Chlorophyta. 相似文献
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叶绿体是植物细胞中一种特殊的细胞器。自1988年开始,人们认识到叶绿体在植物基因工程中的特殊地位。叶绿体基因工程的特点,特别是其高效表达和安全性,使其受到越来越多的重视,本文对叶绿体转化作了较为全面的介绍,包括其优势、方法、用途及不足等内容。Abstract:Chloroplast is a kind of special cell organin plant cells.Since 1988,Scientists have realized its advantages in plant gene enginearing.It′s high efficient expression and safety made it been attached more and more importance to.This paper introduces the chloroplast transfer mation,including its advantages,methods,uses and defects. 相似文献
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Microprojectile bombardment is a powerful method for the transformation of various organisms and tissues. For plants, the
biolistic approach is primarily used for transformation of cereals and other monocotyledons, as well as for dicotyledonous
plants shown to be recalcitrant to Agrobacterium-based transformation of organellar genomes, and transformation of plant and algal chloroplasts has recently been reported.
In this protocol paper we provide methods for nuclear and plastomic transformation of plants using the biolistic technique. 相似文献
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Previous studies have shown that Gnetales exhibit an increase in the rates of substitution in plastid genes. However, the relative roles of selection and drift in driving the observed increase in substitution rate remain unclear. Here we estimated the nonsynonymous (dN) and synonymous (dS) substitution rates and the dN/dS ratios for 59 plastid protein-coding genes conserved across Gnetales and other gymnosperms with maximum likelihood methods. Our results show that: (1) values of dN and dS for 48 and 50 genes, respectively, are significantly higher in Gnetales relative to the other sampled gymnosperms; (2) the acceleration of dN is of lower magnitude than that of dS; (3) dN/dS is significantly reduced for 22 of the 59 plastid genes in Gnetales; and (4) dN/dS is extremely heterogeneous among the Gnetalean genes, varying by up to a factor of 40. We propose that while biological characteristics such as generation time and plant height may contribute to the rate increase in Gnetales, the special habitats that they occupy are linked to the gene-specific reduction of dN/dS. 相似文献
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Sorbus setschwanensis Koehne is a pinnate-leaved Sorbus s.str. species endemic to China with narrow distribution and intriguing phylogeny that needs wider attention. In this paper, the complete chloroplast (cp) genome of S. setschwanensis is reported, and its phylogenetic position is analyzed. The complete cp genome of S. setschwanensis is 160 064 bp in size with 36.50% GC content. It has a typical quadripartite structure including a pair of inverted repeat regions (IRs) of 26 378 bp that separates a large single copy (LSC) region of 86 013 bp and a small single copy (SSC) region of 19 295 bp. The cp genome encodes 108 genes, comprising 76 protein-coding genes, 28 tRNA genes and 4 rRNA genes. Additionally, 52 simple sequence repeats (SSRs) and 43 dispersed repeats were identified. Comparison of the whole cp genome with those of other Sorbus species showed an overall high degree of sequence similarity, but there are six highly variable regions (trnR-atpA, petN-psbM, ndhC-trnV, trnE-trnT, trnT-trnL and rpl32-trnL) located in intergenic spacers that may be useful as molecular markers in future population genetic and phylogenetic studies in the genus. Phylogenetic analyses based on 108 coding genes from 25 species in Rosaceae revealed that S. setschwanensis is nested within Sorbus sect. Sorbus together with other pinnately leaved species, but does not form a sister lineage to S. rufopilosa belonging to the same series Multijugae. Thus, the systematic position of S. setschwanensis and relationships with other species in the genus needs to be further studied. 相似文献
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Chen Yang;Xue-Ying Yao;Zhi-Xiang Chen;Stephen R. Downie;Qi-Zhi Wang; 《Nordic Journal of Botany》2022,2022(8):e03549
Sanicula (Apiaceae subfam. Saniculoideae) is a taxonomically difficult genus of medicinal value. Its distribution center is in China, where there are 18 species (11 of which are endemic). To provide plastid genome resources, whole chloroplast genomes of five Sanicula species (S. flavovirens, S. giraldii, S. lamelligera, S. odorata and S. rubriflora) were sequenced and compared to the previously published S. orthacantha plastome. These genomes exhibit a typical quadripartite structure. All contain 129 different genes, including 84 protein-coding, 37 tRNA and 8 rRNA genes. The loci rpl2, matK, psbA and ycf1 are the most variable. Results of maximum likelihood analysis of 90 whole plastome sequences from Apioideae and Saniculoideae and the outgroup Hydrocotyle (Araliaceae) suggest sectional relationships in Sanicula different from the traditional classification system, but support the monophyly of Apioideae and its sister group relationship to Saniculoideae and show concordant topologies to nrDNA ITS and other plastome-based phylogenies. Sanicula orthacantha and S. chinensis form a sister group to S. lamelligera and S. odorata, consecutively. These four species comprise a sister group to the clade of S. rubriflora and S. flavovirens, with this entire group sister to S. giraldii. The plastid genome resources provided herein will be important for future systematic, evolutionary, phylogenomic and population-level studies of Sanicula. 相似文献
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Traditional sources of taxonomic characters in the large and taxonomically complex subfamily Apioideae (Apiaceae) have been confounding and no classification system of the subfamily has been widely accepted. A restriction site analysis of the chloroplast genome from 78 representatives of Apioideae and related groups provided a data matrix of 990 variable characters (750 of which were potentially parsimony-informative). A comparison of these data to that of three recent DNA sequencing studies of Apioideae (based on ITS, rpoCl intron, and matK sequences) shows that the restriction site analysis provides 2.6–3.6 times more variable characters for a comparable group of taxa. Moreover, levels of divergence appear to be well suited to studies at the subfamilial and tribal levels of Apiaceae. Cladistic and phenetic analyses of the restriction site data yielded trees that are visually congruent to those derived from the other recent molecular studies. On the basis of these comparisons, six lineages and one paraphyletic grade are provisionally recognized as informal groups. These groups can serve as the starting point for future, more intensive studies of the subfamily. 相似文献
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以茜草科(Rubiaceae)植物茜草(Rubia cordifolia L.)为研究对象,采用Illumination高通量测序技术对其叶绿体全基因组进行测序,并运用MAGA11等生信学工具进行全基因组解析及系统发育分析。结果表明,(1)茜草叶绿体基因组呈典型的四分环状结构,总GC含量37.2%,长153 959 bp,其中包含大单拷贝(LSC)区83 844 bp、小单拷贝(SSC)区17 083 bp和2个反向重复(IR)区26 516 bp;共注释得到124个基因,包括79个蛋白质编码基因、37个tRNA和8个rRNA。(2)序列共鉴定到169个SSR位点,以A、T组成为主,包括129个单核苷酸、18个双核苷酸、11个三核苷酸、9个四核苷酸和2个五核苷酸,六核苷酸SSR未检测到;边界分析显示,茜草叶绿体基因组LSC区差异性最大,变异程度最高,而IRa区则差异性最小,最为保守。(3)最大似然法(ML)构建系统发育树显示,样品茜草与同属植物Rubia horrida以100%支持率聚为一类,茜草亚科、仙丹花亚科与金鸡纳亚科聚为姐妹类群,证明茜草科植物在进化过程中保守发育。 相似文献