共查询到20条相似文献,搜索用时 15 毫秒
1.
Gao M Li G McCombie WR Quiros CF 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,111(5):949-955
We compared the sequence of a 96.7 Kb-long BAC clone (B19N3) from Brassica oleracea (broccoli) with its corresponding regions in Arabidopsis
thaliana. B19N3 contains eight genes and 15 transposable elements (TEs). The first two genes in this clone, Bo1 and Bo2, have its
corresponding region at the end of chromosome V of Arabidopsis (24 Mb). The third gene, Bo3, corresponds to an ortholog at
the opposite end (2.6 Mb) of the same chromosome. The other five genes, Bo4 to Bo8 also have a corresponding region on the
same chromosome but at 7.7 Mb . These five genes are colinear with those found in the corresponding region of Arabidopsis,
which contains, however, 15 genes. Therefore, a cluster of 10 genes is missing in B. oleracea clone (B19N3). All five genes in common have the same order and orientation in the genomes of both species. Their 36 exons
constituting the eight homologous genes have high conservation in size and sequence identity in both species. Among these,
there is a major gene involved in aliphatic glucosinolate biosynthesis, BoGSL-ELONG (Bo4). Similar to A. thaliana, this gene, has a tandem duplicate, Bo5. A contig for this region was constructed by primer walking and BAC-end-sequencing,
revealing general gene colinearity between both species. During the 20 million years separating A. thaliana from B. oleracea from a common ancestor both genomes have diverged by chromosomal rearrangements and differential TE activity. These events,
in addition to changes in chromosome number are responsible for the evolution of the genomes of both species. In spite of
these changes, both species conserve general colinearity for their corresponding genes. 相似文献
2.
Zheng Liu Joe Hammerlindl Wilf Keller Peter B. E. McVetty Fouad Daayf Carlos F. Quiros Genyi Li 《Molecular breeding : new strategies in plant improvement》2011,27(4):467-478
Methylthioalkylmalate (MAM) synthases and their associated genes that have been extensively investigated in Arabidopsis control the side-chain elongation of methionine during the synthesis of aliphatic glucosinolates. A Brassica homolog of the Arabidopsis
MAM genes was used in this study to analyze the role of MAM genes in B. napus through RNA interference (RNAi). The silencing of the MAM gene family in B. napus canola and B. napus rapeseed resulted in the reduction of aliphatic glucosinolates and total glucosinolate content. The results indicated that
RNAi has potential for reducing glucosinolate content and improving meal quality in B. napus canola and rapeseed cultivars. Interestingly, MAM gene silencing in B. napus significantly induced the production of 2-propenyl glucosinolate, a 3-carbon side-chain glucosinolate commonly found in B. juncea mustard. Most transgenic plants displayed induction of 2-propenyl glucosinolate; however, the absolute content of this glucosinolate
in transgenic B. napus canola was relatively low (less than 1.00 μmol g−1 seed). In the high glucosinolate content progenies derived from the crosses of B. napus rapeseed and transgenic B. napus canola, MAM gene silencing strongly induced the production of 2-propenyl glucosinolate to high levels (up to 4.45 μmol g−1 seed). 相似文献
3.
The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana 总被引:1,自引:0,他引:1
The goal of this study was to assess the extent to which transposable elements (TEs) have contributed to protein-coding regions
in Arabidopsis thaliana. To do this, we first characterized the extent of chimeric TE-gene constructs. We compared a genome-wide TE database to genomic
sequences, annotated coding regions, and EST data. The comparison revealed that 7.8% of expressed genes contained a region
with close similarity to a known TE sequence. Some groups of TEs, such as helitrons, were underrepresented in exons relative to their genome-wide distribution; in contrast, Copia-like and En/Spm-like sequences were overrepresented in exons. These 7.8% percent of genes were enriched for some GO-based
functions, particularly kinase activity, and lacking in other functions, notably structural molecule activity. We also examined
gene family evolution for these genes. Gene family information helped clarify whether the sequence similarity between TE and
gene was due to a TE contributing to the gene or, instead, the TE co-opting a portion of the gene. Most (66%) of these genes
were not easily assigned to a gene family, and for these we could not infer the direction of the relationship between TE and
gene. For the remainder, where appropriate, we built phylogenetic trees to infer the direction of the TE-gene relationship
by parsimony. By this method, we verified examples where TEs contributed to expressed proteins. Our results are undoubtedly
conservative but suggest that TEs may have contributed small protein segments to as many as 1.2% of all expressed, annotated
A. thaliana genes.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
4.
O. A. Sokolova E. Yu. Yakushev A. D. Stolyarenko E. A. Mikhaleva V. A. Gvozdev M. S. Klenov 《Molecular Biology》2011,45(4):582-590
Complexes of Piwi family proteins with short piRNAs (Piwi-interacting RNAs) are responsible for silencing transposable elements
in animal reproductive organs. In Drosophila melanogaster, three proteins (Piwi, Aub, and Ago3) are members of the Piwi family. Piwi is the nuclear protein of somatic and germinal
ovarian cells, whereas Aub and Ago3 are cytoplasmic proteins involved in piRNA amplification in perinuclear granules that
constitute special organelles of germinal cells called nuage. Mutations in genes of the piRNA system are known to cause derepression
of several transposable elements. In this study, we compared quantitatively changes in expression of a larger number of elements
in the case of mutations in the piwi gene, genes aub, mael, and spn-E, which encode proteins of nuage granules, and armi gene coding an RNA helicase, the lack of which does not interfere with cytoplasmic piRNA amplification but disturbs nuclear
localization of Piwi protein. We found that the genes piwi, armi, aub, spn-E, and mael interact to induce silencing of some retrotransposons (HMS-Beagle, Gate and HeT-A); the same genes, except piwi, are involved in repression of I and G elements. We propose that Armi is involved in control of not only nuclear Piwi localization. Our data suggest the relation
of nuage proteins Aub, Spn-E, and Mael to Piwi-mediated silencing of retrotransposons Gate and HMS-Beagle in the nucleus. In general, our results corroborate the idea of genome stabilization by means of various silencing strategies
specific to different transposable elements. At the same time, our data suggest the existence of yet unknown mechanisms of
interplay between nuclear and cytoplasmic components of the piRNA machinery in germinal cells. 相似文献
5.
We investigated the expression profiles and genomic organisation of the ABA‐responsive genes encoding protein phosphatases 2C (PP2C, group A members) in Brassica oleracea to better understand their functional and genetic relations. Gene expression profiling of drought responsive genes in B. oleracea and Arabidopsis thaliana revealed significant differences in the gene expression pattern of a key regulator of ABA signalling—ABI1 PP2C. This finding prompted us to study genetic relations within the PP2Cs group A in the Brassica species. Twenty homologous B. oleracea sequences were identified and characterised as putative PP2C group A members. Phylogenetic analysis revealed that the B. oleracea homologues were closely related to the particular members of the A. thaliana PP2C. The genetic analysis corroborated the presence of two to three gene copies in B. oleracea in comparison to the nine unique PP2C genes in the A. thaliana genome. Gene expression analyses showed significant differences in PP2C gene expression pattern in B. oleracea. Our results indicate that PP2C‐based drought stress signalling in B. oleracea has evolved distinctly. Different reactions of particular B. oleracea PP2C genes to drought stress and ABA treatment indicate low conservation of gene expression patterns and functional divergence between B. oleracea and A. thaliana homologous genes. 相似文献
6.
Ryoichi Araki Akiko Hasumi Osamu Ishizaki Nishizawa Katsunori Sasaki Ayuko Kuwahara Yuji Sawada Yasushi Totoki Atsushi Toyoda Yoshiyuki Sakaki Yimeng Li Kazuki Saito Toshiya Ogawa Masami Yokota Hirai 《Plant biotechnology journal》2013,11(8):1017-1027
Plants belonging to the Brassicaceae family exhibit species‐specific profiles of glucosinolates (GSLs), a class of defence compounds against pathogens and insects. GSLs also exhibit various human health–promoting properties. Among them, glucoraphanin (aliphatic 4‐methylsulphinylbutyl GSL) has attracted the most attention because it hydrolyses to form a potent anticancer compound. Increased interest in developing commercial varieties of Brassicaceae crops with desirable GSL profiles has led to attempts to identify genes that are potentially valuable for controlling GSL biosynthesis. However, little attention has been focused on genes of kale (Brassica oleracea var. acephala). In this study, we established full‐length kale cDNA libraries containing 59 904 clones, which were used to generate an expressed sequence tag (EST) data set with 119 204 entries. The EST data set clarified genes related to the GSL biosynthesis pathway in kale. We specifically focused on BoMYB29, a homolog of Arabidopsis MYB29/PMG2/HAG3, not only to characterize its function but also to demonstrate its usability as a biological resource. BoMYB29 overexpression in wild‐type Arabidopsis enhanced the expression of aliphatic GSL biosynthetic genes and the accumulation of aliphatic GSLs. When expressed in the myb28myb29 mutant, which exhibited no detectable aliphatic GSLs, BoMYB29 restored the expression of biosynthetic genes and aliphatic GSL accumulation. Interestingly, the ratio of methylsulphinyl GSL content, including glucoraphanin, to that of methylthio GSLs was greatly increased, indicating the suitability of BoMYB29 as a regulator for increasing methylsulphinyl GSL content. Our results indicate that these biological resources can facilitate further identification of genes useful for modifications of GSL profiles and accumulation in kale. 相似文献
7.
C. Hall D. McCallum A. Prescott R. Mithen 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,102(2-3):369-374
Fine mapping of the glucosinolate biosynthesis gene OHP, which regulates the conversion of 3-methylsulphinylpropyl to 3-hydroxypropyl glucosinolate, in an Arabidopsis thaliana Columbia × Landsberg erecta RI line population positioned the gene within 54 kb of DNA on chromosome IV. Sequence data identified a family of genes encoding
2-oxoglutarate-dependent dioxygenases in this region. A probe based on these genes co-segregated with ALK in Brassica oleracea,a gene regulating the synthesis of alkenyl glucosinolates. The reactions catalysed by the OHP and ALK enzymes utilise similar substrates and may have a common mechanism. Thus, these dioxygenases are prime candidates for controlling
the side chain modification of glucosinolates.
Received: 12 May 2000 / Accepted: 29 May 2000 相似文献
8.
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10.
The glucosinolate-degrading enzyme myrosinase in Brassicaceae is encoded by a gene family 总被引:15,自引:0,他引:15
A full-length cDNA clone (MB3) and three partial clones (MA1, MB1 and MB2) which encode myrosinase (thioglucoside glucohydrolase, EC 3.2.3.1) were isolated from a Sinapis alba (white mustard) cDNA library. Nucleotide sequence analysis of these clones revealed that they are encoded by a gene family. Southern blot analysis with gene-specific probes showed that the gene family consists of a least two subfamilies (MA and MB) each with several members both in S. alba and in Brassica napus (oilseed rape). In Arabidopsis thaliana (wall cress) only three myrosinase genes seem to be present. Northern blot analysis indicated that all the myrosinase mRNA species have the same size, approximately 1.95 kb. 相似文献
11.
Lescot M Rombauts S Zhang J Aubourg S Mathé C Jansson S Rouzé P Boerjan W 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2004,109(1):10-22
Poplar has become a model system for functional genomics in woody plants. Here, we report the sequencing and annotation of the first large contiguous stretch of genomic sequence (95 kb) of poplar, corresponding to a bacterial artificial chromosome clone mapped 0.6 centiMorgan from the Melampsora larici-populina resistance locus. The annotation revealed 15 putative genetic objects, of which five were classified as hypothetical genes that were similar only with expressed sequence tags from poplar. Ten putative objects showed similarity with known genes, of which one was similar to a kinase. Three other objects corresponded to the toll/interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant disease resistance genes, of which two were predicted to encode an amino terminal nuclear localization signal. Four objects were homologous to the Ty1/copia family of class I transposable elements, one of which was designated Retropop and interrupted one of the disease resistance genes. Two other objects constituted a novel Spm-like class II transposable element, which we designated Magali.M.L. and S.R. contributed equally to this article 相似文献
12.
Perumal Sampath Jayakodi Murukarthick Nur Kholilatul Izzah Jonghoon Lee Hong-Il Choi Kenta Shirasawa Beom-Soon Choi Shengyi Liu Ill-Sup Nou Tae-Jin Yang 《PloS one》2014,9(4)
Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion. 相似文献
13.
John C. Walker 《The Plant journal : for cell and molecular biology》1993,3(3):451-456
The isolation of a maize cDNA clone that encodes a membrane spanning protein kinase related to the self-incompatibility glycoproteins (SLG) of Brassica and structurally similar to the growth factor receptor tyrosine kinases has recently been reported. Three distinct receptor-like protein kinase (RLK) cDNA clones from Arabidopsis thaliana have now been identified. Two of the Arabidopsis RLK genes encode SLG-related protein kinases but have different patterns of expression: one is expressed predominantly in rosettes while the other is expressed primarily in roots. The third RLK gene contains an extracellular domain that consists of 21 leucine-rich repeats that are analogous to the leucine-rich repeats found in proteins from humans, flies and yeast. The Arabidopsis leucine-rich gene is expressed at equivalent levels in roots and rosettes. These results show that there are several genes in higher plants that encode members of the receptor protein kinase superfamily. The structural diversity and differential expression of these genes suggest that each plays a distinct and possibly important role in cellular signaling in plants. 相似文献
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Meixia Zhao Jianchang Du Feng Lin Chaobo Tong Jingyin Yu Shunmou Huang Xiaowu Wang Shengyi Liu Jianxin Ma 《The Plant journal : for cell and molecular biology》2013,76(2):211-222
Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR‐retrotransposons, the rates of synonymous and non‐synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B. rapa than in B. oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B. rapa than in B. oleracea. Interestingly, non‐synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter‐specific asymmetric evolution. 相似文献
16.
17.
Characterization of the gene encoding ovine beta-lactoglobulin. Similarity to the genes for retinol binding protein and other secretory proteins 总被引:8,自引:0,他引:8
Beta-lactoglobulin is the major whey protein in the milk of ruminants and is expressed in the mammary gland during pregnancy and lactation. Here we describe the isolation and characterization of genomic clones encoding ovine beta-lactoglobulin. Two very similar but non-identical, types of beta-lactoglobulin clone were obtained. DNA sequence analysis of one of these showed that the gene is 4900 bases long and contains seven exons. It codes for a protein of 180 amino acid residues, containing an 18-residue signal peptide, within exons I to VI; exon VII is non-coding. We show that the genes encoding serum retinol binding protein, major urinary protein, alpha-1-acid glycoprotein and apolipoprotein D have a similar organization of exons and introns to beta-lactoglobulin. In particular, a comparison between beta-lactoglobulin and retinol binding protein shows that both genes encode equivalent elements of three-dimensional protein structure within analogous exons. These proteins are all members of a large, diverse family of secretory proteins, many of which function in binding small hydrophobic molecules. 相似文献
18.
The isolation and characterisation of the tapetum-specific Arabidopsis thaliana A9 gene 总被引:11,自引:0,他引:11
Wyatt Paul Rachel Hodge Sarah Smartt John Draper Rod Scott 《Plant molecular biology》1992,19(4):611-622
The Brassica napus cDNA clone A9 and the corresponding Arabidopsis thaliana gene have been sequenced. The B. napus cDNA and the A. thaliana gene encode proteins that are 73% identical and are predicted to be 10.3 kDa and 11.6 kDa in size respectively. Fusions of an RNase gene and the reporter gene -glucuronidase to the A. thaliana A9 promoter demonstrated that in tobacco the A9 promoter is active solely in tapetal cells. Promoter activity is first detectable in anthers prior to sporogenous cell meiosis and ceases during microspore premitotic interphase.The deduced A9 protein sequence has a pattern of cysteine residues that is present in a superfamily of seed plant proteins which contains seed storage proteins and several protease and -amylase inhibitors. 相似文献
19.
E. Pichersky N. E. Hoffman R. Bernatzky B. Piechulla S. D. Tanksley A. R. Cashmore 《Plant molecular biology》1987,9(3):205-216
We report the isolation and characterization of a tomato nuclear gene encoding a chlorophyll a/b-binding (CAB) protein of photosystem I (PSI). The coding nucleotide sequence of the gene, designated Cab-6B, is different at eight positions from that of a previously isolated cDNA clone derived from the Cab-6A gene, but the two genes encode identical proteins. Sequence comparison with the cDNA clone revealed the presence of three short introns in Cab-6B. Genetic mapping experiments demonstrate that Cab-6A and Cab-6B are tightly linked and reside on chromosome 5, but the physical distance between the two genes is at least 7 kilobases. Cab-6A and Cab-6B have been designated Type I PSI CAB genes. They are the only two genes of this branch of the CAB gene family in the tomato genome, and they show substantial divergence to the genes encoding CAB polypeptides of photosystem II. The Type I PSI CAB genes, like the genes encoding PSII CAB proteins, are highly expressed in illuminated leaf tissue and to a lesser extent in other green organs. 相似文献
20.
Lantian Zhang Siyi Wang Yuyu Chen Mengyuan Dong Yunxia Fang Xian Zhang Tao Tong Ziling Zhang Junjun Zheng Dawei Xue Xiaoqin Zhang 《Phyton》2020,89(2):229-251
The F-box protein-encoding gene family plays an essential role in plant
stress resistance. In present study, 126 non-redundant F-box genes were identified
in barley (Hordeum vulgare L., Hv). The corresponding proteins contained 165–
887 amino acid residues and all were amphiphilic, except 5 proteins. Phylogenetic
analysis of F-box protein sequences in barley and stress-related F-box protein
sequences in wheat and Arabidopsis thaliana (At) was used to classify barley
F-box genes are divided into 9 subfamilies (A–I). A structure-based sequence
alignment demonstrated that F-box proteins were highly conserved with a total
of 10 conserved motifs. In total, 124 F-box genes were unevenly distributed on
7 chromosomes; another 2 genes have not been anchored yet. The gene structure
analysis revealed high variability in the number of exons and introns in F-box
genes. Comprehensive analysis of expression profiles and phylogenetic tree analysis, a total of 12 F-box genes that may be related to stress tolerance in barley
were screened. Of the 12 detected F-box genes, 8 and 10 were upregulated
after drought and salt stress treatments, respectively, using quantitative real-time
polymerase chain reaction (qRT-PCR). This study is the first systematic analysis
conducted on the F-box gene family in barley, which is of great importance
for clarifying this family’s bioinformatic characteristics and elucidating its function in barley stress resistance. These results will serve as a theoretical reference
for subsequent research on molecular regulation mechanisms, genetic breeding,
and improvement. 相似文献