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1.
Suresh Reddy Mittapelli Shailendar Kumar Maryada Venkateswara Rao Khareedu Dashavantha Reddy Vudem 《Tree Genetics & Genomes》2014,10(2):399-409
The genus Citrus is an important fruit crop and nutritional source for the good health of humans. Cytochrome P450s represent about 1 % of the proteome and mediate diverse biochemical reactions pertaining to both primary and secondary metabolism. Analysis of Citrus genomic resources identified 296 plant cytochrome P450s (CYP) coding genes in Citrus clementina, 272 in double haploid (dh) Citrus sinensis, and 202 in C. sinensis. In C. clementina and dh C. sinensis, CYP genes are distributed into nine clans. In the three genomes, single intron containing CYP genes are predominant in the A-type families. Among non-A-type CYP families, multiple intron containing genes are predominant. More number of genes in CYP A-type families over non-A-type families is attributed to rapid evolution of A-type genes facilitated by their gene organization. Further, complex gene organization of non-A-type genes with the presence of multiple introns might have contributed to the slower evolvement of paralogs. Majority of introns (1,660) from three genomes showed canonical GT-AG splice sites. However, 33 introns showed non-conventional GC… PyAG splice sites and functionality of these splice sites is confirmed by the ESTs lacking this intron. Across the families, gene organization is conserved between the three genomes. In dh C. sinensis, 22 genes were identified to have alternate splicing. Examination of scaffolds in C. clementina revealed that majority of the Citrus CYP genes are solitary and a few of them are in clusters of 3–8 genes. PCR amplification of C. sinensis genomic DNA with gene-specific primers failed to amplify out-grouped genes Ccl-CYP706A16 and Ccl-CYP706B1, confirming that they are specific to C. clementina. Differential number of CYP genes observed between C. clementina and C. sinensis is attributed to the extent of variability between their parents representing ancestral taxa. 相似文献
2.
Jean C. Cardoso Adriana P. Martinelli Maria Antonieta Germanà Rodrigo R. Latado 《Plant Cell, Tissue and Organ Culture》2014,117(3):455-464
Citrus, and particularly sweet oranges, are very recalcitrant to anther culture. In this paper it was evaluated for the first time the response of 27 genotypes of Citrus sinensis and of one hybrid C. clementina × C. sinensis, to in vitro anther culture. Ten genotypes of sweet oranges showed embryogenic callus induction, mostly blood sweet oranges genotypes, such as Tarocco, Moro and Sanguinelli. In vitro microspore developmental switches from the gamethophytic to the sporophytic pathway were shown by DAPI staining in microspores of these responsive genotypes, after 10 months in culture. However, microsatellite marker analyses showed that these calli were heterozygous. The flow-cytometric analysis of these embryogenic calli showed the presence of two peaks, corresponding to haploid (n) and diploid (2n) genotypes. Differently, anther cultures of the hybrid C. clementina × C. sinensis produced tri-haploid (3n) embryogenic calli and the embryos obtained were homozygous when analyzed by molecular markers (sample sequence repeats), confirming the more responsive characteristic of clementine to microspore embryogenesis through anther culture. 相似文献
3.
Yunsheng Wang Lijuan Zhou Dazhi Li Liangying Dai Amy Lawton-Rauh Pradip K. Srimani Yongping Duan Feng Luo 《PloS one》2015,10(3)
In this study, we identified and compared nucleotide-binding site (NBS) domain-containing genes from three Citrus genomes (C. clementina, C. sinensis from USA and C. sinensis from China). Phylogenetic analysis of all Citrus NBS genes across these three genomes revealed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR) domain and two different Non-TIR groups in which most of proteins contain the Coiled Coil (CC) domain. Motif analysis confirmed that the two groups of CC-containing NBS genes are from different evolutionary origins. We partitioned NBS genes into clades using NBS domain sequence distances and found most clades include NBS genes from all three Citrus genomes. This suggests that three Citrus genomes have similar numbers and types of NBS genes. We also mapped the re-sequenced reads of three pomelo and three mandarin genomes onto the C. sinensis genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pomelo and mandarin genomes. The homologous NBS genes in pomelo and mandarin suggest that the parental species of C. sinensis may contain similar types of NBS genes. This explains why the hybrid C. sinensis and original C. clementina have similar types of NBS genes in this study. Furthermore, we found that sequence variation amongst Citrus NBS genes were shaped by multiple independent and shared accelerated mutation accumulation events among different groups of NBS genes and in different Citrus genomes. Our comparative analyses yield valuable insight into the structure, organization and evolution of NBS genes in Citrus genomes. Furthermore, our comprehensive analysis showed that the non-TIR NBS genes can be divided into two groups that come from different evolutionary origins. This provides new insights into non-TIR genes, which have not received much attention. 相似文献
4.
Gaetano Distefano Stefano La Malfa Alessandra Gentile Shu-Biao Wu 《Tree Genetics & Genomes》2013,9(5):1271-1281
Citrus taxonomy is very complex mainly due to specific aspects of its reproductive biology. A number of studies have been performed using various molecular markers in order to evaluate the level of genetic variability in Citrus. SNP markers have been used for genetic diversity assessment using a variety of different methods. Recently, the availability of EST database and whole genome sequences has made it possible to develop more markers such as SNPs. In the present study, the high-resolution melting curve analysis (HRM) was used to detect SNPs or INDELs in Citrus genus for the first time. We aimed to develop a panel of SNPs to differentiate Citrus genotypes which can also be applied to Citrus biodiversity studies. The results showed that 21 SNP containing markers produced distinct polymorphic melting curves among the Citrus spp. investigated through HRM analysis. It was proved that HRM is an efficient, cost-effective, and accurate method for discriminating citrus SNPs as well as a method to analyze more polymorphisms in a single PCR amplicon, representing a useful tool for genetic, biodiversity, and breeding studies. SNPs developed based on Citrus sinensis EST database showed a good transferability within the Citrus genus. Moreover, HRM analysis allowed the discrimination of citrus genotypes at specific level and the resulting genetic distance analysis clustered these genotypes into three main branches. The results suggested that the panel of SNP markers could be used in a variety of applications in citrus biodiversity assessment and breeding programs using HRM analysis. 相似文献
5.
Mohindra V Singh A Barman AS Tripathi R Sood N Lal KK 《Molecular biology reports》2012,39(5):5921-5931
Clarias batrachus, an Indian catfish species, is endemic to the Indian subcontinent and potential cultivable species. The genomic resources
in C. batrachus in the form of ESTs containing microsatellite repeats (EST-SSR) and single nucleotide polymorphisms (SNPs) that are associated
with the expressed genes from spleen were mined. From a total of 1,937 ESTs generated, 1,698 unique sequences were obtained,
out of which 221 EST-SSRs were identified and 54% could be functionally annotated by similarity searches. A total of 23 contigs
containing 3 or more ESTs were found to contain 31 SNP loci, out of which 8 ESTs showed similarity to genes of known function
and 1 for hypothetical protein. Nine ESTs with SSRs and/or SNPs identified in this study were reported to be associated with
diseases in human and animals. These identified loci can be developed into markers in C. batrachus, which can be useful in linkage mapping, comparative genomics studies and for its genetic improvement programmes. 相似文献
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7.
Livia?Moura?de?Souza Guilherme?Toledo-Silva Claudio?Benicio?Cardoso-Silva Carla?Cristina?da?Silva Isabela?Aparecida?de Araujo?Andreotti Andre?Ricardo?Oliveira?Conson Camila?Campos?Mantello Vincent?Le?Guen Anete?Pereira?de?Souza
The development of single nucleotide polymorphism (SNP) markers provides the opportunity to improve many areas of plant breeding and population genetics. Unfortunately, for species such as the rubber tree (Hevea brasiliensis), the use of next-generation sequencing for genomic SNP discovery is very difficult because of the large genome size and the abundance of repeated sequences. Access to a set of validated SNP markers is a significant advantage for rubber researchers who wish to apply SNPs in scientific research. Here, we performed genomic sequencing of H. brasiliensis and generated 10,993,648 short reads, which were assembled into 10,071 contigs (N50 = 3078) by a de novo assembly strategy. A total of 2446 contigs presented no hits in the current H. brasiliensis genome assembly and may therefore be considered novel genomic sequences of rubber tree. A total of 143 putative polymorphic positions were selected, gene annotations were available for 58.7 % of the markers, and all of the sequences could be anchored to the released H. brasiliensis genome. These SNPs were validated in eight genotypes of H. brasiliensis and 15 F1 plants from a mapping population, resulting in 30 (20.9 %) positions correctly classified. The analysis revealed key candidate genes responsible for defence mechanisms and provided markers for further genetic improvement of Hevea in breeding programmes. 相似文献
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9.
Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. 总被引:20,自引:0,他引:20
Single-nucleotide polymorphisms (SNPs) represent a new form of functional marker, particularly when they are derived from expressed sequence tags (ESTs). A bioinformatics strategy was developed to discover SNPs within a large wheat EST database and to demonstrate the utility of SNPs in genetic mapping and genetic diversity applications. A collection of > 90000 wheat ESTs was assembled into contiguous sequences (contigs), and 45 random contigs were then visually inspected to identify primer pairs capable of amplifying specific alleles. We estimate that homoeologue sequence variants occurred 1 in 24 bp and the frequency of SNPs between wheat genotypes was 1 SNP/540 bp (theta = 0.0069). Furthermore, we estimate that one diagnostic SNP test can be developed from every contig with 10-60 EST members. Thus, EST databases are an abundant source of SNP markers. Polymorphism information content for SNPs ranged from 0.04 to 0.50 and ESTs could be mapped into a framework of microsatellite markers using segregating populations. The results showed that SNPs in wheat can be discovered in ESTs, validated, and be applied to conventional genetic studies. 相似文献
10.
Shaolin Wang Eric Peatman Jason Abernathy Geoff Waldbieser Erika Lindquist Paul Richardson Susan Lucas Mei Wang Ping Li Jyothi Thimmapuram Lei Liu Deepika Vullaganti Huseyin Kucuktas Christopher Murdock Brian C Small Melanie Wilson Hong Liu Yanliang Jiang Yoona Lee Fei Chen Jianguo Lu Wenqi Wang Peng Xu Benjaporn Somridhivej Puttharat Baoprasertkul Jonas Quilang Zhenxia Sha Baolong Bao Yaping Wang Qun Wang Tomokazu Takano Samiran Nandi Shikai Liu Lilian Wong Ludmilla Kaltenboeck Sylvie Quiniou Eva Bengten Norman Miller John Trant Daniel Rokhsar Zhanjiang Liu 《Genome biology》2010,11(1):1-14
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12.
Xinchao Wang Xinyuan Hao Chunlei Ma Hongli Cao Chuan Yue Lu Wang Jianming Zeng Yajun Yang 《Tree Genetics & Genomes》2014,10(5):1149-1159
13.
Putative SNP discovery in interspecific hybrids of catfish by comparative EST analysis 总被引:9,自引:0,他引:9
In this study, we identified putative SNP markers within genes by comparative analysis of expressed sequence tags (ESTs). Comparison of 849 ESTs from blue catfish (Ictalurus furcatus) with >11,000 ESTs from channel catfish (I. punctatus) deposited in GenBank resulted in the identification of 1020 putative SNPs within 161 genes, of which 145 were nuclear genes of known function. The observed frequency of SNPs within ESTs of the two closely related catfish species was 1.32 SNP per 100 bp. The majority of identified SNPs differed between the two species and, therefore, these SNPs are useful for mapping genes in channel catfish x blue catfish interspecific resource families. The SNPs that differed within species were also observed; these can be applied to genome scans in channel catfish resource families. 相似文献
14.
R. M. Green A. Vardi E. Galun 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1986,72(2):170-177
Summary A physical plastome map was constructed for Citrus aurantium, and the plastomes of species and cultivars of Citrus and of two Citrus relatives were analysed by Southern blot-hybridisation of labelled total tobacco cpDNA to digests of total Citrus DNA. A resemblance was found between the plastomes of cultivars of C. limon (lemon), C. sinensis (orange), C. aurantium (sour orange), C. paradisii (grapefruit) and C. grandis (pomello). The plastomes of other Citrus types such as mandarin (C. reticulata) and citron (C. medico) differed from each other as well as from the plastomes of the aforementioned group. The plastomes of Poncirus trifoliata and Microcitrus sp. are distinct from each other as well as from the Citrus types. 相似文献
15.
The genus Citrus contains many economically important fruits that are grown worldwide for their high nutritional and medicinal value. Due to frequent hybridizations among species and cultivars, the exact number of natural species and the taxonomic relationships within this genus are unclear. To compare the differences between the Citrus chloroplast genomes and to develop useful genetic markers, we used a reference-assisted approach to assemble the complete chloroplast genome of Omani lime (C. aurantiifolia). The complete C. aurantiifolia chloroplast genome is 159,893 bp in length; the organization and gene content are similar to most of the rosids lineages characterized to date. Through comparison with the sweet orange (C. sinensis) chloroplast genome, we identified three intergenic regions and 94 simple sequence repeats (SSRs) that are potentially informative markers with resolution for interspecific relationships. These markers can be utilized to better understand the origin of cultivated Citrus. A comparison among 72 species belonging to 10 families of representative rosids lineages also provides new insights into their chloroplast genome evolution. 相似文献
16.
We identified ~13 000 putative single nucleotide polymorphisms (SNPs) by comparison of repeat‐masked BAC‐end sequences from the cattle RPCI‐42 BAC library with whole‐genome shotgun contigs of cattle genome assembly Btau 1.0. Genotyping of a subset of these SNPs was performed on a panel containing 186 DNA samples from 18 cattle breeds including 43 trios. Of 1039 SNPs confirmed as polymorphic in the panel, 998 had minor allele frequency ≥0.25 among unrelated individuals of at least one breed. When Btau 4.0 became available, 974 of these validated SNPs were assigned in silico to known cattle chromosomes, while 41 SNPs were mapped to unassigned sequence scaffolds, yielding one SNP every ~3 Mbp on average. Twenty‐four SNPs identified in Btau 1.0 were not mapped to Btau 4.0. Of the 1015 SNPs mapped to Btau 4.0, 959 SNPs had nucleotide bases identical in Btau 4.0 and Btau 1.0 contigs, whereas 56 bases were changed, resulting in the loss of the in silico SNP in Btau 4.0. Because these 1039 SNPs were all directly confirmed by genotyping on the multi‐breed panel, it is likely that the original polymorphisms were correctly identified. The 1039 validated SNPs identified in this study represent a new and useful resource for genome‐wide association studies and applications in animal breeding. 相似文献
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18.
Bo ZHANG Yan ZHOU Liang ZHANG Qiang ZHUGE Ming-Xiu WANG Min-Ren HUANG 《植物学报(英文版)》2005,47(12):1493-1499
By using assembled expressed sequence tags (ESTs) from 14 different eDNA libraries that contain 84 132 sequences reads, 556 Populus candidate single nucleotide polymorphisms (SNPs) were identified. Because traces were not available from dbEST (http://www.ncbi.nlm.nih.gov/dbEST/index.html), stringent filters were used to identify reliable candidate SNPs. Sequences analysis indicated that the main types of substitutions among candidate SNPs were A/G and T/C transitions, which accounted for 22.0% and 30.8%, respectively. One hundred and ten candidate SNPs were tested. As a result, 38 candidate SNPs were confirmed by directed sequencing of PCR products amplified from six different individuals. Thirteen new SNPs in intron regions were found and multiple SNPs were found to be located in both intron and exon regions of four contigs. Heterozygosis was found in all 47 candidate sites and five SNP sites were heterozygous in all six samples. This is the first report of SNP identification in a tree species which reveals that assembled ESTs from multiple libraries of the public database may provide a rich source of comparative sequences for an SNP search in the poplar genome. 相似文献
19.
Camille Lepoittevin Jean-Marc Frigerio Pauline Garnier-Géré Franck Salin María-Teresa Cervera Barbara Vornam Luc Harvengt Christophe Plomion 《PloS one》2010,5(6)