The complete chloroplast genome sequence of Citrus sinensis(L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms

Bausher, Michael G.; Singh, Nameirakpam D.; Lee, Seung Bum; Jansen, Robert K.; Daniell, Henry

doi:10.1186/1471-2229-6-21

Cited by 180 publications

(98 citation statements)

References 71 publications

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“…DQ864733) [41] by searching candidate SSR regions using mreps [76] as described in the previous section. Oligonucleotide primer sets for citrus mitochondrial genomes [53], and universal primer sets for the chloroplast genomes of dicotyledonous angiosperms [81] were also used for genotyping organelle genomes.…”

Section: Methodsmentioning

confidence: 99%

“…Nowadays, codominant precision simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers have been developed and used in most studies (see the reviews [34,37–40]). In addition, the chloroplast genome sequence of sweet orange has been released [41], and genome sequences of major citrus varieties are now public [42,43]. These genome sequence resources enable the design of precision DNA markers, and have revealed the parentage of Clementine, grapefruit, sweet orange, and limes and lemons [43–48].…”

Section: Introductionmentioning

confidence: 99%

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Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

et al. 2016

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Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy–Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

et al. 2016

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“…Only b2seq alignments with an E-value of <0.01 were considered homologous. All sequences passing this criteria were then aligned together using ClustalW (version 1.82), back-translated, and assessed for purifying selection against nonsynonymous mutations using PAML (version 3.14) (Yang 1997) according to the protocol in Nekrutenko et al (2002) and a tree topology based on Figure 2A (Bausher et al 2006). In brief, a likelihood ratio test was evaluated for a model in which the nonsynonymous (dN) to synonymous substitution (dS) ratio was allowed to vary and another model in which it was fixed at 1.…”

Section: Motif Categorizationmentioning

confidence: 99%

Known and novel post-transcriptional regulatory sequences are conserved across plant families

Vaughn¹,

Ellingson²,

Mignone³

et al. 2012

RNA

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The sequence elements that mediate post-transcriptional gene regulation often reside in the 59 and 39 untranslated regions (UTRs) of mRNAs. Using six different families of dicotyledonous plants, we developed a comparative transcriptomics pipeline for the identification and annotation of deeply conserved regulatory sequences in the 59 and 39 UTRs. Our approach was robust to confounding effects of poor UTR alignability and rampant paralogy in plants. In the 39 UTR, motifs resembling PUMILIObinding sites form a prominent group of conserved motifs. Additionally, Expansins, one of the few plant mRNA families known to be localized to specific subcellular sites, possess a core conserved RCCCGC motif. In the 59 UTR, one major subset of motifs consists of purine-rich repeats. A distinct and substantial fraction possesses upstream AUG start codons. Half of the AUG containing motifs reveal hidden protein-coding potential in the 59 UTR, while the other half point to a peptideindependent function related to translation. Among the former, we added four novel peptides to the small catalog of conserved-peptide uORFs. Among the latter, our case studies document patterns of uORF evolution that include gain and loss of uORFs, switches in uORF reading frame, and switches in uORF length and position. In summary, nearly three hundred posttranscriptional elements show evidence of purifying selection across the eudicot branch of flowering plants, indicating a regulatory function spanning at least 70 million years. Some of these sequences have experimental precedent, but many are novel and encourage further exploration.

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“…The diversity of Citrus L. genus is credited (in part) to the presence of transposable elements, especially retrotransposons as reported by Bretó et al (2001). It is important to note that the chloroplast genome of the sweet orange has recently been sequenced completely by Bausher et al (2006). In recent years, the expressed sequence tags (ESTs) have been identified by several research groups from a number of Citrus species (Terol et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Assessment of genetic diversity of Tunisian orange, Citrus sinensis (L.) Osbeck using microsatellite (SSR) markers

et al. 2016

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ABSTRACT. Citrus are one of the most cultivated crops in the world. Economically, they are very important fruit trees in Tunisia. Little is known about the genetic diversity of the Tunisian Citrus germplasm. Exploring this diversity is a prerequisite for the identification and characterization of the local germplasm to circumvent and controlling genetic erosion caused by biotic and abiotic stress to aid its conservation and use. In the present study, we explored the genetic diversity of 20 Tunisian orange cultivars [Citrus sinensis (L.) Osbeck] and established their relationships by using seven simple sequence repeat (SSR) loci. In total, 37 alleles and 44 genotypes were scored. The sizes of alleles ranged from 90 to 280 bp. The number of alleles per locus was from 4 to 7, with an average of 5.28. Polymorphic information content value changed from 0.599 to 0.769 with an average of 0.675. Analysis of the genotypes revealed a heterozygote deficiency across all the genotypes. The observed heterozygosity varied from 0 to 1 (average of 0.671). Cluster analysis showed that three groups could be distinguished and the polymorphism occurred independently of the geographical origin of the studied orange cultivars. The detected SSR genotypes allowed the establishment of an identification key with a discriminating power of 100%. Multivariate analysis and the neighbor-joining phylogenetic tree indicated a narrow genetic base for the orange cultivars. The usefulness of SSR markers for orange fingerprinting and evaluation of the genetic diversity in the Tunisian germplasm are discussed in this paper.

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The complete chloroplast genome sequence of Citrus sinensis(L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms

Cited by 180 publications

References 71 publications

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

Known and novel post-transcriptional regulatory sequences are conserved across plant families

Assessment of genetic diversity of Tunisian orange, Citrus sinensis (L.) Osbeck using microsatellite (SSR) markers

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