Eucalyptus microsatellites mined in silico: survey and evaluation

Yasodha, R.; Sumathi, R.; Chezhian, P.; Kavitha, S.; Ghosh, Modhumita

doi:10.1007/s12041-008-0003-9

Cited by 32 publications

(23 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this current study, the repeat motifs of AG/TC and GA/CT accounted for the vast majority (94.3%) of dinucleotide repeat motifs, and CCG/CGG repeat motifs were the most common (16.4%) trinucleotide repeat motifs. These results are in perfect agreement with the results of other studies in Eucalyptus (Zhou 2011;Yasodha et al 2008).…”

Section: Discussion Characterization Of Ssrs In Eucalyptussupporting

confidence: 93%

“…This frequency is consistent with results obtained by Ellis and Burke (2007) and Yasodha et al (2008) Dinucleotide repeat motifs are generally the most common types of repeat motifs in dicotyledons, and trinucleotide repeat motifs are most common in graminaceous plants (Biet et al 1999). In this current study, dinucleotide and trinucleotide repeat motifs were found to be the most frequent in Eucalyptus, accounting for 44.4 and 32.8%,respectively, of the total repeat motifs.…”

Section: Discussion Characterization Of Ssrs In Eucalyptussupporting

confidence: 91%

See 1 more Smart Citation

Analysis of SSR loci and development of SSR primers in Eucalyptus

et al. 2017

View full text Add to dashboard Cite

In this study, 28,691 genome sequences and 16,566 expressed sequence tags (ESTs) of Eucalyptus were derived from the GenBank database. A total of 2292 SSR loci were sought out from 1785 effective sequences. Through analyses of SSR loci information, the SSR motif length was negatively correlated with the abundance of the SSRs. In the EST sequences of Eucalyptus, triplet repeat motifs were the most abundant, and dinucleotide repeats motifs had the highest frequencies. Subsequently, 395 pairs of primers were designed based on the SSR loci. Using optimized SSR-PCR conditions, 340 pairs of primers were successfully screened, with a success rate of 86.1%. By construction of a maximum likelihood phylogenetic tree of six eucalypt species, represented by five species of the genus Eucalyptus and one of the genus Corymbia, the genetic relationships of Eucalyptus urophylla and E. camaldulensis suggested by this tree was found to differ from that suggested by traditional morphological taxonomy. The results provide insights for evaluating genetic diversity of Eucalyptus and analysis of Eucalyptus phylogenetics using SSR markers.

show abstract

Section: Discussion Characterization Of Ssrs In Eucalyptussupporting

confidence: 93%

Section: Discussion Characterization Of Ssrs In Eucalyptussupporting

confidence: 91%

Analysis of SSR loci and development of SSR primers in Eucalyptus

et al. 2017

View full text Add to dashboard Cite

show abstract

“…For five Eucalyptus species, average frequency of microsatellite-containing EST was 12.9% with AG motif most common (Yasodha et al, 2008). Quercus mongolica var.…”

Section: Microsatellite Mining and Est-ssr Markersmentioning

confidence: 99%

Generation de marqueurs de séquences exprimées et développement de marqueurs microsatellites pour Castanopsis sieboldii var. sieboldii (Fagaceae)

Ueno¹,

Aoki²,

Tsumura³

2009

Ann. For. Sci.

View full text Add to dashboard Cite

Abstract• Castanopsis sieboldii var. sieboldii is an evergreen broadleaved canopy tree that grows on Honshu, Shikoku and Kyushu Islands in Japan. A closely-related, hybridizing, congener species, C. cuspidata var. cuspidata, has different leaf epidermis structure and different seed nuts morphology compared to C. sieboldii var. sieboldii. Furthermore, the habitats in which the two species grow often indicate different water requirements.• Analysis of genetic diversity, using transcribed sequences, will provide a sound basis for the management of this species, allowing successful reforestation, incorporating phylogeographic conservation. In order to obtain transcripts sequences for the species and to develop transcript-based markers, we constructed and analyzed a cDNA library, surveyed microsatellite sequences within it and designed PCR primers for the microsatellites.• The cDNA library was constructed using tissue from the inner bark of C. sieboldii var. sieboldii; 3 354 Expressed Sequence Tags (ESTs) were identified. We constructed 2 417 putative unigenes and assigned putative functions to 1 856 of them. Three hundred and fourteen microsatellites were found within the putative unigenes and 16 EST-SSR (Simple Sequence Repeat) markers were developed. The EST-SSR markers developpe in this study should facilitate future analysis of the genetic diversity of this and related species. Mots-clés :arbre feuillu sempervirent / Castanopsis cuspidata var. cuspidata / Castanopsis sieboldii var. lutchuensis / Castanopsis sieboldii var. carlesii Résumé -Generation de marqueurs de séquences exprimées et développement de marqueurs microsatellites pour Castanopsis sieboldii var. sieboldii (Fagaceae).• Castanopsis sieboldii var. sieboldii est un feuillu sempervirent qui pousse sur les îles japonaises de Honshu, Shikoku et Kyushu. C. cuspidata var. cuspidata une espèce congénère, étroitement liée, hybridée, a une structure de l'épiderme des feuilles différente et une morphologie différente des noix semences par rapport à C. sieboldii var. sieboldii. En outre, les habitats dans lesquels les deux espèces poussent indiquent souvent des besoins en eau différents.• L'analyse de la diversité génétique, en utilisant des séquences transcrites, fournira une base solide pour la gestion de cette espèce, ce qui permettra le succès des reboisements, en intégrant une conservation phylogéographique. Afin d'obtenir les transcriptions des séquences de l'espèce et de mettre au point des marqueurs à base de transcription, nous avons construit et analysé une banque d'ADNc, étudié des séquences microsatellites et conçu des amorces PCR pour les microsatellites.• La banque d'ADNc a été construite en utilisant les tissus de l'écorce interne de C. sieboldii var. sieboldii, 3 354 marqueurs de séquences exprimées (EST) ont été identifiés. Nous avons construit 2 417 unigènes putatifs et assigné des fonctions putatives à 1 856 d'entre eux. Trois cents quatorze microsatellites ont été trouvés à l'intérieur des unigènes putatifs et 16 EST-SSR (Simple Sequence Re...

show abstract

“…SSRs originate from unequal crossing over or replication errors resulting in the formation of unusual secondary structures such as hairpins or slipped strands (Pearson et al 1998). Molecular markers developed from ESTs are known as genic markers, are highly useful in developing linkage maps and in marker assisted breeding programmes (Varshney et al 2005;Yasodha et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools

Riju

Rajesh

Sherin

et al. 2009

J Genet

View full text Add to dashboard Cite

Expressed sequence tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, data on gene expression and regulation, and also provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences, as available in the public domain, were downloaded and made into contigs. Microsatellites were located in these ESTs and contigs using five softwares (MISA, TRA, TROLL, SSRIT and SSR primer). MISA gave maximum coverage of SSRs in cacao ESTs and contigs, although TRA was able to detect higher order (5-mer) repeats. The frequency of SSRs was one per 26.9 kb in the known set of ESTs. One-third of the repeats in EST-contigs were found to be trimeric. A few rare repeats like 21-mer repeat were also located. A/T repeats were most abundant among the mononucleotide repeats and the AG/GA/TC/CT type was the most frequent among dimerics. Flanking primers were designed using Primer3 program and verified experimentally for PCR amplification. The results of the study are made available freely online database (http://riju.byethost31.com/cocoa/). Seven primer pairs amplified genomic DNA isolated from leaves were used to screen a representative set of 12 accessions of cacao.

show abstract

Eucalyptus microsatellites mined in silico: survey and evaluation

Cited by 32 publications

References 24 publications

Analysis of SSR loci and development of SSR primers in Eucalyptus

Analysis of SSR loci and development of SSR primers in Eucalyptus

Generation de marqueurs de séquences exprimées et développement de marqueurs microsatellites pour Castanopsis sieboldii var. sieboldii (Fagaceae)

Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools

Contact Info

Product

Resources

About