Development and characterization of Simple Sequence Repeats (SSRs) markers in durian kura-kura (Durio testudinarius Becc.) using NGS data

Abstract Durian Kura-kura (Durio testudinarius Becc.) belongs to the Malvaceae family and is an endemic species of Borneo. Recently, genomic-based next-generation sequencing (NGS) approaches have been carried out for germplasm conservation and plant breeding programs. The NGS technologies allow plant genomes to be sequenced quickly and inexpensively and enable the efficient development of SSR markers through the in-silico approaches. This study aimed to develop and characterize simple sequence repeats (SSRs) from the assembled genome. The 1203929 scaffolds of the assembled genome were produced from the Ray assembler. The SSRs were identified and extracted using the MISA program produced 4315 sequences containing SSRs. The six motif repeats of SSRs were identified; consist of 431 sequences of dinucleotide (the most motif is AT), 3257 sequences of trinucleotide (the most motif is TTA), 516 sequences of tetranucleotide (the most motif is AAAT), 89 sequences of pentanucleotide (the most motif is ATTTT), 18 sequences of hexanucleotide and four sequences of heptanucleotide. The new SSRs markers will be used in further studies of genetic population of D. testudinarius and plant breeding programs.

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DNA Fingerprinting and Characterization of some Egyptian Date Palm Cultivars Using Simple Sequence Repeats (SSRs)

Journal of Plant Production Sciences ◽

10.21608/jpps.2015.7402 ◽

2015 ◽

Vol 3 (1) ◽

pp. 31-41

Author(s):

Mohammed Hussein ◽

Samah Sabry ◽

Manal Eid

Keyword(s):

Dna Fingerprinting ◽

Simple Sequence Repeats ◽

Date Palm ◽

Simple Sequence

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Ampelographic characterization of white grapevine cul-tivars (Vitis vinifera L.) grown in Palestine

مجلة جامعة فلسطين التقنية للأبحاث ◽

10.53671/pturj.v3i1.34 ◽

2015 ◽

Vol 3 (1) ◽

pp. 1-11

Author(s):

Rezq Basheer-Salimia

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Germplasm Conservation ◽

Genetic Distances ◽

Vitis Vinifera L ◽

Similarity Matrix ◽

Breeding Programs ◽

Local Varieties ◽

Synonymies And Homonymies

Abstract: In Palestine, grape culture consists of ecotypes and cultivars (also called local varieties), for which a large number of homonymous and synonymous designations exist as well as misnaming of cultivars. The present study is the first report using detailed ampelographic characterizations (39 informative traits) to assess genetic diversity and detect similarities among sixteen accessions collected from putative diverse grape genotypes In general, 30 descriptors presented highly and satisfactory divergent genotypes, whereas the remaining traits showed no or very little ampelographic variation. Based on the similarity matrix and the resulting dendrogram of these ampelographic data, distinguishable genotypes as well as some cases of synonymies and homonymies clearly exist. A synonymy case seemed to be in four genotypes including Jandali-Mfarad, Jan-dali-Mrazraz, Jandali, and Hamadani-Mattar, which indeed showed genetic distances of less than 0.5, sug-gesting their relatedness, and the possibility that they are the same genotype, but with different names. In addition, homonym cases also occur in the following pairs of “Marawi’s, Hamadani’s, and Zaini’s genotypes, in which each pair seems to be two distinctive genotypes. Finally, among the 16 examined genotypes, the Zaini-Baladi genotype tended to show the highest genetic distance values from the others and thus could be potentially incorporated into any further local or regional breeding programs as well as germplasm conservation.

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Genetic Diversity and Characterization of a Core Collection of Malus Germplasm Using Simple Sequence Repeats (SSRs)

Plant Molecular Biology Reporter ◽

10.1007/s11105-011-0399-x ◽

2011 ◽

Vol 30 (4) ◽

pp. 827-837 ◽

Cited By ~ 35

Author(s):

Sarah M. Potts ◽

Yuepeng Han ◽

M. Awais Khan ◽

Mosbah M. Kushad ◽

A. Lane Rayburn ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Core Collection ◽

Simple Sequence

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SIMPLE SEQUENCE REPEATS (SSRS) FOR DIVERSITY CHARACTERIZATION OF GUAVA (PSIDIUM GUAJAVA L.)

Acta Horticulturae ◽

10.17660/actahortic.2010.849.17 ◽

2010 ◽

pp. 155-162 ◽

Cited By ~ 3

Author(s):

J. Valdés-Infante ◽

N.N. Rodríguez ◽

B. Velásquez ◽

D. Rivero ◽

F. Martínez ◽

...

Keyword(s):

Simple Sequence Repeats ◽

Psidium Guajava ◽

Simple Sequence

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Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics

Microorganisms ◽

10.3390/microorganisms8050662 ◽

2020 ◽

Vol 8 (5) ◽

pp. 662 ◽

Cited By ~ 1

Author(s):

Yuan Li ◽

Xiao Chen ◽

Kun Wu ◽

Jiao Pan ◽

Hongan Long ◽

...

Keyword(s):

Simple Sequence Repeats ◽

Evolutionary History ◽

Rapid Evolution ◽

Genome Diversity ◽

Unicellular Eukaryotes ◽

Genome Wide ◽

Species Analysis ◽

Simple Sequence ◽

High Diversity

Simple sequence repeats (SSRs) are prevalent in the genomes of all organisms. They are widely used as genetic markers, and are insertion/deletion mutation hotspots, which directly influence genome evolution. However, little is known about such important genomic components in ciliated protists, a large group of unicellular eukaryotes with extremely long evolutionary history and genome diversity. With recent publications of multiple ciliate genomes, we start to get a chance to explore perfect SSRs with motif size 1–100 bp and at least three motif repeats in nine species of two ciliate classes, Oligohymenophorea and Spirotrichea. We found that homopolymers are the most prevalent SSRs in these A/T-rich species, with AAA (lysine, charged amino acid; also seen as an SSR with one-adenine motif repeated three times) being the codons repeated at the highest frequencies in coding SSR regions, consistent with the widespread alveolin proteins rich in lysine repeats as found in Tetrahymena. Micronuclear SSRs are universally more abundant than the macronuclear ones of the same motif-size, except for the 8-bp-motif SSRs in extensively fragmented chromosomes. Both the abundance and A/T content of SSRs decrease as motif-size increases, while the abundance is positively correlated with the A/T content of the genome. Also, smaller genomes have lower proportions of coding SSRs out of all SSRs in Paramecium species. This genome-wide and cross-species analysis reveals the high diversity of SSRs and reflects the rapid evolution of these simple repetitive elements in ciliate genomes.

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