Genome-wide characterization of simple sequence repeats in Palmae genomes

Manee, Manee M.; Al-Shomrani, Badr M.; Al-Fageeh, Mohamed B.

doi:10.1007/s13258-020-00924-w

Cited by 9 publications

(11 citation statements)

References 37 publications

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“…Six classes of perfect SSRs were evaluated (from mono-to hexanucleotide) for their abundance in the assembled genome. Dinucleotides were the most abundant, in accordance with what has been previously reported in literature [30][31][32][33][34][35][36][37][38][39], representing 60.2% of the identified SSRs. Trinucleotides were the second most abundant class (23.7%), followed by tetranucleotides (6.8%).…”

Section: The Ssr Content Of the Poppy Anemone Draft Genomesupporting

confidence: 91%

Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

Martina

Acquadro

Barchi

et al. 2022

IJMS

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Anemone coronaria L. (2n = 2x = 16) is a perennial, allogamous, highly heterozygous plant marketed as a cut flower or in gardens. Due to its large genome size, limited efforts have been made in order to develop species-specific molecular markers. We obtained the first draft genome of the species by Illumina sequencing an androgenetic haploid plant of the commercial line “MISTRAL® Magenta”. The genome assembly was obtained by applying the MEGAHIT pipeline and consisted of 2 × 106 scaffolds. The SciRoKo SSR (Simple Sequence Repeats)-search module identified 401.822 perfect and 188.987 imperfect microsatellites motifs. Following, we developed a user-friendly “Anemone coronaria Microsatellite DataBase” (AnCorDB), which incorporates the Primer3 script, making it possible to design couples of primers for downstream application of the identified SSR markers. Eight genotypes belonging to eight cultivars were used to validate 62 SSRs and a subset of markers was applied for fingerprinting each cultivar, as well as to assess their intra-cultivar variability. The newly developed microsatellite markers will find application in Breeding Rights disputes, developing genetic maps, marker assisted breeding (MAS) strategies, as well as phylogenetic studies.

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Section: The Ssr Content Of the Poppy Anemone Draft Genomesupporting

confidence: 91%

Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

Martina

Acquadro

Barchi

et al. 2022

IJMS

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“…Our findings suggest that in weevils, the number of SSRs is significantly positively correlated with genome size; this is inconsistent with the results reported in [ 35 , 42 ]. Nonetheless, a study reported that the number of SSRs was significantly associated with genome size in 136 insects [ 43 ], which agrees with our results.…”

Section: Discussioncontrasting

confidence: 99%

“…This finding is consistent with previous reports that mono- to trinucleotide SSR repeats are more frequent in 23 mosquito species [ 44 ] and six plant species [ 45 ]. Meanwhile, tetra- to hexanucleotide SSRs were the least frequent types in these draft genomes, an observation similar to what has been found in Palmae genomes [ 35 ] and Gossypium species [ 46 ]. More specifically, we observed dinucleotide SSRs to be the most frequent repeat type in R. ferrugineus and I. nitidus , consistent with dicotyledons [ 47 ] and Drosophila [ 14 ].…”

Section: Discussionsupporting

confidence: 82%

“…SSR repeat content differs between species, which might be a general phenomenon across taxa [ 33 ]. Previous studies reported SSRs to comprise 3% of the human genome [ 34 ], 0.04–0.44% of plant and fungal genomes [ 35 , 36 , 37 ], and 0.44–0.88% of primate genomes [ 22 , 38 ]. Here, our results showed that identified SSRs differ with the degree of coverage and comprise 0.02–1.44% of the draft genomes for these nine weevil species.…”

Section: Discussionmentioning

confidence: 99%

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Microsatellite Variation in the Most Devastating Beetle Pests (Coleoptera: Curculionidae) of Agricultural and Forest Crops

Manee

Al-Shomrani

Altammami

et al. 2022

IJMS

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Weevils, classified in the family Curculionidae (true weevils), constitute a group of phytophagous insects of which many species are considered significant pests of crops. Within this family, the red palm weevil (RPW), Rhynchophorus ferrugineus, has an integral role in destroying crops and has invaded all countries of the Middle East and many in North Africa, Southern Europe, Southeast Asia, Oceania, and the Caribbean Islands. Simple sequence repeats (SSRs), also termed microsatellites, have become the DNA marker technology most applied to study population structure, evolution, and genetic diversity. Although these markers have been widely examined in many mammalian and plant species, and draft genome assemblies are available for many species of true weevils, very little is yet known about SSRs in weevil genomes. Here we carried out a comparative analysis examining and comparing the relative abundance, relative density, and GC content of SSRs in previously sequenced draft genomes of nine true weevils, with an emphasis on R. ferrugineus. We also used Illumina paired-end sequencing to generate draft sequence for adult female RPW and characterized it in terms of perfect SSRs with 1–6 bp nucleotide motifs. Among weevil genomes, mono- to trinucleotide SSRs were the most frequent, and mono-, di-, and hexanucleotide SSRs exhibited the highest GC content. In these draft genomes, SSR number and genome size were significantly correlated. This work will aid our understanding of the genome architecture and evolution of Curculionidae weevils and facilitate exploring SSR molecular marker development in these species.

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“…Eukaryotic genomes are known to be densely populated with different types of repetitive elements, including tandem repeats [1] and transposable elements (TEs) [2]. TEs were first characterized in plant genomes over 65 years ago by B. McClintock, who discovered genes that move from one chromosome to another and, in so doing, affect the phenotype of the host organism [3,4].…”

Section: Introductionmentioning

confidence: 99%