A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops

Microsatellites, or simple sequences repeat (SSRs), are distributed in genes, intergenic regions and transposable elements in the genome. SSRs were identified for developing markers from draft genome assemblies, transcriptome sequences and genome survey sequences in plant and animals. The identifica...

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Autores principales:	Manosh Kumar Biswas, Dhiman Biswas, Mita Bagchi, Ganjun Yi, Guiming Deng
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	microsatellite microRNA pre-miRNA simple sequence repeat marker database legumes Agriculture S
Acceso en línea:	https://doaj.org/article/43b9ebe7422e4d1b96ff6ba48406c54b
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id	oai:doaj.org-article:43b9ebe7422e4d1b96ff6ba48406c54b
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spelling	oai:doaj.org-article:43b9ebe7422e4d1b96ff6ba48406c54b2021-11-25T16:10:44ZA Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops10.3390/agronomy111122982073-4395https://doaj.org/article/43b9ebe7422e4d1b96ff6ba48406c54b2021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4395/11/11/2298https://doaj.org/toc/2073-4395Microsatellites, or simple sequences repeat (SSRs), are distributed in genes, intergenic regions and transposable elements in the genome. SSRs were identified for developing markers from draft genome assemblies, transcriptome sequences and genome survey sequences in plant and animals. The identification, distribution, and density of microsatellites in pre-microRNAs (miRNAs) are not well documented in plants. In this study, SSRs were identified in 16,892 pre-miRNA sequences from 292 plant species in six taxonomic groups (algae to dicots). Fifty-one percent of pre-miRNA sequences contained SSRs. Mononucleotide repeats were the most abundant, followed by di- and trinucleotide repeats. Tetra-, penta-, and hexarepeats were rare. A total of 9,498 (57.46%) microsatellite loci had potential as pre-miRNA SSR markers. Of the markers, 3,573 (37.62%) were non-redundant, and 2,341 (65.51%) primer pairs could be transferred to at least one of the plant taxonomic groups. All data and primer pairs were deposited in a user-friendly, freely accessible plant miRNA SSR marker database. The data presented in this study, accelerate the understanding of pre-miRNA evolution and serve as valuable genomic treasure for genetic improvements in a wide range of crops, including legumes, cereals, and cruciferous crops.Manosh Kumar BiswasDhiman BiswasMita BagchiGanjun YiGuiming DengMDPI AGarticlemicrosatellitemicroRNApre-miRNAsimple sequence repeatmarker databaselegumesAgricultureSENAgronomy, Vol 11, Iss 2298, p 2298 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	microsatellite microRNA pre-miRNA simple sequence repeat marker database legumes Agriculture S
spellingShingle	microsatellite microRNA pre-miRNA simple sequence repeat marker database legumes Agriculture S Manosh Kumar Biswas Dhiman Biswas Mita Bagchi Ganjun Yi Guiming Deng A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops
description	Microsatellites, or simple sequences repeat (SSRs), are distributed in genes, intergenic regions and transposable elements in the genome. SSRs were identified for developing markers from draft genome assemblies, transcriptome sequences and genome survey sequences in plant and animals. The identification, distribution, and density of microsatellites in pre-microRNAs (miRNAs) are not well documented in plants. In this study, SSRs were identified in 16,892 pre-miRNA sequences from 292 plant species in six taxonomic groups (algae to dicots). Fifty-one percent of pre-miRNA sequences contained SSRs. Mononucleotide repeats were the most abundant, followed by di- and trinucleotide repeats. Tetra-, penta-, and hexarepeats were rare. A total of 9,498 (57.46%) microsatellite loci had potential as pre-miRNA SSR markers. Of the markers, 3,573 (37.62%) were non-redundant, and 2,341 (65.51%) primer pairs could be transferred to at least one of the plant taxonomic groups. All data and primer pairs were deposited in a user-friendly, freely accessible plant miRNA SSR marker database. The data presented in this study, accelerate the understanding of pre-miRNA evolution and serve as valuable genomic treasure for genetic improvements in a wide range of crops, including legumes, cereals, and cruciferous crops.
format	article
author	Manosh Kumar Biswas Dhiman Biswas Mita Bagchi Ganjun Yi Guiming Deng
author_facet	Manosh Kumar Biswas Dhiman Biswas Mita Bagchi Ganjun Yi Guiming Deng
author_sort	Manosh Kumar Biswas
title	A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops
title_short	A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops
title_full	A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops
title_fullStr	A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops
title_full_unstemmed	A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops
title_sort	comprehensive plant microrna simple sequence repeat marker database to accelerate genetic improvements in crops
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/43b9ebe7422e4d1b96ff6ba48406c54b
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A Comprehensive Plant microRNA Simple Sequence Repeat Marker Database to Accelerate Genetic Improvements in Crops

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