RiTE database: A resource database for genus-wide rice genomics and evolutionary biology

Dario Copetti; Jianwei Zhang; Moaine El Baidouri; Dongying Gao; Jun Wang; Elena Barghini; Rosa M. Cossu; Angelina Angelova; Carlos E. Maldonado L.; Stefan Roffler; Hajime Ohyanagi; Thomas Wicker; Chuanzhu Fan; Andrea Zuccolo; Mingsheng Chen; Antonio Costa de Oliveira; Bin Han; Robert Henry; Yue ie Hsing; Nori Kurata; Wen Wang; Scott A. Jackson; Olivier Panaud; Rod A. Wing

doi:10.1186/s12864-015-1762-3

RiTE database: A resource database for genus-wide rice genomics and evolutionary biology

Dario Copetti, Jianwei Zhang, Moaine El Baidouri, Dongying Gao, Jun Wang, Elena Barghini, Rosa M. Cossu, Angelina Angelova, Carlos E. Maldonado L., Stefan Roffler, Hajime Ohyanagi, Thomas Wicker, Chuanzhu Fan, Andrea Zuccolo, Mingsheng Chen, Antonio Costa de Oliveira, Bin Han, Robert Henry, Yue ie Hsing, Nori KurataWen Wang, Scott A. Jackson, Olivier Panaud, Rod A. Wing

Research output: Contribution to journal › Article › peer-review

57 Scopus citations

Abstract

Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. Results: Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. Conclusions: This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.

Original language	English (US)
Journal	BMC Genomics
Volume	16
Issue number	1
DOIs	https://doi.org/10.1186/s12864-015-1762-3
State	Published - Jul 22 2015
Externally published	Yes

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Copetti, D., Zhang, J., El Baidouri, M., Gao, D., Wang, J., Barghini, E., Cossu, R. M., Angelova, A., Maldonado L., C. E., Roffler, S., Ohyanagi, H., Wicker, T., Fan, C., Zuccolo, A., Chen, M., Costa de Oliveira, A., Han, B., Henry, R., Hsing, Y. I., ... Wing, R. A. (2015). RiTE database: A resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics, 16(1). https://doi.org/10.1186/s12864-015-1762-3

@article{a4f2df347b6f48668da5ec5a7da4bc37,

title = "RiTE database: A resource database for genus-wide rice genomics and evolutionary biology",

abstract = "Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. Results: Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. Conclusions: This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.",

author = "Dario Copetti and Jianwei Zhang and {El Baidouri}, Moaine and Dongying Gao and Jun Wang and Elena Barghini and Cossu, {Rosa M.} and Angelina Angelova and {Maldonado L.}, {Carlos E.} and Stefan Roffler and Hajime Ohyanagi and Thomas Wicker and Chuanzhu Fan and Andrea Zuccolo and Mingsheng Chen and {Costa de Oliveira}, Antonio and Bin Han and Robert Henry and Hsing, {Yue ie} and Nori Kurata and Wen Wang and Jackson, {Scott A.} and Olivier Panaud and Wing, {Rod A.}",

note = "Generated from Scopus record by KAUST IRTS on 2019-11-20",

year = "2015",

month = jul,

day = "22",

doi = "10.1186/s12864-015-1762-3",

language = "English (US)",

volume = "16",

journal = "BMC Genomics",

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Copetti, D, Zhang, J, El Baidouri, M, Gao, D, Wang, J, Barghini, E, Cossu, RM, Angelova, A, Maldonado L., CE, Roffler, S, Ohyanagi, H, Wicker, T, Fan, C, Zuccolo, A, Chen, M, Costa de Oliveira, A, Han, B, Henry, R, Hsing, YI, Kurata, N, Wang, W, Jackson, SA, Panaud, O & Wing, RA 2015, 'RiTE database: A resource database for genus-wide rice genomics and evolutionary biology', BMC Genomics, vol. 16, no. 1. https://doi.org/10.1186/s12864-015-1762-3

TY - JOUR

T1 - RiTE database: A resource database for genus-wide rice genomics and evolutionary biology

AU - Copetti, Dario

AU - Zhang, Jianwei

AU - El Baidouri, Moaine

AU - Gao, Dongying

AU - Wang, Jun

AU - Barghini, Elena

AU - Cossu, Rosa M.

AU - Angelova, Angelina

AU - Maldonado L., Carlos E.

AU - Roffler, Stefan

AU - Ohyanagi, Hajime

AU - Wicker, Thomas

AU - Fan, Chuanzhu

AU - Zuccolo, Andrea

AU - Chen, Mingsheng

AU - Costa de Oliveira, Antonio

AU - Han, Bin

AU - Henry, Robert

AU - Hsing, Yue ie

AU - Kurata, Nori

AU - Wang, Wen

AU - Jackson, Scott A.

AU - Panaud, Olivier

AU - Wing, Rod A.

N1 - Generated from Scopus record by KAUST IRTS on 2019-11-20

PY - 2015/7/22

Y1 - 2015/7/22

N2 - Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. Results: Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. Conclusions: This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.

AB - Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. Results: Here we present the Rice TE database (RiTE-db) - a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. Conclusions: This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.

UR - http://www.biomedcentral.com/1471-2164/16/538

UR - http://www.scopus.com/inward/record.url?scp=84937232446&partnerID=8YFLogxK

U2 - 10.1186/s12864-015-1762-3

DO - 10.1186/s12864-015-1762-3

M3 - Article

SN - 1471-2164

VL - 16

JO - BMC Genomics

JF - BMC Genomics

IS - 1

ER -

RiTE database: A resource database for genus-wide rice genomics and evolutionary biology

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