Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93-11 and evaluation of the two rice reference sequence assemblies

Yonglong Pan, Ying Deng, Haiyan Lin, David A Kudrna, Rod A Wing, Lijia Li, Qifa Zhang, Meizhong Luo

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Reference sequences are sequences that are used for public consultation, and therefore must be of high quality. Using the whole-genome shotgun/next-generation sequencing approach, many genome sequences of complex higher plants have been generated in recent years, and are generally considered reference sequences. However, none of these sequences has been experimentally evaluated at the whole-genome sequence assembly level. Rice has a relatively simple plant genome, and the genome sequences for its two sub-species obtained using different sequencing approaches were published approximately 10 years ago. This provides a unique system for a case study to evaluate the qualities and utilities of published plant genome sequences. We constructed a robust BAC physical map embedding a large number of BAC end sequences forrice variety 93-11. Through BAC end sequence alignments and tri-assembly comparisons of the 93-11 physical map and the two reference sequences, we found that the Nipponbare reference sequence generated using the clone-by-clone approach has a high quality but still contains small artifact inversions and missing sequences. In contrast, the 93-11 reference sequence generated using the whole-genome shotgun approach contains many large and varied assembly errors, such as inversions, duplications and translocations, as well as missing sequences. The 93-11 physical map provides an invaluable resource for evaluation and improvements toward completion of both Nipponbare and 93-11 reference sequences.

Original languageEnglish (US)
Pages (from-to)795-805
Number of pages11
JournalPlant Journal
Volume77
Issue number5
DOIs
StatePublished - Mar 2014

Fingerprint

physical chromosome mapping
Oryza sativa
Genome
rice
genome
Plant Genome
Firearms
Clone Cells
Sequence Inversion
clones
Sequence Alignment
genome assembly
Artifacts
sequence alignment
Referral and Consultation
Oryza
case studies

Keywords

  • 93-11
  • BAC
  • Nipponbare
  • physical map
  • reference sequence
  • rice
  • technical advance

ASJC Scopus subject areas

  • Plant Science
  • Cell Biology
  • Genetics
  • Medicine(all)

Cite this

Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93-11 and evaluation of the two rice reference sequence assemblies. / Pan, Yonglong; Deng, Ying; Lin, Haiyan; Kudrna, David A; Wing, Rod A; Li, Lijia; Zhang, Qifa; Luo, Meizhong.

In: Plant Journal, Vol. 77, No. 5, 03.2014, p. 795-805.

Research output: Contribution to journalArticle

Pan, Yonglong ; Deng, Ying ; Lin, Haiyan ; Kudrna, David A ; Wing, Rod A ; Li, Lijia ; Zhang, Qifa ; Luo, Meizhong. / Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93-11 and evaluation of the two rice reference sequence assemblies. In: Plant Journal. 2014 ; Vol. 77, No. 5. pp. 795-805.
@article{f118f15eb00849718f89069245fed56f,
title = "Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93-11 and evaluation of the two rice reference sequence assemblies",
abstract = "Reference sequences are sequences that are used for public consultation, and therefore must be of high quality. Using the whole-genome shotgun/next-generation sequencing approach, many genome sequences of complex higher plants have been generated in recent years, and are generally considered reference sequences. However, none of these sequences has been experimentally evaluated at the whole-genome sequence assembly level. Rice has a relatively simple plant genome, and the genome sequences for its two sub-species obtained using different sequencing approaches were published approximately 10 years ago. This provides a unique system for a case study to evaluate the qualities and utilities of published plant genome sequences. We constructed a robust BAC physical map embedding a large number of BAC end sequences forrice variety 93-11. Through BAC end sequence alignments and tri-assembly comparisons of the 93-11 physical map and the two reference sequences, we found that the Nipponbare reference sequence generated using the clone-by-clone approach has a high quality but still contains small artifact inversions and missing sequences. In contrast, the 93-11 reference sequence generated using the whole-genome shotgun approach contains many large and varied assembly errors, such as inversions, duplications and translocations, as well as missing sequences. The 93-11 physical map provides an invaluable resource for evaluation and improvements toward completion of both Nipponbare and 93-11 reference sequences.",
keywords = "93-11, BAC, Nipponbare, physical map, reference sequence, rice, technical advance",
author = "Yonglong Pan and Ying Deng and Haiyan Lin and Kudrna, {David A} and Wing, {Rod A} and Lijia Li and Qifa Zhang and Meizhong Luo",
year = "2014",
month = "3",
doi = "10.1111/tpj.12412",
language = "English (US)",
volume = "77",
pages = "795--805",
journal = "Plant Journal",
issn = "0960-7412",
publisher = "Wiley-Blackwell",
number = "5",

}

TY - JOUR

T1 - Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93-11 and evaluation of the two rice reference sequence assemblies

AU - Pan, Yonglong

AU - Deng, Ying

AU - Lin, Haiyan

AU - Kudrna, David A

AU - Wing, Rod A

AU - Li, Lijia

AU - Zhang, Qifa

AU - Luo, Meizhong

PY - 2014/3

Y1 - 2014/3

N2 - Reference sequences are sequences that are used for public consultation, and therefore must be of high quality. Using the whole-genome shotgun/next-generation sequencing approach, many genome sequences of complex higher plants have been generated in recent years, and are generally considered reference sequences. However, none of these sequences has been experimentally evaluated at the whole-genome sequence assembly level. Rice has a relatively simple plant genome, and the genome sequences for its two sub-species obtained using different sequencing approaches were published approximately 10 years ago. This provides a unique system for a case study to evaluate the qualities and utilities of published plant genome sequences. We constructed a robust BAC physical map embedding a large number of BAC end sequences forrice variety 93-11. Through BAC end sequence alignments and tri-assembly comparisons of the 93-11 physical map and the two reference sequences, we found that the Nipponbare reference sequence generated using the clone-by-clone approach has a high quality but still contains small artifact inversions and missing sequences. In contrast, the 93-11 reference sequence generated using the whole-genome shotgun approach contains many large and varied assembly errors, such as inversions, duplications and translocations, as well as missing sequences. The 93-11 physical map provides an invaluable resource for evaluation and improvements toward completion of both Nipponbare and 93-11 reference sequences.

AB - Reference sequences are sequences that are used for public consultation, and therefore must be of high quality. Using the whole-genome shotgun/next-generation sequencing approach, many genome sequences of complex higher plants have been generated in recent years, and are generally considered reference sequences. However, none of these sequences has been experimentally evaluated at the whole-genome sequence assembly level. Rice has a relatively simple plant genome, and the genome sequences for its two sub-species obtained using different sequencing approaches were published approximately 10 years ago. This provides a unique system for a case study to evaluate the qualities and utilities of published plant genome sequences. We constructed a robust BAC physical map embedding a large number of BAC end sequences forrice variety 93-11. Through BAC end sequence alignments and tri-assembly comparisons of the 93-11 physical map and the two reference sequences, we found that the Nipponbare reference sequence generated using the clone-by-clone approach has a high quality but still contains small artifact inversions and missing sequences. In contrast, the 93-11 reference sequence generated using the whole-genome shotgun approach contains many large and varied assembly errors, such as inversions, duplications and translocations, as well as missing sequences. The 93-11 physical map provides an invaluable resource for evaluation and improvements toward completion of both Nipponbare and 93-11 reference sequences.

KW - 93-11

KW - BAC

KW - Nipponbare

KW - physical map

KW - reference sequence

KW - rice

KW - technical advance

UR - http://www.scopus.com/inward/record.url?scp=84896718165&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84896718165&partnerID=8YFLogxK

U2 - 10.1111/tpj.12412

DO - 10.1111/tpj.12412

M3 - Article

C2 - 24330235

AN - SCOPUS:84896718165

VL - 77

SP - 795

EP - 805

JO - Plant Journal

JF - Plant Journal

SN - 0960-7412

IS - 5

ER -