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Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding

BACKGROUND: Bottle gourd [Lagenaria siceraria (Mol.) Standl.] is an important cucurbit crop worldwide. Archaeological research indicates that bottle gourd was domesticated more than 10,000 years ago, making it one of the earliest plants cultivated by man. In spite of its widespread importance and lo...

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Autores principales: Xu, Pei, Wu, Xiaohua, Luo, Jie, Wang, Baogen, Liu, Yonghua, Ehlers, Jeffrey D, Wang, Sha, Lu, Zhongfu, Li, Guojing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188536/
https://www.ncbi.nlm.nih.gov/pubmed/21942996
http://dx.doi.org/10.1186/1471-2164-12-467
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author Xu, Pei
Wu, Xiaohua
Luo, Jie
Wang, Baogen
Liu, Yonghua
Ehlers, Jeffrey D
Wang, Sha
Lu, Zhongfu
Li, Guojing
author_facet Xu, Pei
Wu, Xiaohua
Luo, Jie
Wang, Baogen
Liu, Yonghua
Ehlers, Jeffrey D
Wang, Sha
Lu, Zhongfu
Li, Guojing
author_sort Xu, Pei
collection PubMed
description BACKGROUND: Bottle gourd [Lagenaria siceraria (Mol.) Standl.] is an important cucurbit crop worldwide. Archaeological research indicates that bottle gourd was domesticated more than 10,000 years ago, making it one of the earliest plants cultivated by man. In spite of its widespread importance and long history of cultivation almost nothing has been known about the genome of this species thus far. RESULTS: We report here the partial sequencing of bottle gourd genome using the 454 GS-FLX Titanium sequencing platform. A total of 150,253 sequence reads, which were assembled into 3,994 contigs and 82,522 singletons were generated. The total length of the non-redundant singletons/assemblies is 32 Mb, theoretically covering ~ 10% of the bottle gourd genome. Functional annotation of the sequences revealed a broad range of functional types, covering all the three top-level ontologies. Comparison of the gene sequences between bottle gourd and the model cucurbit cucumber (Cucumis sativus) revealed a 90% sequence similarity on average. Using the sequence information, 4395 microsatellite-containing sequences were identified and 400 SSR markers were developed, of which 94% amplified bands of anticipated sizes. Transferability of these markers to four other cucurbit species showed obvious decline with increasing phylogenetic distance. From analyzing polymorphisms of a subset of 14 SSR markers assayed on 44 representative China bottle gourd varieties/landraces, a principal coordinates (PCo) analysis output and a UPGMA-based dendrogram were constructed. Bottle gourd accessions tended to group by fruit shape rather than geographic origin, although in certain subclades the lines from the same or close origin did tend to cluster. CONCLUSIONS: This work provides an initial basis for genome characterization, gene isolation and comparative genomics analysis in bottle gourd. The SSR markers developed would facilitate marker assisted breeding schemes for efficient introduction of desired traits.
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spelling pubmed-31885362011-10-07 Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding Xu, Pei Wu, Xiaohua Luo, Jie Wang, Baogen Liu, Yonghua Ehlers, Jeffrey D Wang, Sha Lu, Zhongfu Li, Guojing BMC Genomics Research Article BACKGROUND: Bottle gourd [Lagenaria siceraria (Mol.) Standl.] is an important cucurbit crop worldwide. Archaeological research indicates that bottle gourd was domesticated more than 10,000 years ago, making it one of the earliest plants cultivated by man. In spite of its widespread importance and long history of cultivation almost nothing has been known about the genome of this species thus far. RESULTS: We report here the partial sequencing of bottle gourd genome using the 454 GS-FLX Titanium sequencing platform. A total of 150,253 sequence reads, which were assembled into 3,994 contigs and 82,522 singletons were generated. The total length of the non-redundant singletons/assemblies is 32 Mb, theoretically covering ~ 10% of the bottle gourd genome. Functional annotation of the sequences revealed a broad range of functional types, covering all the three top-level ontologies. Comparison of the gene sequences between bottle gourd and the model cucurbit cucumber (Cucumis sativus) revealed a 90% sequence similarity on average. Using the sequence information, 4395 microsatellite-containing sequences were identified and 400 SSR markers were developed, of which 94% amplified bands of anticipated sizes. Transferability of these markers to four other cucurbit species showed obvious decline with increasing phylogenetic distance. From analyzing polymorphisms of a subset of 14 SSR markers assayed on 44 representative China bottle gourd varieties/landraces, a principal coordinates (PCo) analysis output and a UPGMA-based dendrogram were constructed. Bottle gourd accessions tended to group by fruit shape rather than geographic origin, although in certain subclades the lines from the same or close origin did tend to cluster. CONCLUSIONS: This work provides an initial basis for genome characterization, gene isolation and comparative genomics analysis in bottle gourd. The SSR markers developed would facilitate marker assisted breeding schemes for efficient introduction of desired traits. BioMed Central 2011-09-27 /pmc/articles/PMC3188536/ /pubmed/21942996 http://dx.doi.org/10.1186/1471-2164-12-467 Text en Copyright ©2011 Xu et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Xu, Pei
Wu, Xiaohua
Luo, Jie
Wang, Baogen
Liu, Yonghua
Ehlers, Jeffrey D
Wang, Sha
Lu, Zhongfu
Li, Guojing
Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding
title Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding
title_full Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding
title_fullStr Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding
title_full_unstemmed Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding
title_short Partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding
title_sort partial sequencing of the bottle gourd genome reveals markers useful for phylogenetic analysis and breeding
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188536/
https://www.ncbi.nlm.nih.gov/pubmed/21942996
http://dx.doi.org/10.1186/1471-2164-12-467
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