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De novo assembly of a wild pear (Pyrus betuleafolia) genome

China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia‐Shanxi Duli using an integrated strate...

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Autores principales: Dong, Xingguang, Wang, Zheng, Tian, Luming, Zhang, Ying, Qi, Dan, Huo, Hongliang, Xu, Jiayu, Li, Zhe, Liao, Rui, Shi, Miao, Wahocho, Safdar Ali, Liu, Chao, Zhang, Simeng, Tian, Zhixi, Cao, Yufen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6953202/
https://www.ncbi.nlm.nih.gov/pubmed/31368610
http://dx.doi.org/10.1111/pbi.13226
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author Dong, Xingguang
Wang, Zheng
Tian, Luming
Zhang, Ying
Qi, Dan
Huo, Hongliang
Xu, Jiayu
Li, Zhe
Liao, Rui
Shi, Miao
Wahocho, Safdar Ali
Liu, Chao
Zhang, Simeng
Tian, Zhixi
Cao, Yufen
author_facet Dong, Xingguang
Wang, Zheng
Tian, Luming
Zhang, Ying
Qi, Dan
Huo, Hongliang
Xu, Jiayu
Li, Zhe
Liao, Rui
Shi, Miao
Wahocho, Safdar Ali
Liu, Chao
Zhang, Simeng
Tian, Zhixi
Cao, Yufen
author_sort Dong, Xingguang
collection PubMed
description China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia‐Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi‐C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein‐coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide‐binding site (NBS)‐type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR‐NBS‐LRR (TNL)‐type genes, which represented the greatest number of TNL‐type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism‐related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high‐quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.
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spelling pubmed-69532022020-01-14 De novo assembly of a wild pear (Pyrus betuleafolia) genome Dong, Xingguang Wang, Zheng Tian, Luming Zhang, Ying Qi, Dan Huo, Hongliang Xu, Jiayu Li, Zhe Liao, Rui Shi, Miao Wahocho, Safdar Ali Liu, Chao Zhang, Simeng Tian, Zhixi Cao, Yufen Plant Biotechnol J Research Articles China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia‐Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi‐C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein‐coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide‐binding site (NBS)‐type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR‐NBS‐LRR (TNL)‐type genes, which represented the greatest number of TNL‐type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism‐related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high‐quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding. John Wiley and Sons Inc. 2019-08-12 2020-02 /pmc/articles/PMC6953202/ /pubmed/31368610 http://dx.doi.org/10.1111/pbi.13226 Text en © 2019 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle Research Articles
Dong, Xingguang
Wang, Zheng
Tian, Luming
Zhang, Ying
Qi, Dan
Huo, Hongliang
Xu, Jiayu
Li, Zhe
Liao, Rui
Shi, Miao
Wahocho, Safdar Ali
Liu, Chao
Zhang, Simeng
Tian, Zhixi
Cao, Yufen
De novo assembly of a wild pear (Pyrus betuleafolia) genome
title De novo assembly of a wild pear (Pyrus betuleafolia) genome
title_full De novo assembly of a wild pear (Pyrus betuleafolia) genome
title_fullStr De novo assembly of a wild pear (Pyrus betuleafolia) genome
title_full_unstemmed De novo assembly of a wild pear (Pyrus betuleafolia) genome
title_short De novo assembly of a wild pear (Pyrus betuleafolia) genome
title_sort de novo assembly of a wild pear (pyrus betuleafolia) genome
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6953202/
https://www.ncbi.nlm.nih.gov/pubmed/31368610
http://dx.doi.org/10.1111/pbi.13226
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