Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses.

<h4>Background</h4>The isochore, a large DNA sequence with relatively small GC variance, is one of the most important structures in eukaryotic genomes. Although the isochore has been widely studied in humans and other species, little is known about its distribution in pigs.<h4>Prin...

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Autores principales:	Wenqian Zhang, Wenwu Wu, Wenchao Lin, Pengfang Zhou, Li Dai, Yang Zhang, Jingfei Huang, Deli Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0bde72470b4c440c8892598cce3c8e64
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spelling	oai:doaj.org-article:0bde72470b4c440c8892598cce3c8e642021-11-18T07:03:31ZDeciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses.1932-620310.1371/journal.pone.0013303https://doaj.org/article/0bde72470b4c440c8892598cce3c8e642010-10-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20948965/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>The isochore, a large DNA sequence with relatively small GC variance, is one of the most important structures in eukaryotic genomes. Although the isochore has been widely studied in humans and other species, little is known about its distribution in pigs.<h4>Principal findings</h4>In this paper, we construct a map of long homogeneous genome regions (LHGRs), i.e., isochores and isochore-like regions, in pigs to provide an intuitive version of GC heterogeneity in each chromosome. The LHGR pattern study not only quantifies heterogeneities, but also reveals some primary characteristics of the chromatin organization, including the followings: (1) the majority of LHGRs belong to GC-poor families and are in long length; (2) a high gene density tends to occur with the appearance of GC-rich LHGRs; and (3) the density of LINE repeats decreases with an increase in the GC content of LHGRs. Furthermore, a portion of LHGRs with particular GC ranges (50%-51% and 54%-55%) tend to have abnormally high gene densities, suggesting that biased gene conversion (BGC), as well as time- and energy-saving principles, could be of importance to the formation of genome organization.<h4>Conclusion</h4>This study significantly improves our knowledge of chromatin organization in the pig genome. Correlations between the different biological features (e.g., gene density and repeat density) and GC content of LHGRs provide a unique glimpse of in silico gene and repeats prediction.Wenqian ZhangWenwu WuWenchao LinPengfang ZhouLi DaiYang ZhangJingfei HuangDeli ZhangPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 10, p e13303 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wenqian Zhang Wenwu Wu Wenchao Lin Pengfang Zhou Li Dai Yang Zhang Jingfei Huang Deli Zhang Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses.
description	<h4>Background</h4>The isochore, a large DNA sequence with relatively small GC variance, is one of the most important structures in eukaryotic genomes. Although the isochore has been widely studied in humans and other species, little is known about its distribution in pigs.<h4>Principal findings</h4>In this paper, we construct a map of long homogeneous genome regions (LHGRs), i.e., isochores and isochore-like regions, in pigs to provide an intuitive version of GC heterogeneity in each chromosome. The LHGR pattern study not only quantifies heterogeneities, but also reveals some primary characteristics of the chromatin organization, including the followings: (1) the majority of LHGRs belong to GC-poor families and are in long length; (2) a high gene density tends to occur with the appearance of GC-rich LHGRs; and (3) the density of LINE repeats decreases with an increase in the GC content of LHGRs. Furthermore, a portion of LHGRs with particular GC ranges (50%-51% and 54%-55%) tend to have abnormally high gene densities, suggesting that biased gene conversion (BGC), as well as time- and energy-saving principles, could be of importance to the formation of genome organization.<h4>Conclusion</h4>This study significantly improves our knowledge of chromatin organization in the pig genome. Correlations between the different biological features (e.g., gene density and repeat density) and GC content of LHGRs provide a unique glimpse of in silico gene and repeats prediction.
format	article
author	Wenqian Zhang Wenwu Wu Wenchao Lin Pengfang Zhou Li Dai Yang Zhang Jingfei Huang Deli Zhang
author_facet	Wenqian Zhang Wenwu Wu Wenchao Lin Pengfang Zhou Li Dai Yang Zhang Jingfei Huang Deli Zhang
author_sort	Wenqian Zhang
title	Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses.
title_short	Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses.
title_full	Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses.
title_fullStr	Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses.
title_full_unstemmed	Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses.
title_sort	deciphering heterogeneity in pig genome assembly sscrofa9 by isochore and isochore-like region analyses.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/0bde72470b4c440c8892598cce3c8e64
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Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses.

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