Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)

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	Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)
	Zhang, Li-Na 1,2,3; Zhang, Xian-Zhi1,2,3 ; Zhang, Yu-Xiao 1,2; Zeng, Chun-Xia 2; Ma, Peng-Fei 1,2; Zhao, Lei 2; Guo, Zhen-Hua2 ; Li, De-Zhu1,2
刊名	MOLECULAR ECOLOGY RESOURCES
	2014-09-01
卷号	14 期号:5 页码:988-999
关键词	Arundinarieae Fargesia orthologous genes Phyllostachys phylogeny
ISSN号	1755-098X
通讯作者	Li, DZ (reprint author), Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Div & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China. ; dzl@mail.kib.ac.cn
产权排序	第一
英文摘要	The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared with nuclear data. In this study, we intended to identify a set of desirable nuclear genes for resolving the phylogeny of the temperate woody bamboos. Using two different methodologies, we identified 209 and 916 genes, respectively, as putative single copy orthologous genes. A total of 112 genes was successfully amplified and sequenced by next-generation sequencing technologies in five species sampled from the tribe. As most of the genes exhibited intra-individual allele heterozygotes, we investigated phylogenetic utility by reconstructing the phylogeny based on individual genes. Discordance among gene trees was observed and, to resolve the conflict, we performed a range of analyses using BUCKy and HybTree. While caution should be taken when inferring a phylogeny from multiple conflicting genes, our analysis indicated that 74 of the 112 investigated genes are potential markers for resolving the phylogeny of the temperate woody bamboos.
学科主题	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
类目[WOS]	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
研究领域[WOS]	Biochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
关键词[WOS]	COPY NUCLEAR GENES ; SPECIES TREES ; AGGLOMERATIVE METHOD ; EUKARYOTIC GENOMES ; GBSSI GENE ; SEQUENCES ; INCONGRUENCE ; EVOLUTION ; NETWORKS ; UTILITY
收录类别	SCI
资助信息	National Natural Science Foundation of China [31100148, 30990244, U1136603]; Yunnan Provincial Government
语种	英语
WOS记录号	WOS:000340425100010
公开日期	2014-10-11
内容类型	期刊论文
源URL	[http://ir.kib.ac.cn/handle/151853/18318]
专题	昆明植物研究所_中国西南野生生物种质资源库
作者单位	1.Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Div & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China 2.Chinese Acad Sci, Kunming Inst Bot, Plant Germplasm & Genom Ctr, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China 3.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Li-Na,Zhang, Xian-Zhi,Zhang, Yu-Xiao,et al. Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)[J]. MOLECULAR ECOLOGY RESOURCES,2014,14(5):988-999.
APA	Zhang, Li-Na.,Zhang, Xian-Zhi.,Zhang, Yu-Xiao.,Zeng, Chun-Xia.,Ma, Peng-Fei.,...&Li, De-Zhu.(2014).Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae).MOLECULAR ECOLOGY RESOURCES,14(5),988-999.
MLA	Zhang, Li-Na,et al."Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)".MOLECULAR ECOLOGY RESOURCES 14.5(2014):988-999.