De novo transcriptome analysis of the rare fern Monachosorum maximowiczii (Dennstaedtiaceae) endemic to East Asia

doi:10.17520/biods.2016231

Abstract

Abstract:

Monachosorum maximowiczii, which belongs to the family Dennstaedtiaceae, is a unique fern rarely distributed in the middle-high altitudinal areas in East Asia. In order to identify the molecular basis of this species at the transcriptome level, a second generation sequencing technology (RNA-seq) was employed here for the first time. Using Illumina Hiseq 2500 platform, a total of 4.95 Gb raw data were obtained. After filtration, 4.83 Gb clean reads were kept and 101,448 unigene were generated using de novo assembly. Among them, 54,106 unigene were predicted to have a complete open reading frame. The functional annotation of the unigene obtained here was carried out using the Phytozome v11.0 databases. The gene function pattern and participated pathway were further explored based on GO, COG and KEGG annotation. Meanwhile, transcription factors prediction and analysis will provide preliminary insights into mechanisms of Monachosorum maximowiczii for environmental adaptation.

Key words: ferns, transcriptomics, high-throughput sequencing, biodiversity, adaptation

Li Liu, Jiangping Shu, Hongjin Wei, Rui Zhang, Hui Shen, Yuehong Yan. De novo transcriptome analysis of the rare fern Monachosorum maximowiczii (Dennstaedtiaceae) endemic to East Asia[J]. Biodiv Sci, 2016, 24(12): 1325-1334.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2016231

https://www.biodiversity-science.net/EN/Y2016/V24/I12/1325

Figures/Tables 9

References 27

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物种名 Species	测序部位 Description	测序平台 Platform	数据总量 Total size (Mb)	单基因簇或转录本数目 No. of unigene or transcript	文献 References
欧洲蕨 Pteridium aquilinum	配子体 Gametophyte	Roche 454	254	56,256	Der et al, 2011
水蕨 Ceratopteris richardii	孢子 Spore	Roche 454	266	15,730	Bushart et al, 2013
鸟巢蕨 Asplenium nidus	叶片 Leaf	Illumina HiSeq 2000	5,910	42,907	贾新平等, 2014
海金沙 Lygodium japonicum	原叶体、营养叶、孢子体、根状茎 Pro- thalli, trophophylls, sporophylls, rhizomes	Roche 454 Illumina HiSeq 2000	28 268	18,999 381,814	Aya et al, 2015
巨木贼 Equisetum giganteum	茎、叶、孢子囊 Stem, leaf, strobili	Illumina RNA-Seq	8,800	34,282	Vannesta et al, 2015

物种名 Species	测序部位 Description	测序平台 Platform	数据总量 Total size (Mb)	单基因簇或转录本数目 No. of unigene or transcript	文献 References
欧洲蕨 Pteridium aquilinum	配子体 Gametophyte	Roche 454	254	56,256	Der et al, 2011
水蕨 Ceratopteris richardii	孢子 Spore	Roche 454	266	15,730	Bushart et al, 2013
鸟巢蕨 Asplenium nidus	叶片 Leaf	Illumina HiSeq 2000	5,910	42,907	贾新平等, 2014
海金沙 Lygodium japonicum	原叶体、营养叶、孢子体、根状茎 Pro- thalli, trophophylls, sporophylls, rhizomes	Roche 454 Illumina HiSeq 2000	28 268	18,999 381,814	Aya et al, 2015
巨木贼 Equisetum giganteum	茎、叶、孢子囊 Stem, leaf, strobili	Illumina RNA-Seq	8,800	34,282	Vannesta et al, 2015

	原始数据 Raw data	有效数据 Clean data
序列数目 Number of sequences	49,027,722	48,497,004
全长 Total length (Gb)	4.95	4.83
Q20值 Q20%	96.54%	98.61%
Q30值 Q30%	91.54%	93.58%
GC值 GC%	47.82%	47.71%

	原始数据 Raw data	有效数据 Clean data
序列数目 Number of sequences	49,027,722	48,497,004
全长 Total length (Gb)	4.95	4.83
Q20值 Q20%	96.54%	98.61%
Q30值 Q30%	91.54%	93.58%
GC值 GC%	47.82%	47.71%

	转录本 Transcript	单基因簇 Unigene
序列数目 Sequence number	107,197	101,448
平均长度 Mean length (bp)	955	900
最大长度 Max. length (bp)	14,804	14,804
最小长度 Min. length (bp)	201	201
N50值 N50	1,907	1,817
GC含量 GC content	0.44	0.44