De novo transcriptome and small RNA analyses of two amorphophallus species.
De novo transcriptome and small RNA analyses of two amorphophallus species.
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DOI：
10.1371/journal.pone.0095428
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Hu Z
中科院分区：
文献类型：
--
作者：
Diao Y;Yang C;Yan M;Zheng X;Jin S;Wang Y;Hu Z
魔芋是世界上最重要的葡甘露聚糖作物之一。魔芋的遗传基础限制了其育种和基因组学研究。本研究对A.魔芋和A.使用高通量Illumina测序平台构建了bulbifer。所有108，651个单基因平均长度为430 nt。在过滤和组装后，分别从54，986，020个读段和52，334，098个读段产生了平均长度为439 nt的cDNAac和119，678个unigenes。A. 55，525人在A.在去除外源污染序列后，通过与Nr、Swiss-Prot、KEGG和COG数据库比较来注释bulbifier。共检测到80，332个A.魔芋和A.珠芽植物鉴定了与葡甘露聚糖生物合成途径相关的大多数基因。此外，A.还通过深度测序技术获得了苜蓿叶。共获得5，499，903条小RNA序列，长度范围在18 ~ 30 nt之间。根据miRNAs的转录本预测了miRNAs的潜在靶点。我们的研究提供了一个系统的概述魔芋葡甘露聚糖的生物合成基因，参与魔芋叶，并应促进进一步了解碳水化合物的合成和其他重要的代谢途径的关键作用。
Konjac is one of the most important glucomannan crops worldwide. The breeding and genomic researches are largely limited by the genetic basis of Amorphophallus. In this study, the transcriptomes of A. konjac and A. bulbifer were constructed using a high-throughput Illumina sequencing platform. All 108,651 unigenes with average lengths of 430 nt in A. konjac and 119,678 unigenes with average lengths of 439 nt were generated from 54,986,020 reads and 52,334,098 reads after filtering and assembly, respectively. A total of 54,453 transcripts in A. konjac and 55,525 in A. bulbifier were annotated by comparison with Nr, Swiss-Prot, KEGG, and COG databases after removing exogenous contaminated sequences. A total of 80,332 transcripts differentially expressed between A. konjac and A. bulbifer. The majority of the genes that are associated with konjac glucomannan biosynthetic pathway were identified. Besides, the small RNAs in A. konjac leaves were also obtained by deep sequencing technology. All of 5,499,903 sequences of small RNAs were obtained with the length range between 18 and 30 nt. The potential targets for the miRNAs were also predicted according to the konjac transcripts. Our study provides a systematic overview of the konjac glucomannan biosynthesis genes that are involved in konjac leaves and should facilitate further understanding of the crucial roles of carbohydrate synthesis and other important metabolism pathways in Amorphophallus.
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