De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits.
De novo transcriptome analysis and comparative expression profiling of genes associated with the taste-modifying protein neoculin in Curculigo latifolia and Curculigo capitulata fruits.
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DOI：
10.1186/s12864-021-07674-3
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发表时间：
2021-05-13
期刊：
影响因子：
4.4
通讯作者：
Asakura T
中科院分区：
文献类型：
--
作者：
Okubo S;Terauchi K;Okada S;Saito Y;Yamaura T;Misaka T;Nakajima KI;Abe K;Asakura T
宽叶胡枝子是一种东南亚内源性多年生植物，其果实含有味觉调节蛋白质新oculin，它与甜味受体结合，使酸味水果尝起来很甜。虽然与雪花莲（Galanthus nivalis）凝集素（GNA）相似，在其序列和3D结构中含有甘露糖结合位点，但新oculin缺乏这些位点，并且没有凝集素活性。C. latifolia和其它含有新oculin和/或GNA家族成员的石花菜植物中的蛋白质含量尚不清楚。通过从头RNA-seq组装C. latifolia和近缘种C. capitulata和两个物种的neoculin和neoculin样基因的表达模式的详细分析，我们组装了85，697个转录本，从C. latifolia和C. capitulata使用Trinity和注释他们使用公共数据库。我们在C. latifolia和C.头状的其中，38.6%的单基因来自C. latifolia和C. capitulata在两个种之间具有很高的相似性。我们在C. latifolia和C. capitulata，编码两种植物中新oculin的碱性和酸性亚基。我们将这25个转录本进行比对并生成系统发育树。这两个物种中的许多直系同源物具有高度的相似性，尽管共同基因的数量很少，这表明这些基因可能在两个物种分化之前就存在了。这些基因的相对表达水平在两个物种之间有很大差异：新oculin基因的每百万转录本（TPM）值在C中高60倍。latifolia比C. capitulata中GNA家族成员的遗传多样性比C. latifolia比C.头状的neoculin相关基因的遗传多样性强有力地表明，neoculin基因在进化过程中经历了复制。C. latifolia和C. capitulata的突变可能是由于参与转录调控的区域的突变。通过对这两种胡枝子果实中表达基因的综合分析，有助于从分子水平上阐明新oculin的起源。在线版本包含补充材料，可通过10.1186/s12864-021-07674-3获得。
Curculigo latifolia is a perennial plant endogenous to Southeast Asia whose fruits contain the taste-modifying protein neoculin, which binds to sweet receptors and makes sour fruits taste sweet. Although similar to snowdrop (Galanthus nivalis) agglutinin (GNA), which contains mannose-binding sites in its sequence and 3D structure, neoculin lacks such sites and has no lectin activity. Whether the fruits of C. latifolia and other Curculigo plants contain neoculin and/or GNA family members was unclear. Through de novo RNA-seq assembly of the fruits of C. latifolia and the related C. capitulata and detailed analysis of the expression patterns of neoculin and neoculin-like genes in both species, we assembled 85,697 transcripts from C. latifolia and 76,775 from C. capitulata using Trinity and annotated them using public databases. We identified 70,371 unigenes in C. latifolia and 63,704 in C. capitulata. In total, 38.6% of unigenes from C. latifolia and 42.6% from C. capitulata shared high similarity between the two species. We identified ten neoculin-related transcripts in C. latifolia and 15 in C. capitulata, encoding both the basic and acidic subunits of neoculin in both plants. We aligned these 25 transcripts and generated a phylogenetic tree. Many orthologs in the two species shared high similarity, despite the low number of common genes, suggesting that these genes likely existed before the two species diverged. The relative expression levels of these genes differed considerably between the two species: the transcripts per million (TPM) values of neoculin genes were 60 times higher in C. latifolia than in C. capitulata, whereas those of GNA family members were 15,000 times lower in C. latifolia than in C. capitulata. The genetic diversity of neoculin-related genes strongly suggests that neoculin genes underwent duplication during evolution. The marked differences in their expression profiles between C. latifolia and C. capitulata may be due to mutations in regions involved in transcriptional regulation. Comprehensive analysis of the genes expressed in the fruits of these two Curculigo species helped elucidate the origin of neoculin at the molecular level. The online version contains supplementary material available at 10.1186/s12864-021-07674-3.
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影响因子：
--
作者：
Babaei N;Abdullah NA;Saleh G;Abdullah TL
通讯作者：
Abdullah TL
DOI：
10.1093/bioinformatics/bts565
发表时间：
2012-12-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fu L;Niu B;Zhu Z;Wu S;Li W
通讯作者：
Li W
影响因子：
3.4
作者：
Jiang SY;Ma Z;Ramachandran S
通讯作者：
Ramachandran S
影响因子：
4.8
作者：
Kurimoto, Eiji;Suzuki, Maiko;Kato, Koichi
通讯作者：
Kato, Koichi
影响因子：
6.5
作者：
Dang, Liuyi;Van Damme, Els J. M.
通讯作者：
Van Damme, Els J. M.