Comparative transcriptomics of leaves of five mulberry accessions and cataloguing structural and expression variants for future prospects.
Comparative transcriptomics of leaves of five mulberry accessions and cataloguing structural and expression variants for future prospects.
复制标题
DOI：
10.1371/journal.pone.0252246
复制
发表时间：
2021
期刊：
影响因子：
3.7
通讯作者：
Khurana P
中科院分区：
文献类型：
--
作者：
Baranwal VK;Negi N;Khurana P
家蚕（Bombyx mori）是一种单食性昆虫，它比其他桑属植物更喜欢某些桑属植物的叶子。这种偏好归因于形态和解剖特征以及生化化合物。在本手稿中，对两种优选栽培品种和三种野生类型物种的叶子转录组进行了比较。组装时，分别从 ML、MN、MS、K2 和 V1 样本中构建了总共 100930、151245、89724、181761 和 102908 个转录本，构建了五种基因型的高质量转录组。此外，为了比较它们，从这些组装的转录组中鉴定出直系同源物。在KvsN、KvsL、KvsS、KvsV、LvsN、LvsS中一对一比较中总共发现了22462、23413、23685、24371、18362、22326、20058、18049、17567和20518个直系同源簇，分别为 LvsV、NvsS、NvsV 和 SvsV。然后使用代数连通性为 1.0 的 4236 个直向同源物来比较并找出所有基因型的差异表达转录本。总共表达了 1037 个转录本，其中包括一些调节转录因子（AP2/ERF 和 C2H2 锌指）的重要形态、解剖和生化途径以及信号传导成分，经鉴定存在差异表达。此外，使用这些转录组找出标记（SSR）和变异，总共发现了 1101013、537245、970877、310437、675772、338400、581189、751477、514999 和 257107 个变异，包括 SNP、MNP、插入和缺失。一对一的比较。总而言之，我们的数据对于全世界的桑树社区非常有用，因为它可以用于桑树育种计划。
Bombyx mori, a monophagous insect, prefers leaves of the certain species of Morus more than others. The preference has been attributed to morphological and anatomical features and biochemical compounds. In the present manuscript a comparison has been made among the transcriptome of leaves of the two preferred cultivated varieties and three wild types species. While assembling, high quality transcriptomes of five genotypes were constructed with a total of 100930, 151245, 89724, 181761 and 102908 transcripts from ML, MN, MS, K2 and V1 samples respectively. Further, to compare them, orthologs were identified from these assembled transcriptome. A total of 22462, 23413, 23685, 24371, 18362, 22326, 20058, 18049, 17567 and 20518 clusters of orthologs were found in one to one comparison in KvsN, KvsL, KvsS, KvsV, LvsN, LvsS, LvsV, NvsS, NvsV, and SvsV respectively. 4236 orthologs with algebraic connectivity of 1.0 were then used to compare and to find out differentially expressed transcripts from all the genotypes. A total of 1037 transcripts expressed that include some of the important morphology, anatomy and biochemical pathways regulating transcription factors (AP2/ERFs and C2H2 Zinc fingers) and signalling components were identified to express differentially. Further, these transcriptomes were used find out markers (SSR) and variants and a total of 1101013, 537245, 970877, 310437, 675772, 338400, 581189, 751477, 514999 and 257107 variants including SNP, MNP, Insertions and deletions were found in one to one comparisons. Taken together, our data could be highly useful for mulberry community worldwide as it could be utilized in mulberry breeding programs.
登录
查看更多内容
影响因子：
3.7
作者：
Honaas LA;Wafula EK;Wickett NJ;Der JP;Zhang Y;Edger PP;Altman NS;Pires JC;Leebens-Mack JH;dePamphilis CW
通讯作者：
dePamphilis CW
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
3.1
作者：
Baranwal, Vinay Kumar;Khurana, Paramjit
通讯作者：
Khurana, Paramjit
影响因子：
7.3
作者：
Hamanishi, Erin T.;Raj, Sherosha;Campbell, Malcolm M.
通讯作者：
Campbell, Malcolm M.
影响因子：
3
作者：
Checker, Vibha G.;Chhibbar, Anju K.;Khurana, Paramjit
通讯作者：
Khurana, Paramjit