Abstract
Long non-coding RNAs (lncRNAs) are defined as transcripts of greater than 200 nucleotides that play a crucial role in various cellular processes such as the development, differentiation and gene regulation across all eukaryotes, including plant cells. Since the last decade, there has been a significant rise in our understanding of lncRNA molecular functions in plants, resulting in an exponential increase in lncRNA transcripts, while these went unannounced from the major Angiosperm plant species despite the availability of large-scale high throughput sequencing data in public repositories. We, therefore, developed a user-friendly, open-access web interface, AlnC (Angiosperm lncRNA Catalogue) for the exploration of lncRNAs in diverse Angiosperm plant species using recent 1000 plant (1KP) trancriptomes data. The current version of AlnC offers 10,855,598 annotated lncRNA transcripts across 682 Angiosperm plant species encompassing 809 tissues. To improve the user interface, we added features for browsing, searching, and downloading lncRNA data, interactive graphs, and an online BLAST service. Additionally, each lncRNA record is annotated with possible small open reading frames (sORFs) to facilitate the study of peptides encoded within lncRNAs. With this user-friendly interface, we anticipate that AlnC will provide a rich source of lncRNAs for small-and large-scale studies in a variety of flowering plants, as well as aid in the improvement of key characteristics in relevance to their economic importance. Database URL: http://www.nipgr.ac.in/AlnC
Highlights
Angiosperms are flowering plants that constitute an exceptionally large group of plants that grow in a wide variety of habitats
We found the median length of identified Long non-coding RNAs (lncRNAs) is smaller than the median length of the coding sequences (Figs 1(B) and 4(E))
We found the AU content of AlnC lncRNAs varied from 50–90% with an average of 75% in comparison to the coding transcripts which ranged 30–80% with an average of 60% (Fig 1(D))
Summary
Angiosperms are flowering plants that constitute an exceptionally large group of plants that grow in a wide variety of habitats. It comprises of more than 3,000,000 recorded species worldwide, encompassing one of the most diverse group within the plant kingdom [1, 2]. Most angiosperms are a main source of consumer goods like textile fibres, herbs and spices, fuel and pharmaceuticals, as well as a major source of food. Research in Angiosperms exploded with the advent of generation sequencing (NGS) resulting in an improved picture of transcriptome, especially from the point of noncoding RNAs (ncRNAs). LncRNAs are a major RNA class of greater research
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