Long non-coding RNAs of the trematode Himasthla Elongata (Mehlis, 1831) (Trematoda, Himasthlidae)

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The molecular mechanisms regulating the life cycle of trematodes remain largely unexplored to date. It is hypothesized that the non-coding portion of the genome, particularly long non-coding RNAs (lncRNAs) and repetitive elements, plays a key role in this regulation. In this study, we present the first identification of lncRNAs in the trematode Himasthla elongata based on transcriptome analysis combined with repeat homology assessment. Approximately half of the identified lncRNAs contain transposon-derived regions, reflecting the fact that transposable elements occupy 57.5% of the genome. The expression of several lncRNAs was confirmed across the redia, cercaria, and metacercaria life stages. These findings provide a basis for further study of the role of mobile elements in the formation of regulatory RNAs and in the evolution of transcription regulation mechanisms in trematodes.

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作者简介

A. Smolyaninova

Институт цитологии РАН

Email: orcinuca@gmail.com
俄罗斯联邦, Тихорецкий пр., 4, Санкт-Петербург, 194064

M. Gabdrakhmanova

Институт цитологии РАН

Email: orcinuca@gmail.com
俄罗斯联邦, Тихорецкий пр., 4, Санкт-Петербург, 194064

A. Romanovich

Санкт-Петербургский государственный университет

Email: orcinuca@gmail.com
俄罗斯联邦, Университетская наб. 7/9, Санкт-Петербург, 199034

B. Efeykin

Институт проблем экологии и эволюции имени А.Н. Северцова РАН

Email: orcinuca@gmail.com
俄罗斯联邦, Ленинский пр-т, 33, Москва, 119071

A. Solovyeva

Институт цитологии РАН; Зоологический институт РАН

编辑信件的主要联系方式.
Email: orcinuca@gmail.com
俄罗斯联邦, Тихорецкий пр., 4, Санкт-Петербург, 194064; Университетская наб. 1, Санкт-Петербург, 199034

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2. Figure 1. Workflow for lncRNA identification in the H. elongata transcriptome. A – lncRNAs identified based on sequence homology with transposable elements of H. elongata; B – lncRNAs obtained through direct H. elongata transcriptome filtering. ORF – Open reading frame.

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3. Figure 2. The piechart illustrating the percentage of repetitive and unique sequences in the genome of H. elongata.

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4. Figure 3. Piechart representing composition of lncRNAs in the redia-stage transcriptome of H. elongata that share homology with lncRNAs from other trematodes, classified by type: true lncRNAs – 73%, transposable element and viral ORF fragments – 24.7%, and housekeeping gene fragments – 2.3%.

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5. Figure 4. Comparison of two approaches for lncRNA identification in the H. elongata transcriptome: A – direct transcriptome filtering, which primarily identified short lncRNAs; B – еhomology-based search against transposable elements, which predominantly detected longer lncRNAs.

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6. Figure 5. Results of PCR, performed with genomic DNA from rediae (DNA) and cDNA from cercariae (C), metacercariae (M), and rediae (R) as templates, with primers specific to the identified lncRNAs. L – ladder, DNA size marker, b.p. – base pairs, K- – negative control. Primer names corresponding to the selected lncRNAs (see Table 1) are labeled above each lane.

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7. Figure 6. Alignment of nucleotide sequences of PCR products corresponding to putative H. elongata lncRNAs (bottom row) with their respective transcripts (top row) derived from the transcriptome assembly. A–C – are examples of alignments for delnc2.2, delnc1.2 and delnc4.1 amplicons with corresponding transcripts. The colour shows the degree of similarity as determined by the T-Coffe software.

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8. Figure 7. Differential expression of lncRNAs in the trematode H. elongata at the redia, cercaria, and metacercaria stages, based on real-time PCR analysis. Statistical analysis was performed using the Kruskal–Wallis test (for overall group comparisons) and the Mann–Whitney U test (for pairwise comparisons). * p < 0.05. Primer names corresponding to each lncRNA are indicated above the graphs.

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