Previous Article in Journal
Agrobacterium-Mediated Transient Expression Methods to Validate Gene Functions in Strawberry (F. × ananassa)
Previous Article in Special Issue
Evaluation of the Spike Diversity of Seven Hexaploid Wheat Species and an Artificial Amphidiploid Using a Quadrangle Model Obtained from 2D Images
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Plants
Volume 13
Issue 23
10.3390/plants13233291
plants-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Full-Length Transcriptomes Reconstruction Reveals Intraspecific Diversity in Hairy Vetch (Vicia villosa Roth) and Smooth Vetch (V. villosa Roth var. glabrescens)

by
Weiyi Kong
1,2,
Bohao Geng
1,
Wenhui Yan
1,
Jun Xia
1,
Wenkai Xu
1,
Na Zhao
1 and
Zhenfei Guo
1,*
1
College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
2
The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China
*
Author to whom correspondence should be addressed.
Plants 2024, 13(23), 3291; https://doi.org/10.3390/plants13233291
Submission received: 6 August 2024 / Revised: 19 November 2024 / Accepted: 20 November 2024 / Published: 22 November 2024
(This article belongs to the Special Issue Genetic and Biological Diversity of Plants)
Versions Notes

Abstract

Hairy vetch (Vicia villosa Roth) and smooth vetch (V. villosa Roth var. glabrescens) are important cover crops and legume forage with great economic and ecological values. Due to the large and highly heterozygous genome, full-length transcriptome reconstruction is a cost-effective route to mining their genetic resources. In this study, a hybrid sequencing approach combining SMRT and NGS technologies was applied. The results showed that 28,747 and 40,600 high-quality non-redundant transcripts with an average length of 1808 bp and 1768 bp were generated from hairy vetch and smooth vetch, including 24,864 and 35,035 open reading frames (ORFs), respectively. More than 96% of transcripts were annotated to the public databases, and around 25% of isoforms underwent alternative splicing (AS) events. In addition, 987 and 1587 high-confidence lncRNAs were identified in two vetches. Interestingly, smooth vetch contains more specific transcripts and orthologous clusters than hairy vetch, revealing intraspecific transcript diversity. The phylogeny revealed that they were clustered together and closely related to the genus Pisum. Furthermore, the estimation of Ka/Ks ratios showed that purifying selection was the predominant force. A putative 3-dehydroquinate dehydratase/shikimate dehydrogenase (DHD/SDH) gene underwent strong positive selection and might regulate phenotypic differences between hairy vetch and smooth vetch. Overall, our study provides a vital characterization of two full-length transcriptomes in Vicia villosa, which will be valuable for their molecular research and breeding.
Keywords: hairy vetch; full-length transcriptome; alternative splicing; LncRNA; positive selection hairy vetch; full-length transcriptome; alternative splicing; LncRNA; positive selection

Share and Cite

MDPI and ACS Style

Kong, W.; Geng, B.; Yan, W.; Xia, J.; Xu, W.; Zhao, N.; Guo, Z. Full-Length Transcriptomes Reconstruction Reveals Intraspecific Diversity in Hairy Vetch (Vicia villosa Roth) and Smooth Vetch (V. villosa Roth var. glabrescens). Plants 2024, 13, 3291. https://doi.org/10.3390/plants13233291

AMA Style

Kong W, Geng B, Yan W, Xia J, Xu W, Zhao N, Guo Z. Full-Length Transcriptomes Reconstruction Reveals Intraspecific Diversity in Hairy Vetch (Vicia villosa Roth) and Smooth Vetch (V. villosa Roth var. glabrescens). Plants. 2024; 13(23):3291. https://doi.org/10.3390/plants13233291

Chicago/Turabian Style

Kong, Weiyi, Bohao Geng, Wenhui Yan, Jun Xia, Wenkai Xu, Na Zhao, and Zhenfei Guo. 2024. "Full-Length Transcriptomes Reconstruction Reveals Intraspecific Diversity in Hairy Vetch (Vicia villosa Roth) and Smooth Vetch (V. villosa Roth var. glabrescens)" Plants 13, no. 23: 3291. https://doi.org/10.3390/plants13233291

APA Style

Kong, W., Geng, B., Yan, W., Xia, J., Xu, W., Zhao, N., & Guo, Z. (2024). Full-Length Transcriptomes Reconstruction Reveals Intraspecific Diversity in Hairy Vetch (Vicia villosa Roth) and Smooth Vetch (V. villosa Roth var. glabrescens). Plants, 13(23), 3291. https://doi.org/10.3390/plants13233291

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop