A Chromosome-level Genome Assembly for Onobrychis Viciifolia Reveals Gene Copy Number Gain Underlying Enhanced Proanthocyanidin Biosynthesis

Overview

Journal Commun Biol

Specialty Biology

Date 2024 Jan 5

PMID 38182881

Authors

Junyi He

Danyang Tian

Xue Li

Xuemeng Wang

Tingting Wang

Ziyao Wang

Hui Zang

Xiaofan He

TieJun Zhang

Quanzheng Yun

Rengang Zhang

Jishan Jiang

Shangang Jia

Yunwei Zhang

Affiliations

Soon will be listed here.

Abstract

Sainfoin (Onobrychis viciifolia), which belongs to subfamily Papilionoideae of Leguminosae, is a vital perennial forage known as "holy hay" due to its high contents of crude proteins and proanthocyanidins (PAs, also called condensed tannins) that have various pharmacological properties in animal feed, such as alleviating rumen tympanic disease in ruminants. In this study, we select an autotetraploid common sainfoin (2n = 4x = 28) and report its high-quality chromosome-level genome assembly with 28 pseudochromosomes and four haplotypes (~1950.14 Mb, contig N50 = 10.91 Mb). The copy numbers of genes involved in PA biosynthesis in sainfoin are significantly greater than those in four selected Fabales species, namely, autotetraploid Medicago sativa and three other diploid species, Lotus japonicus, Medicago truncatula, and Glycine max. Furthermore, gene expansion is confirmed to be the key contributor to the increased expression of these genes and subsequent PA enhancement in sainfoin. Transcriptomic analyses reveal that the expression of genes involved in the PA biosynthesis pathway is significantly increased in the lines with high PA content compared to the lines with medium and low PA content. The sainfoin genome assembly will improve our understanding of leguminous genome evolution and biosynthesis of secondary metabolites in sainfoin.

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References

Kreplak J, Madoui M, Capal P, Novak P, Labadie K, Aubert G . A reference genome for pea provides insight into legume genome evolution. Nat Genet. 2019; 51(9):1411-1422. DOI: 10.1038/s41588-019-0480-1. View

Simao F, Waterhouse R, Ioannidis P, Kriventseva E, Zdobnov E . BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19):3210-2. DOI: 10.1093/bioinformatics/btv351. View

Ellinghaus D, Kurtz S, Willhoeft U . LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008; 9:18. PMC: 2253517. DOI: 10.1186/1471-2105-9-18. View

Durand N, Robinson J, Shamim M, Machol I, Mesirov J, Lander E . Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom. Cell Syst. 2016; 3(1):99-101. PMC: 5596920. DOI: 10.1016/j.cels.2015.07.012. View

Shen C, Du H, Chen Z, Lu H, Zhu F, Chen H . The Chromosome-Level Genome Sequence of the Autotetraploid Alfalfa and Resequencing of Core Germplasms Provide Genomic Resources for Alfalfa Research. Mol Plant. 2020; 13(9):1250-1261. DOI: 10.1016/j.molp.2020.07.003. View

Patra A, Saxena J . Exploitation of dietary tannins to improve rumen metabolism and ruminant nutrition. J Sci Food Agric. 2010; 91(1):24-37. DOI: 10.1002/jsfa.4152. View

Fu L, Niu B, Zhu Z, Wu S, Li W . CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23):3150-2. PMC: 3516142. DOI: 10.1093/bioinformatics/bts565. View

Marais J, Mueller-Harvey I, Brandt E, Ferreira D . Polyphenols, condensed tannins, and other natural products in Onobrychis viciifolia (Sainfoin). J Agric Food Chem. 2000; 48(8):3440-7. DOI: 10.1021/jf000388h. View

Wang F, Xia Z, Zou M, Zhao L, Jiang S, Zhou Y . The autotetraploid potato genome provides insights into highly heterozygous species. Plant Biotechnol J. 2022; 20(10):1996-2005. PMC: 9491450. DOI: 10.1111/pbi.13883. View

10.

Li H, Jiang F, Wu P, Wang K, Cao Y . A High-Quality Genome Sequence of Model Legume (MG-20) Provides Insights into the Evolution of Root Nodule Symbiosis. Genes (Basel). 2020; 11(5). PMC: 7290416. DOI: 10.3390/genes11050483. View

11.

Siren J, Valimaki N, Makinen V . Indexing Graphs for Path Queries with Applications in Genome Research. IEEE/ACM Trans Comput Biol Bioinform. 2015; 11(2):375-88. DOI: 10.1109/TCBB.2013.2297101. View

12.

Yan Q, Wu F, Xu P, Sun Z, Li J, Gao L . The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth. Mol Ecol Resour. 2020; 21(2):526-542. PMC: 7821259. DOI: 10.1111/1755-0998.13271. View

13.

Ou S, Jiang N . LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 2017; 176(2):1410-1422. PMC: 5813529. DOI: 10.1104/pp.17.01310. View

14.

He F, Pan Q, Shi Y, Duan C . Biosynthesis and genetic regulation of proanthocyanidins in plants. Molecules. 2008; 13(10):2674-703. PMC: 6245171. DOI: 10.3390/molecules13102674. View

15.

Dixon R, Xie D, Sharma S . Proanthocyanidins--a final frontier in flavonoid research?. New Phytol. 2005; 165(1):9-28. DOI: 10.1111/j.1469-8137.2004.01217.x. View

16.

Gou L, Zhang R, Ma L, Zhu F, Dong J, Wang T . Multigene synergism increases the isoflavone and proanthocyanidin contents of Medicago truncatula. Plant Biotechnol J. 2015; 14(3):915-25. PMC: 11629816. DOI: 10.1111/pbi.12445. View

17.

Sun X, Jia X, Huo L, Che R, Gong X, Wang P . MdATG18a overexpression improves tolerance to nitrogen deficiency and regulates anthocyanin accumulation through increased autophagy in transgenic apple. Plant Cell Environ. 2017; 41(2):469-480. DOI: 10.1111/pce.13110. View

18.

Verma S, Salminen J, Taube F, Malisch C . Large Inter- and Intraspecies Variability of Polyphenols and Proanthocyanidins in Eight Temperate Forage Species Indicates Potential for Their Exploitation as Nutraceuticals. J Agric Food Chem. 2021; 69(42):12445-12455. DOI: 10.1021/acs.jafc.1c03898. View

19.

Jonker A, Yu P . The Role of Proanthocyanidins Complex in Structure and Nutrition Interaction in Alfalfa Forage. Int J Mol Sci. 2016; 17(5). PMC: 4881609. DOI: 10.3390/ijms17050793. View

20.

Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z . clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb). 2021; 2(3):100141. PMC: 8454663. DOI: 10.1016/j.xinn.2021.100141. View