A High-Quality Reference Genome Assembly of (Rosaceae)

Overview

Journal Genes (Basel)

Publisher MDPI

Date 2023 Nov 25

PMID 38002978

Authors

Lei Zhang

Chaopan Zhang

Yajing An

Qiang Zhu

Mingcheng Wang

Affiliations

Soon will be listed here.

Abstract

This study introduces a meticulously constructed genome assembly at the chromosome level for the Rosaceae family species , a traditional Chinese medicinal herb. The final assembly encompasses 1272.71 megabases (Mb) distributed across 16 pseudochromosomes, boasting contig and super-scaffold N50 values of 2.77 and 79.32 Mb, respectively. Annotated within this genome is a substantial 875.99 Mb of repetitive sequences, with transposable elements occupying 777.28 Mb, constituting 61.07% of the entire genome. Our predictive efforts identified 49,261 protein-coding genes within the repeat-masked assembly, with 45,256 (91.87%) having functional annotations, 5127 (10.41%) demonstrating tandem duplication, and 2373 (4.82%) classified as transcription factor genes. Additionally, our investigation unveiled 3080 non-coding RNAs spanning 0.51 Mb of the genome sequences. According to our evolutionary study, underwent recent whole-genome duplication following its separation from . The presented reference-level genome assembly and annotation for will significantly facilitate the in-depth exploration of genomic information pertaining to this species, offering substantial utility in comparative genomics and evolutionary analyses involving Rosaceae species.

References

Wang M, Zhang L, Tong S, Jiang D, Fu Z . Chromosome-level genome assembly of a xerophytic plant, Haloxylon ammodendron. DNA Res. 2022; 29(2). PMC: 8946665. DOI: 10.1093/dnares/dsac006. 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

Louwers M, Splinter E, van Driel R, de Laat W, Stam M . Studying physical chromatin interactions in plants using Chromosome Conformation Capture (3C). Nat Protoc. 2009; 4(8):1216-29. DOI: 10.1038/nprot.2009.113. View

Bairoch A, Apweiler R . The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 1999; 28(1):45-8. PMC: 102476. DOI: 10.1093/nar/28.1.45. View

Jung S, Lee T, Cheng C, Buble K, Zheng P, Yu J . 15 years of GDR: New data and functionality in the Genome Database for Rosaceae. Nucleic Acids Res. 2018; 47(D1):D1137-D1145. PMC: 6324069. DOI: 10.1093/nar/gky1000. View

Emms D, Kelly S . OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019; 20(1):238. PMC: 6857279. DOI: 10.1186/s13059-019-1832-y. View

Hodel R, Zimmer E, Liu B, Wen J . Synthesis of Nuclear and Chloroplast Data Combined With Network Analyses Supports the Polyploid Origin of the Apple Tribe and the Hybrid Origin of the Maleae-Gillenieae Clade. Front Plant Sci. 2022; 12:820997. PMC: 8822239. DOI: 10.3389/fpls.2021.820997. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

10.

Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B . AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006; 34(Web Server issue):W435-9. PMC: 1538822. DOI: 10.1093/nar/gkl200. View

11.

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

12.

Shirasawa K, Isuzugawa K, Ikenaga M, Saito Y, Yamamoto T, Hirakawa H . The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. DNA Res. 2017; 24(5):499-508. PMC: 5737369. DOI: 10.1093/dnares/dsx020. View

13.

DAmico-Willman K, Ouma W, Meulia T, Sideli G, Gradziel T, Fresnedo-Ramirez J . Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar 'Nonpareil'. G3 (Bethesda). 2022; 12(5). PMC: 9073694. DOI: 10.1093/g3journal/jkac065. View

14.

Wang M, Huang J, Liu S, Liu X, Li R, Luo J . Improved assembly and annotation of the sesame genome. DNA Res. 2022; 29(6). PMC: 9724774. DOI: 10.1093/dnares/dsac041. View

15.

Wang Y, Tang H, DeBarry J, Tan X, Li J, Wang X . MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012; 40(7):e49. PMC: 3326336. DOI: 10.1093/nar/gkr1293. View

16.

Zhou H, Zhao R, Yang J . Two new alkaloid galactosides from the kernel of Prinsepia uniflora. Nat Prod Res. 2012; 27(8):687-90. DOI: 10.1080/14786419.2012.691487. View

17.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

18.

Dudchenko O, Batra S, Omer A, Nyquist S, Hoeger M, Durand N . De novo assembly of the genome using Hi-C yields chromosome-length scaffolds. Science. 2017; 356(6333):92-95. PMC: 5635820. DOI: 10.1126/science.aal3327. View

19.

Durand N, Shamim M, Machol I, Rao S, Huntley M, Lander E . Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 2016; 3(1):95-8. PMC: 5846465. DOI: 10.1016/j.cels.2016.07.002. View

20.

Jurka J, Kapitonov V, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J . Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005; 110(1-4):462-7. DOI: 10.1159/000084979. View