The phased telomere-to-telomere reference genome of <i>Musa acuminata</i>, a main contributor to banana cultivars

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Abstract

Musa acuminata is a main wild contributor to banana cultivars. Here, we reported a haplotype-resolved and telomere-to-telomere reference genome of M. acuminata by incorporating PacBio HiFi reads, Nanopore ultra-long reads, and Hi-C data. The genome size of the two haploid assemblies was estimated to be 469.83 Mb and 470.21 Mb, respectively. Multiple assessments confirmed the contiguity (contig N50: 16.53 Mb and 18.58 Mb; LAI: 20.18 and 19.48), completeness (BUSCOs: 98.57% and 98.57%), and correctness (QV: 45.97 and 46.12) of the genome. The repetitive sequences accounted for about half of the genome size. In total, 40,889 and 38,269 protein-coding genes were annotated in the two haploid assemblies, respectively, of which 9.56% and 3.37% were newly predicted. Genome comparison identified a large reciprocal translocation involving 3 Mb and 10 Mb from chromosomes 01 and 04 within M. acuminata. This reference genome of M. acuminata provides a valuable resource for further understanding of subgenome evolution of Musa species, and precise genetic improvement of banana.

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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2009)

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk

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fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen, Yanqing Zhou, Yaru Chen … (2018)

Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.

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Minimap2: pairwise alignment for nucleotide sequences

Heng Li (2018)

Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.

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Author and article information

Contributors

Hui-Run Huang:

ORCID: http://orcid.org/0000-0002-4656-5627

huirun.huang@scbg.ac.cn

Journal

Journal ID (nlm-ta): Sci Data

Journal ID (iso-abbrev): Sci Data

Title: Scientific Data

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2052-4463

Publication date (Electronic): 16 September 2023

Publication date PMC-release: 16 September 2023

Publication date Collection: 2023

Volume: 10

Electronic Location Identifier: 631

Affiliations

[1 ]GRID grid.9227.e, ISNI 0000000119573309, Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, , Chinese Academy of Sciences, ; Guangzhou, 510650 China

[2 ]South China National Botanical Garden, Guangzhou, 510650 China

[3 ]University of Chinese Academy of Sciences, ( https://ror.org/05qbk4x57) Beijing, 100049 China

[4 ]GRID grid.410727.7, ISNI 0000 0001 0526 1937, National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, , Chinese Academy of Agricultural Sciences, ; Shenzhen, 518120 China

[5 ]School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, ( https://ror.org/0495efn48) Nanning, 530008 China

[6 ]GRID grid.453499.6, ISNI 0000 0000 9835 1415, National Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, , Chinese Academy of Tropical Agricultural Sciences, ; Haikou, 571101 China

Author information

Xin Liu http://orcid.org/0000-0003-4175-9358

Yongfeng Zhou http://orcid.org/0000-0003-0780-2973

Hui-Run Huang http://orcid.org/0000-0002-4656-5627

Article

Publisher ID: 2546

DOI: 10.1038/s41597-023-02546-9

PMC ID: 10505225

PubMed ID: 37716992

SO-VID: 985b6309-e020-480e-813f-d9e22f6d6b7c

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 6 June 2023

Date accepted : 5 September 2023

Funding

Funded by: FundRef https://doi.org/10.13039/501100001809, National Natural Science Foundation of China (National Science Foundation of China);

Award ID: 32070237, 31261140366

Award Recipient : Xue-Jun Ge

Funded by: Strategic Priority Research Program of Chinese Academy of Sciences, Grant No. XDB31000000

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Keywords: structural variation,comparative genomics,dna sequencing,natural variation in plants

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Keywords: structural variation, comparative genomics, dna sequencing, natural variation in plants

The phased telomere-to-telomere reference genome of Musa acuminata, a main contributor to banana cultivars

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Arabidopsis genomics

Most cited references 47

Fast and accurate short read alignment with Burrows–Wheeler transform

fastp: an ultra-fast all-in-one FASTQ preprocessor

Minimap2: pairwise alignment for nucleotide sequences

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