SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango,<i>Mangifera indica</i>

Li, Wei; Zhu, Xun-Ge; Zhang, Qun‐Jie; Li, Kui; Zhang, Dan; Shi, Cong; Gao, Li‐Zhi

doi:10.1101/2020.02.22.960880

Cited by 17 publications

(25 citation statements)

References 55 publications

(61 reference statements)

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“…As a result, a total of 97.19% (375 Mb) sequences in the mango genome were anchored to 20 chromosomes, and the chromosome size ranged from 12.8 to 29.8 Mb (Supplementary Tables 3, 4, and Figure 1A). These results are consistent with those of studies by Li et al (2020) and Wang et al (2020). Two independent methods were used to evaluate assembly quality.…”

Section: Genome Sequencing and Assemblysupporting

confidence: 88%

“…After heterozygosis was accounted for, a draft genome of 396 Mb was assembled, with N50 of 1.03 Mb (Table 1). The assembly of our genome was comparable to that of the recently published genome of the traditional Indian cultivar "Alphonso" (392.9 Mb) (Wang et al, 2020), but better than that of the Southeast Asian variety "Hong Xiang Ya" (∼372 Mb) (Li et al, 2020). Then, Hi-C contact frequency derived from Hi-C sequencing was used to order and orient the polished contigs into Hi-C scaffolds.…”

Section: Genome Sequencing and Assemblymentioning

confidence: 64%

“…Hence, a single genome may not fully display the genetic diversity of the species. Recently, genome assemblies for the two mango cultivars "Hong Xiang Ya" (Li et al, 2020) and "Alphonso" (Wang et al, 2020) have been published, providing insights on mango genome evolution. In the current study, the whole genome of the mango cultivar "Irwin" was sequenced using the third-generation PacBio technique, which generated a high-quality genome with contig N50 and 1.03 Mb long.…”

Section: Discussionmentioning

confidence: 99%

“…Genetic analysis of mango germplasm diversity has shown that the whole mango group can be divided into two subgroups: Indian and Southeast Asia groups (Warschefsky and Wettberg, 2019). Recently, the genomes of Indian cultivars (variety "Alphonso") (Wang et al, 2020) and Southeast Asian cultivars (variety "Hong Xiang Ya") (Li et al, 2020) have been sequenced, expanding our understanding of mango genome evolution. The Florida mango cultivars are generally considered hybrids between Indian cultivars and Southeast Asian cultivars.…”

Section: Introductionmentioning

confidence: 99%

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Chromosome-Scale Genome and Comparative Transcriptomic Analysis Reveal Transcriptional Regulators of β-Carotene Biosynthesis in Mango

Luo

Wei

et al. 2021

Front. Plant Sci.

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Mango (2n = 2x = 40) is an important tropical/subtropical evergreen fruit tree grown worldwide and yields nutritionally rich and high-value fruits. Here, a high-quality mango genome (396 Mb, contig N50 = 1.03 Mb) was assembled using the cultivar “Irwin” from Florida, USA. A total of 97.19% of the sequences were anchored to 20 chromosomes, including 36,756 protein-coding genes. We compared the β-carotene content, in two different cultivars (“Irwin” and “Baixiangya”) and growth periods. The variation in β-carotene content mainly affected fruit flesh color. Additionally, transcriptome analysis identified genes related to β-carotene biosynthesis. MiPSY1 was proved to be a key gene regulating β-carotene biosynthesis. Weighted gene co-expression network analysis, dual luciferase, and yeast one-hybrid assays confirmed that transcription factors (TFs) MibZIP66 and MibHLH45 activate MiPSY1 transcription by directly binding to the CACGTG motif of the MiPSY1 promoter. However, the two TFs showed no significant synergistic effect on promoter activity. The results of the current study provide a genomic platform for studying the molecular basis of the flesh color of mango fruit.

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Section: Genome Sequencing and Assemblysupporting

confidence: 88%

Section: Genome Sequencing and Assemblymentioning

confidence: 64%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Chromosome-Scale Genome and Comparative Transcriptomic Analysis Reveal Transcriptional Regulators of β-Carotene Biosynthesis in Mango

Luo

Wei

et al. 2021

Front. Plant Sci.

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“…In addition, we used LAI, which estimates the quality of a genome assembly by counting identifiable intact LTR retroelements, to evaluate the genome of T. sinensis (Ou et al., 2018). The LAI score of T. sinensis was 12.21 (Figure S2), suggesting that the genome assembly is of high quality (Li et al, 2020).…”

Section: Resultsmentioning

confidence: 99%

Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome‐level reference genome for the family Meliaceae

Xiu

Chen

et al. 2021

Molecular Ecology Resources

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Chinese mahogany (Toona sinensis) is a woody plant that is widely cultivated in China and Malaysia. Toona sinensis is important economically, including as a nutritious food source, as material for traditional Chinese medicine and as a high‐quality hardwood. However, the absence of a reference genome has hindered in‐depth molecular and evolutionary studies of this plant. In this study, we report a high‐quality T. sinensis genome assembly, with scaffolds anchored to 28 chromosomes and a total assembled length of 596 Mb (contig N50 = 1.5 Mb and scaffold N50 = 21.5 Mb). A total of 34,345 genes were predicted in the genome after homology‐based and de novo annotation analyses. Evolutionary analysis showed that the genomes of T. sinensis and Populus trichocarpa diverged ~99.1–103.1 million years ago, and the T. sinensis genome underwent a recent genome‐wide duplication event at ~7.8 million years and one more ancient whole genome duplication event at ~71.5 million years. These results provide a high‐quality chromosome‐level reference genome for T. sinensis and confirm its evolutionary position at the genomic level. Such information will offer genomic resources to study the molecular mechanism of terpenoid biosynthesis and the formation of flavour compounds, which will further facilitate its molecular breeding. As the first chromosome‐level genome assembled in the family Meliaceae, it will provide unique insights into the evolution of members of the Meliaceae.

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A chromosome‐level genome of mango exclusively from long‐read sequence data

Wijesundara,

Masouleh,

Furtado

et al. 2024

The Plant Genome

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Improvements in long‐read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long‐read sequence data into contigs that are assembled to chromosome level by chromatin conformation capture. We report here a chromosome‐level mango genome using only PacBio high‐fidelity (HiFi) long reads. HiFi reads at high coverage (204x) resulted in the assembly of 17 chromosomes, each as a single contig with telomeres at both ends. The remaining three chromosomes were represented each by two contigs, with telomeres at one end and ribosomal repeats at the other end. Analyzing contig ends allowed them to be paired and linked to generate the remaining three complete chromosomes, telomere‐to‐telomere but with ribosomal repeats of uncertain length. The assembled genome was 365 Mb with 100% completeness as assessed by Benchmarking Universal Single‐Copy Orthologs analysis. The haplotypes assembled demonstrated extensive structural differences. This approach using very high genome coverage may be useful for assembling high‐quality genomes for many other plants.

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SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango,Mangifera indica

Cited by 17 publications

References 55 publications

Chromosome-Scale Genome and Comparative Transcriptomic Analysis Reveal Transcriptional Regulators of β-Carotene Biosynthesis in Mango

Chromosome-Scale Genome and Comparative Transcriptomic Analysis Reveal Transcriptional Regulators of β-Carotene Biosynthesis in Mango

Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome‐level reference genome for the family Meliaceae

A chromosome‐level genome of mango exclusively from long‐read sequence data

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