The genome evolution and domestication of tropical fruit mango

Wang, Peng; Luo, Yingfeng; Huang, Jianfeng; Gao, Shenghan; Zhu, Guopeng; Zhiguo, Dang; Gai, Jiangtao; Yang, Meng; Zhu, Min; Zhang, Huangkai; Ye, Xiuxu; Gao, Aiping; Tan, Xinyu; Wang, Sen; Wu, Shizhou; Cahoon, Edgar B.; Bai, Beibei; Zhong, Zhao; Li, Qian; Wei, June; Chen, Huarui; Luo, Ruibang; Gong, D.; Tang, Kexuan; Zhang, Bing; ZhangGuang, Ni; Huang, Guodi; Hu, Songnian; Chen, Yeyuan

doi:10.1186/s13059-020-01959-8

Cited by 161 publications

(143 citation statements)

References 120 publications

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“…Recently, the genome sequence of a mango cultivar ‘Alphonso’ was published [ 52 ]. The methods of sequencing, assembly, and annotation of the two genomes are significantly different.…”

Section: Discussionmentioning

confidence: 99%

The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality

Bally¹,

Bombarely

Chambers

et al. 2021

BMC Plant Biol

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Background Mango, Mangifera indica L., an important tropical fruit crop, is grown for its sweet and aromatic fruits. Past improvement of this species has predominantly relied on chance seedlings derived from over 1000 cultivars in the Indian sub-continent with a large variation for fruit size, yield, biotic and abiotic stress resistance, and fruit quality among other traits. Historically, mango has been an orphan crop with very limited molecular information. Only recently have molecular and genomics-based analyses enabled the creation of linkage maps, transcriptomes, and diversity analysis of large collections. Additionally, the combined analysis of genomic and phenotypic information is poised to improve mango breeding efficiency. Results This study sequenced, de novo assembled, analyzed, and annotated the genome of the monoembryonic mango cultivar ‘Tommy Atkins’. The draft genome sequence was generated using NRGene de-novo Magic on high molecular weight DNA of ‘Tommy Atkins’, supplemented by 10X Genomics long read sequencing to improve the initial assembly. A hybrid population between ‘Tommy Atkins’ x ‘Kensington Pride’ was used to generate phased haplotype chromosomes and a highly resolved phased SNP map. The final ‘Tommy Atkins’ genome assembly was a consensus sequence that included 20 pseudomolecules representing the 20 chromosomes of mango and included ~ 86% of the ~ 439 Mb haploid mango genome. Skim sequencing identified ~ 3.3 M SNPs using the ‘Tommy Atkins’ x ‘Kensington Pride’ mapping population. Repeat masking identified 26,616 genes with a median length of 3348 bp. A whole genome duplication analysis revealed an ancestral 65 MYA polyploidization event shared with Anacardium occidentale. Two regions, one on LG4 and one on LG7 containing 28 candidate genes, were associated with the commercially important fruit size characteristic in the mapping population. Conclusions The availability of the complete ‘Tommy Atkins’ mango genome will aid global initiatives to study mango genetics.

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“…Recently, the genome sequence of a mango cultivar ‘Alphonso’ was published [ 52 ]. The methods of sequencing, assembly, and annotation of the two genomes are significantly different.…”

Section: Discussionmentioning

confidence: 99%

The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality

Bally¹,

Bombarely

Chambers

et al. 2021

BMC Plant Biol

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“…This is especially true given the identification of an atypical PIP T version of the mango IDA/IDL protein. The recent release of different mango genome sequences [48,49], opens now new avenues to explore the mango IDA-HAE/HSL2-like module. As such, a BLAST search using 'Tommy Atkins' mango genome led us to identifying three HAESA-like predicted proteins.…”

Section: Discussionmentioning

confidence: 99%

Characterization of Two Ethephon-Induced IDA-Like Genes from Mango, and Elucidation of Their Involvement in Regulating Organ Abscission

Chandra

Halon

Zemach

et al. 2021

Genes

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In mango (Mangifera indica L.), fruitlet abscission limits productivity. The INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) peptide acts as a key component controlling abscission events in Arabidopsis. IDA-like peptides may assume similar roles in fruit trees. In this study, we isolated two mango IDA-like encoding-genes, MiIDA1 and MiIDA2. We used mango fruitlet-bearing explants and fruitlet-bearing trees, in which fruitlets abscission was induced using ethephon. We monitored the expression profiles of the two MiIDA-like genes in control and treated fruitlet abscission zones (AZs). In both systems, qRT-PCR showed that, within 24 h, both MiIDA-like genes were induced by ethephon, and that changes in their expression profiles were associated with upregulation of different ethylene signaling-related and cell-wall modifying genes. Furthermore, ectopic expression of both genes in Arabidopsis promoted floral-organ abscission, and was accompanied by an early increase in the cytosolic pH of floral AZ cells—a phenomenon known to be linked with abscission, and by activation of cell separation in vestigial AZs. Finally, overexpression of both genes in an Atida mutant restored its abscission ability. Our results suggest roles for MiIDA1 and MiIDA2 in affecting mango fruitlet abscission. Based on our results, we propose new possible modes of action for IDA-like proteins in regulating organ abscission.

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“…We explored three popularly used software applications for merging transcriptome assemblies -StringTie-merge [76,[126][127][128][129][130][131][132], TACO [133][134][135][136][137][138] and Cuffmerge [139][140][141][142][143][144] to combine 116 A. thaliana assemblies constructed by StringTie [59], Scallop [61] and Strawberry [60] (Please check section 3 of Additional file 9 for more details). The best assembly was reported by StringTie-merge and was hence used for all other organisms.…”

Section: Psiclass Meta-assembly Work Better Than Other Approachesmentioning

confidence: 99%

FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

Banerjee

Bhandary

Woodhouse

et al. 2021

Preprint

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Background: Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available gene annotation software applications depend on pre-constructed full-length gene sequence assemblies which are not guaranteed to be error-free. The origins of these sequences are often uncertain, making it difficult to identify and rectify errors in them. This hinders the creation of an accurate and holistic representation of the transcriptomic landscape across multiple tissue types and experimental conditions. Therefore, to gauge the extent of diversity in gene structures, a comprehensive analysis of genome-wide expression data is imperative. Results: We present FINDER, a fully automated computational tool that optimizes the entire process of annotating genes and transcript structures. Unlike current state-of-the-art pipelines, FINDER automates the RNA-Seq pre-processing step by working directly with raw sequence reads and optimizes gene prediction from BRAKER2 by supplementing these reads with associated proteins. The FINDER pipeline (1) reports transcripts and recognizes genes that are expressed under specific conditions, (2) generates all possible alternatively spliced transcripts from expressed RNA-Seq data, (3) analyzes read coverage patterns to modify existing transcript models and create new ones, and (4) scores genes as high- or low-confidence based on the available evidence across multiple datasets. We demonstrate the ability of FINDER to automatically annotate a diverse pool of genomes from eight species. Conclusions: FINDER takes a completely automated approach to annotate genes directly from raw expression data. It is capable of processing eukaryotic genomes of all sizes and requires no manual supervision - ideal for bench researchers with limited experience in handling computational tools.

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The genome evolution and domestication of tropical fruit mango

Cited by 161 publications

References 120 publications

The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality

The ‘Tommy Atkins’ mango genome reveals candidate genes for fruit quality

Characterization of Two Ethephon-Induced IDA-Like Genes from Mango, and Elucidation of Their Involvement in Regulating Organ Abscission

FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

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