Methods and Tools for Plant Organelle Genome Sequencing, Assembly, and Downstream Analysis

Sandhya, Sankaran; Srivastava, Harsha; Kaila, Tanvi; Tyagi, Anshika; Gaikwad, Kishor

doi:10.1007/978-1-0716-0235-5_4

Cited by 14 publications

(9 citation statements)

References 87 publications

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“…In avocado, the plastid genome was of intermediate size (153 kb) with respect to the known range of plastid genomes, i.e. 100–220 kb [ 45 ]. Mitochondrial genomes in plants can vary greatly in size (100–10 000 kb), with the size in avocado being small compared to those of most flowering plants [ 17 ].…”

Section: Discussionmentioning

confidence: 99%

A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes

Nath

Fletcher

Hayward

et al. 2022

Horticulture Research

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Avocado (Persea americana) is a member of the magnoliids, an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious. Here, we report a chromosome-level genome assembly for the commercial avocado cultivar Hass, which represents 80% of the world’s avocado consumption. The DNA contigs produced from Pacific Biosciences HiFi reads were further assembled using a previously published version of the genome supported by a genetic map. The total assembly was 913 Mb with a contig N50 of 84 Mb. Contigs assigned to the 12 chromosomes represented 874 Mb and covered 98.8% of benchmarked single-copy genes from embryophytes. Annotation of protein coding sequences identified 48 915 avocado genes of which 39 207 could be ascribed functions. The genome contained 62.6% repeat elements. Specific biosynthetic pathways of interest in the genome were investigated. The analysis suggested that the predominant pathway of heptose biosynthesis in avocado may be through sedoheptulose 1,7 bisphosphate rather than via alternative routes. Endoglucanase genes were high in number, consistent with avocado using cellulase for fruit ripening. The avocado genome appeared to have a limited number of translocations between homeologous chromosomes, despite having undergone multiple genome duplication events. Proteome clustering with related species permitted identification of genes unique to avocado and other members of the Lauraceae family, as well as genes unique to species diverged near or prior to the divergence of monocots and eudicots. This genome provides a tool to support future advances in the development of elite avocado varieties with higher yields and fruit quality.

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Section: Discussionmentioning

confidence: 99%

A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes

Nath

Fletcher

Hayward

et al. 2022

Horticulture Research

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“…For example, more conserved genes in the organelle can more clearly reflect the evolutionary history, and sequences with a higher evolution rate encoded by the organelle can be used to study the systemic relationship at the species level ( 47 ). The small organelle genome and closed loop feature mean that the de novo sequencing is relatively simple and easy to splice, and subsequent analysis can facilitate the operation, resulting in faster accumulation of organelle genome data, which leads to challenges related to genome ‘big data’ ( 48 ). Therefore, the development of a professional database will help more scientists skillfully use genomic data.…”

Section: Discussionmentioning

confidence: 99%

OGDA: a comprehensive organelle genome database for algae

et al. 2020

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Algae are the oldest taxa on Earth, with an evolutionary relationship that spans prokaryotes (Cyanobacteria) and eukaryotes. A long evolutionary history has led to high algal diversity. Their organelle DNAs are characterized by uniparental inheritance and a compact genome structure compared with nuclear genomes; thus, they are efficient molecular tools for the analysis of gene structure, genome structure, organelle function and evolution. However, an integrated organelle genome database for algae, which could enable users to both examine and use relevant data, has not previously been developed. Therefore, to provide an organelle genome platform for algae, we have developed a user-friendly database named Organelle Genome Database for Algae (OGDA, http://ogda.ytu.edu.cn/). OGDA contains organelle genome data either retrieved from several public databases or sequenced in our laboratory (Laboratory of Genetics and Breeding of Marine Organism [MOGBL]), which are continuously updated. The first release of OGDA contains 1055 plastid genomes and 755 mitochondrial genomes. Additionally, a variety of applications have been integrated into this platform to analyze the structural characteristics, collinearity and phylogeny of organellar genomes for algae. This database represents a useful tool for users, enabling the rapid retrieval and analysis of information related to organellar genomes for biological discovery.

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“…A global scaling process is developed to solve this problem (Figure 2b). If l adj_g is greater than l g , we use Formulas (van Dijk et al, 2014) and (Sandhya et al, 2020) to adjust the start and end positions of all exons:…”

Section: Developing a Coordinate Scaling Algorithm For Drawing Cis-sp...mentioning

confidence: 99%

“…genome" and "plastome." Ensuring the correct assembly and annotation of many chloroplast genome sequences has become increasingly challenging (Sandhya et al, 2020).…”

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confidence: 99%

CPGView: A package for visualizing detailed chloroplast genome structures

Liu

et al. 2023

Molecular Ecology Resources

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Chloroplast genomes have been widely used in studying plant phylogeny and evolution. Several chloroplast genome visualization tools have been developed to display the distribution of genes on the genome. However, these tools do not draw features, such as exons, introns, repetitive elements, and variable sites, disallowing in‐depth examination of the genome structures. Here, we developed and validated a software package called Chloroplast Genome Viewers (CPGView). CPGView can draw three maps showing (i) the distributions of genes, variable sites, and repetitive sequences, including microsatellites, tandem and dispersed repeats; (ii) the structure of the cis‐splicing genes after adjusting the exon‐intron boundary positions using a coordinate scaling algorithm, and (iii) the structure of the trans‐splicing gene rps12. To test the accuracy of CPGView, we sequenced, assembled, and annotated 31 chloroplast genomes from 31 genera of 22 families. CPGView drew maps correctly for all the 31 chloroplast genomes. Lastly, we used CPGView to examine 5998 publicly released chloroplast genomes from 2513 genera of 553 families. CPGView succeeded in plotting maps for 5882 but failed to plot maps for 116 chloroplast genomes. Further examination showed that the annotations of these 116 genomes had various errors needing manual correction. The test on newly generated data and publicly available data demonstrated the ability of CPGView to identify errors in the annotations of chloroplast genomes. CPGView will become a widely used tool to study the detailed structure of chloroplast genomes. The web version of CPGView can be accessed from http://www.1kmpg.cn/cpgview.

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Methods and Tools for Plant Organelle Genome Sequencing, Assembly, and Downstream Analysis

Cited by 14 publications

References 87 publications

A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes

A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes

OGDA: a comprehensive organelle genome database for algae

CPGView: A package for visualizing detailed chloroplast genome structures

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