High level of somatic mutations detected in a diploid banana wild relative Musa basjoo

Ji, Yilun; Chen, Xiaonan; Lin, Shi Ying; Traw, M. Brian; Tian, Dacheng; Yang, Sihai; Wang, Long; Huang, Ju

doi:10.1007/s00438-022-01959-2

Cited by 4 publications

(2 citation statements)

References 51 publications

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“…Asexual propagation leads to developing and accumulating somatic mutations in bananas (Mertens et al, 2021;Sardos et al, 2022;Ji et al, 2023).…”

Section: Chitinase Gene Sequence Variation In 'Lakatan'/'mapilak' And...mentioning

confidence: 99%

Sequence Variability and in Vitro Cleavage of Chitinase Homologs Toward Crispr/Cas9-Based Genome-Editing in Philippine Bananas

GARDOCE

2024

SABRAOJBG

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The technology based on CRISPR/Cas9, one of the potential solutions recognized for addressing the worsening situation of fusarium wilt caused by Fusarium oxysporum f. sp. cubense 'Tropical Race 4" (TR4) plaguing the Philippine banana industry, still lacks information on its use to target host resistance in Philippine bananas. This study reports the elucidation of the gene sequence of chitinase homologs chit6 and chac in the leading Philippine dessert banana varieties, "Lakatan" and "Latundan," and the design, selection, and pre-validation of sgRNAs using in vitro cleavage assay. Multiple sequence alignment revealed the conserved sites, SNPs, and indels. Evolutionary analysis disclosed that the pattern of nucleotide substitution resulted in an overall bias in favor of adenine and thymine changing to cytosine and guanine. It said transitions outnumber transversions typical of clonally propagated crops. The in silico prediction initially identified a total of 58 sgRNAs for chit6 and 68 sgRNAs for chac, with 58.62% and 58.97% found across "Latundan" and "Lakatan"/"Mapilak" backgrounds, respectively. A design criteria imposition for plants and consideration of the predicted efficiency and localization of sgRNAs along the targets narrowed down the sgRNAs. Four selected efficient sgRNAs were demonstrated to cleave all targets under in vitro assay with Cas9, showing its potential for gene editing by the SDN-1 or SDN-2 mechanism. With unavailable protocols for embryogenic cell suspension and corresponding delivery systems for these varieties, this in vitro approach provides a strategy to identify potential sgRNAs to streamline resources for the gene-editing pipeline and a guide to employing CRISPR/Cas9 for elucidation of the functional role of chit6 and chac in host resistance response to TR4 in bananas.

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“…Asexual propagation leads to developing and accumulating somatic mutations in bananas (Mertens et al, 2021;Sardos et al, 2022;Ji et al, 2023).…”

Section: Chitinase Gene Sequence Variation In 'Lakatan'/'mapilak' And...mentioning

confidence: 99%

Sequence Variability and in Vitro Cleavage of Chitinase Homologs Toward Crispr/Cas9-Based Genome-Editing in Philippine Bananas

GARDOCE

2024

SABRAOJBG

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“…Multiple studies have analysed genomic mosaicism within individual plants and discussed various aspects of somatic mutations like mutation rates, allelic frequencies, genome-wide distribution, and distribution across branches (14)(15)(16)(17)(18)(19)(20)(21)(22). However, most analyses were limited to bulked samples where cells from all layers were sequenced and analysed together.…”

Section: Introductionmentioning

confidence: 99%

The vast majority of somatic mutations in plants are layer-specific

Goel,

Campoy,

Krause

et al. 2024

Preprint

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Plant meristems consist of three distinct stem cells layers. The identities of these layers are maintained in developing organs. Somatic mutations in the meristem thus propagate only into the respective layers of the differentiated organs. We analysed the genomes of individual cell layers in an apricot tree and found an unexpectedly high mutation load, where >90% of the somatic mutations were layer-specific. The layers had similar mutation spectra but layer 1 (epidermis) had substantially more mutations than layer 2 (mesocarp). Most somatic mutations were shared between fruits and neighbouring leaves corroborating their meristematic origin. Single-cell transcriptomics revealed their layer-specific effects forming the basis for layer-specific phenotypes. Our work unveils the hidden abundance of layer-specific meristematic mutations and provides insights into their identification and understanding.

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A clock for clonal organisms

Wang

2024

Nat Ecol Evol

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High level of somatic mutations detected in a diploid banana wild relative Musa basjoo

Cited by 4 publications

References 51 publications

Sequence Variability and in Vitro Cleavage of Chitinase Homologs Toward Crispr/Cas9-Based Genome-Editing in Philippine Bananas

Sequence Variability and in Vitro Cleavage of Chitinase Homologs Toward Crispr/Cas9-Based Genome-Editing in Philippine Bananas

The vast majority of somatic mutations in plants are layer-specific

A clock for clonal organisms

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