Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi

Ribeiro, Tiago; Vasconcelos, Emanuelle Varão; Santos, Karla G. B. dos; Vaio, Magdalena; Brasileiro-Vidal, Ana Christina; Pedrosa‐Harand, Andrea

doi:10.1007/s10577-019-09618-w

Cited by 29 publications

(23 citation statements)

References 58 publications

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“…We have applied short read sequencing followed by read clustering to efficiently gain insights into both genomes’ satDNA contents (as laid out by Weiss-Schneeweiss et al, 2015 ; Novák et al, 2017 ). This approach has been successfully used to characterize the repeat landscapes of many non-model plant species as for example beans, various grasses, camellias, crocuses, quinoa, and ferns ( Cai et al, 2014 ; Heitkam et al, 2015 ; Ávila Robledillo et al, 2018 ; Kirov et al, 2018 ; Liu et al, 2019 ; Schmidt et al, 2019 ; Heitkam et al, 2020 ; Ribeiro et al, 2020 ), and also of non-model animals, such as locusts, grasshoppers, or fishes ( Ruiz-Ruano et al, 2016 ; Ferretti et al, 2020 ; Boštjančić et al, 2021 ). For larch genomes, we provided evidence that LTR retrotransposons and derived fragments are their main components, well in line with reports for the related pines and spruces ( Kamm et al, 1996 ; Kossack and Kinlaw, 1999 ; Nystedt et al, 2013 ; Stevens et al, 2016 ; Voronova et al, 2017 ; Perera et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs

et al. 2021

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In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 giga base pairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers’ accumulative genome evolution mode. For this, we applied low-coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs’ organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.

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Section: Discussionmentioning

confidence: 99%

Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs

et al. 2021

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“…We have applied short read sequencing followed by read clustering to efficiently gain insights into both genomes’ satDNA contents (as laid out by Weiss-Schneeweiss et al, 2015; Novák et al, 2017). This approach has been successfully used to characterize the repeat landscapes of many non-model plant species as for example beans, various grasses, camellias, crocuses, quinoa, and ferns (Cai et al, 2014; Heitkam et al, 2015; Ávila Robledillo et al, 2018; Kirov et al, 2018; Liu et al, 2019; Schmidt et al, 2019; Heitkam et al, 2020; Ribeiro et al, 2020), and also of non-model animals such as locusts, grasshoppers, or fishes (Ruiz-Ruano et al, 2016; Ferretti et al, 2020; Boštjancić et al, 2021). For larch genomes, we provided evidence that LTR retrotransposons and derived fragments are their main components, well in line with reports for the related pines and spruces (Kamm et al, 1996; Kossack and Kinlaw, 1999; Nystedt et al, 2013; Stevens et al, 2016; Perera et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Comparative repeat profiling of two closely related conifers (Larix decidua and Larix kaempferi) reveals high genome similarity with only few fast-evolving satellite DNAs

Heitkam

Schulte

Weber

et al. 2021

Preprint

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In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 gigabasepairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers' accumulative genome evolution mode. For this, we applied low coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs' organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.

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“…The copyright holder for this this version posted December 11, 2020. ; https://doi.org/10.1101/2020.12.10.419515 doi: bioRxiv preprint 21 grossly underestimate the true abundance of this repeat type (i.e. Ribeiro et al, 2020), caution is needed when interpreting TCS-yielded genomic abundances, though similar caution is needed with GS data as well.…”

Section: Tcs Data Can Be Used To Characterize the Repeat Composition mentioning

confidence: 99%

“…The activity of transposable elements in the host genome can also cause modifications to gene regulation and the formation of retrogenes, generating morphological innovations and impacting speciation processes (Schrader & Schmitz, 2019). Moreover, lineage-specific satellite DNAs have been widely used as efficient cytomolecular markers, allowing the identification of chromosome pairs and elucidating chromosome rearrangement and duplication events (Koo et al, 2011;Čížková et al, 2013;Ávila Robledillo et al, 2018;Ribeiro et al, 2020) .…”

Section: Introductionmentioning

confidence: 99%

“…The fast evolution of repetitive DNA, with many satellite families being genus-or species-specific, impair their use in phylogenetic studies, as concerted evolution and homogenisation reduces sequence variability for comparative studies across taxa (Macas et al, 2015;Mascagni et al, 2020;Ribeiro et al, 2020). Their abundances, however, have preprint (which was not certified by peer review) is the author/funder.…”

Section: Introductionmentioning

confidence: 99%

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Aiming off the target: studying repetitive DNA using target capture sequencing reads

Costa

Marques

Buddenhagen

et al. 2020

Preprint

Self Cite

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SUMMARYWith the advance of high-throughput sequencing (HTS), reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information. As the off-target reads from such sequencing are expected to be similar to genome skims (GS), we assessed the quality of repeat characterization using this data.For this, repeat composition from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa.All the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01% in the GS data. Rank correlation between GS and TCS repeat abundances were moderately high (r = 0.58-0.85), increasing after filtering out the targeted loci from the raw TCS reads (r = 0.66-0.92). Repeat data obtained by TCS was also reliable to develop a cytogenetic probe and solve phylogenetic relationships of Rhynchospora species with high support.In light of our results, TCS data can be effectively used for cyto- and phylogenomic investigations of repetitive DNA. Given the growing availability of HTS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity.

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Diversity of repetitive sequences within compact genomes of Phaseolus L. beans and allied genera Cajanus L. and Vigna Savi

Cited by 29 publications

References 58 publications

Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs

Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs

Comparative repeat profiling of two closely related conifers (Larix decidua and Larix kaempferi) reveals high genome similarity with only few fast-evolving satellite DNAs

Aiming off the target: studying repetitive DNA using target capture sequencing reads

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