A Bioinformatics Approach to Identify Telomere Sequences

Somanathan, Indira; Baysdorfer, Chris

doi:10.2144/btn-2018-0057

Cited by 12 publications

(11 citation statements)

References 41 publications

(52 reference statements)

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“…Centromeres were predicted using the distribution of repeated sequences on chromosomes according to a previous report (Melters et al ., 2013). Telomeres were identified using SERF to find repeated sequences (bioserf.org) (Somanathan and Baysdorfer, 2018).…”

Section: Methodsmentioning

confidence: 99%

The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales

Song

Sun

Yuan

et al. 2020

Plant Biotechnology Journal

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Summary Celery (Apium graveolens L. 2n = 2x = 22), a member of the Apiaceae family, is among the most important and globally grown vegetables. Here, we report a high‐quality genome sequence assembly, anchored to 11 chromosomes, with total length of 3.33 Gb and N50 scaffold length of 289.78 Mb. Most (92.91%) of the genome is composed of repetitive sequences, with 62.12% of 31 326 annotated genes confined to the terminal 20% of chromosomes. Simultaneous bursts of shared long‐terminal repeats (LTRs) in different Apiaceae plants suggest inter‐specific exchanges. Two ancestral polyploidizations were inferred, one shared by Apiales taxa and the other confined to Apiaceae. We reconstructed 8 Apiales proto‐chromosomes, inferring their evolutionary trajectories from the eudicot common ancestor to extant plants. Transcriptome sequencing in three tissues (roots, leaves and petioles), and varieties with different‐coloured petioles, revealed 4 and 2 key genes in pathways regulating anthocyanin and coumarin biosynthesis, respectively. A remarkable paucity of NBS disease‐resistant genes in celery (62) and other Apiales was explained by extensive loss and limited production of these genes during the last ~10 million years, raising questions about their biotic defence mechanisms and motivating research into effects of chemicals, for example coumarins, that give off distinctive odours. Celery genome sequencing and annotation facilitates further research into important gene functions and breeding, and comparative genomic analyses in Apiales.

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Section: Methodsmentioning

confidence: 99%

The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales

Song

Sun

Yuan

et al. 2020

Plant Biotechnology Journal

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“…To identify telomeric repeats we used trf finder (Benson, ) and searched for tandem repeats with a unit length between 5 and 15 bp (usual length of telomeric repeats in plants) (Somanathan and Baysdorfer, ) using the following options (trf input.fasta 2 7 7 80 10 50 500). We assessed both copy number and localization of the detected tandem repeats to assess their association with telomeric regions.…”

Section: Methodsmentioning

confidence: 99%

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

et al. 2019

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Summary Marchantia polymorpha has recently become a prime model for cellular, evo‐devo, synthetic biological, and evolutionary investigations. We present a pseudomolecule‐scale assembly of the M. polymorpha genome, making comparative genome structure analysis and classical genetic mapping approaches feasible. We anchored 88% of the M. polymorpha draft genome to a high‐density linkage map resulting in eight pseudomolecules. We found that the overall genome structure of M. polymorpha is in some respects different from that of the model moss Physcomitrella patens. Specifically, genome collinearity between the two bryophyte genomes and vascular plants is limited, suggesting extensive rearrangements since divergence. Furthermore, recombination rates are greatest in the middle of the chromosome arms in M. polymorpha like in most vascular plant genomes, which is in contrast with P. patens where recombination rates are evenly distributed along the chromosomes. Nevertheless, some other properties of the genome are shared with P. patens. As in P. patens, DNA methylation in M. polymorpha is spread evenly along the chromosomes, which is in stark contrast with the angiosperm model Arabidopsis thaliana, where DNA methylation is strongly enriched at the centromeres. Nevertheless, DNA methylation and recombination rate are anticorrelated in all three species. Finally, M. polymorpha and P. patens centromeres are of similar structure and marked by high abundance of retroelements unlike in vascular plants. Taken together, the highly contiguous genome assembly we present opens unexplored avenues for M. polymorpha research by linking the physical and genetic maps, making novel genomic and genetic analyses, including map‐based cloning, feasible.

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“…Total percentages of genomic nucleic acid residues present as low-complexity repeats were determined using RepeatModeler2 24 . Tandemly repeated telomer sequences were identified using BioSerf 85 .…”

Section: Methodsmentioning

confidence: 99%

Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

Oliver

Podell

Pinowska

et al. 2021

Sci Rep

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A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.

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A Bioinformatics Approach to Identify Telomere Sequences

Cited by 12 publications

References 41 publications

The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales

The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales

A pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha

Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

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