CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data

Abramova, Anna; Osińska, Adriana; Kunche, Haveela; Burman, Emil; Bengtsson‐Palme, Johan

doi:10.1093/bioinformatics/btaa1086

Cited by 5 publications

(4 citation statements)

References 9 publications

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“…The divergence time of different Syringa species were also estimated by mcmctree based on the divergence time from timetree ( Fraxinus excelsior versus S. oblata , Forsythia suspensa versus S. oblata ) and related studies (Kim & Jansen, 1998), and all divergence time were using 95% HPD. Gene expansion was processed using café , version 3.1 (Abramova et al., 2021). The orthmcl results and the divergence tree were used as the input in the gene expansion determination step.…”

Section: Methodsmentioning

confidence: 99%

A chromosome‐level genome of Syringa oblata provides new insights into chromosome formation in Oleaceae and evolutionary history of lilacs

Wang

et al. 2022

The Plant Journal

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Lilacs (Syringa L.), a group of well-known ornamental and aromatic woody plants, have long been used for gardening, essential oils and medicine purposes in East Asia and Europe. The lack of knowledge about the complete genome of Syringa not only hampers effort to better understand its evolutionary history, but also prevents genome-based functional gene mining that can help in the variety improvement and medicine development. Here, a chromosome-level genome of Syringa oblata is presented, which has a size of 1.12 Gb including 53 944 protein coding genes. Synteny analysis revealed that a recent duplication event and parallel evolution of two subgenomes formed the current karyotype. Evolutionary analysis, transcriptomics and metabolic profiling showed that segment and tandem duplications contributed to scent formation in the woody aromatic species. Moreover, phylogenetic analysis indicated that S. oblata shared a common ancestor with Osmanthus fragrans and Olea europaea approximately 27.61 million years ago (Mya). Biogeographic reconstruction based on a resequenced data set of 26 species suggested that Syringa originated in the northern part of East Asia during the Miocene (approximately 14.73 Mya) and that the five Syringa groups initially formed before the Late Miocene (approximately 9.97 Mya). Furthermore, multidirectional dispersals accompanied by gene introgression among Syringa species from Northern China during the Miocene were detected by biogeographic reconstruction. Taken together, the results showed that complex gene introgression, which occurred during speciation history, greatly contributed to Syringa diversity.

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Section: Methodsmentioning

confidence: 99%

A chromosome‐level genome of Syringa oblata provides new insights into chromosome formation in Oleaceae and evolutionary history of lilacs

Wang

et al. 2022

The Plant Journal

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“…The divergence time between different species was calculated by MCMCtree (4.8a) from the PAML package 35 based on four calibrations ( P. persica vs P. mume , C. pseudocerasus vs P. persica , M. domestica vs P. bretschneideri , R. chinensis vs F. ananassa ) from TimeTree 36 ( http://www.timetree.org ). CAFÉ 37 (v3.1) was used to estimate the gene expansion based on the OrthMCL results and times divergence tree.…”

Section: Methodsmentioning

confidence: 99%

The genome of Prunus humilis provides new insights to drought adaption and population diversity

Wang

Xie²,

Zhang

et al. 2022

DNA Research

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Prunus humilis (2n =2x = 16) is dwarf shrub fruit tree native to China and distributed widely in the cold and arid northern region. In this study, we obtained the whole genome sequences of P. humilis by combining Illumina, Pacbio and HiC sequencing technologies. This genome was 254.38Mb long and encodes 28,301 putative proteins. Phylogenetic analysis indicated that P. humilis shares the same ancestor with Prunus mume and Prunus armeniaca at ∼ 29.03 Mya. Gene expansion analysis implied that the expansion of WAX-related and LEA genes might be associated with high drought tolerance of P. humilis and LTR maybe one of the driver factors for the drought adaption by increase the copy number of LEAs. Population diversity analysis among 20 P. humilis accessions found that the genetic diversity of P. humilis populations was limited, only 1.40% base pairs were different with each other, more wild resources need to be collected and utilized in the breeding and improvement. This study provides new insights to the drought adaption and population diversity of P. humilis, that could be used as a potential model plant for horticultural research.

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“…Time calibration points (correction points) were from the Timetree website [ 99 ]. The gene family was then analyzed using CAFE v. 3.1 software and GO functional enrichment analysis for the genes in these families (Table S3 ) [ 100 – 102 ]. A branch-site model can detect positive selection that occurs in a particular clade and only affects a portion of the locus.…”

Section: Methodsmentioning

confidence: 99%

Genome assembly of Melilotus officinalis provides a new reference genome for functional genomics

Meng,

Li,

et al. 2024

BMC Genom Data

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Background Sweet yellow clover (Melilotus officinalis) is a diploid plant (2n = 16) that is native to Europe. It is an excellent legume forage. It can both fix nitrogen and serve as a medicine. A genome assembly of Melilotus officinalis that was collected from Best corporation in Beijing is available based on Nanopore sequencing. The genome of Melilotus officinalis was sequenced, assembled, and annotated. Results The latest PacBio third generation HiFi assembly and sequencing strategies were used to produce a Melilotus officinalis genome assembly size of 1,066 Mbp, contig N50 = 5 Mbp, scaffold N50 = 130 Mbp, and complete benchmarking universal single-copy orthologs (BUSCOs) = 96.4%. This annotation produced 47,873 high-confidence gene models, which will substantially aid in our research on molecular breeding. A collinear analysis showed that Melilotus officinalis and Medicago truncatula shared conserved synteny. The expansion and contraction of gene families showed that Melilotus officinalis expanded by 565 gene families and shrank by 56 gene families. The contacted gene families were associated with response to stimulus, nucleotide binding, and small molecule binding. Thus, it is related to a family of genes associated with peptidase activity, which could lead to better stress tolerance in plants. Conclusions In this study, the latest PacBio technology was used to assemble and sequence the genome of the Melilotus officinalis and annotate its protein-coding genes. These results will expand the genomic resources available for Melilotus officinalis and should assist in subsequent research on sweet yellow clover plants.

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CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data

Cited by 5 publications

References 9 publications

A chromosome‐level genome of Syringa oblata provides new insights into chromosome formation in Oleaceae and evolutionary history of lilacs

A chromosome‐level genome of Syringa oblata provides new insights into chromosome formation in Oleaceae and evolutionary history of lilacs

The genome of Prunus humilis provides new insights to drought adaption and population diversity

Genome assembly of Melilotus officinalis provides a new reference genome for functional genomics

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