scholarly journals Validation of Automated Chromosome Recovery in the Reconstruction of Ancestral Gene Order

Algorithms ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 160
Author(s):  
Qiaoji Xu ◽  
Lingling Jin ◽  
James H. Leebens-Mack ◽  
David Sankoff
Keyword(s):  
Phylogenetic Tree ◽  
Gene Order ◽  
Evolutionary Process ◽  
Gene Content ◽  
Ancestral Genome ◽  
Maximum Weight ◽  
Ancestral Gene ◽  
Maximum Weight Matching

The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process giving rise to the gene content and order of a set of extant genomes (six distantly related monocots), and to assess to what extent an updated version of RACCROCHE can recover the artificial ancestral genome at the root of the phylogenetic tree relating to the simulated genomes.

scholarly journals Chloroplast genome features of Moricandia arvensis (Brassicaceae), a C3-C4 intermediate photosynthetic species

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254109
Author(s):  
Bin Zhu ◽  
Lijuan Hu ◽  
Fang Qian ◽  
Zuomin Gao ◽  
Chenchen Gan ◽  
...  
Keyword(s):  
Gene Order ◽  
De Novo ◽  
Genomic Structure ◽  
Evolutionary Process ◽  
Single Copy ◽  
Synonymous Substitution ◽  
Gene Content ◽  
Moricandia Arvensis ◽  
Ssr Loci ◽  
Cp Genome

Moricandia arvensis, a plant species originating from the Mediterranean, has been classified as a rare C3-C4 intermediate species, and it is a possible bridge during the evolutionary process from C3 to C4 plant photosynthesis in the family Brassicaceae. Understanding the genomic structure, gene order, and gene content of chloroplasts (cp) of such species can provide a glimpse into the evolution of photosynthesis. In the present study, we obtained a well-annotated cp genome of M. arvensis using long PacBio and short Illumina reads with a de novo assembly strategy. The M. arvensis cp genome was a quadripartite circular molecule with the length of 153,312 bp, including two inverted repeats (IR) regions of 26,196 bp, divided by a small single copy (SSC) region of 17,786 bp and a large single copy (LSC) region of 83,134 bp. We detected 112 unigenes in this genome, comprising 79 protein-coding genes, 29 tRNAs, and four rRNAs. Forty-nine long repeat sequences and 51 simple sequence repeat (SSR) loci of 15 repeat types were identified. The analysis of Ks (synonymous) and Ka (non-synonymous) substitution rates indicated that the genes associated with “subunits of ATP synthase” (atpB), “subunits of NADH-dehydrogenase” (ndhG and ndhE), and “self-replication” (rps12 and rpl16) showed relatively higher Ka/Ks values than those of the other genes. The gene content, gene order, and LSC/IR/SSC boundaries and adjacent genes of the M. arvensis cp genome were highly conserved compared to those in related C3 species. Our phylogenetic analysis demonstrated that M. arvensis was clustered into a subclade with cultivated Brassica species and Raphanus sativus, indicating that M. arvensis was not involved in an independent evolutionary origin event. These results will open the way for further studies on the evolutionary process from C3 to C4 photosynthesis and hopefully provide guidance for utilizing M. arvensis as a resource for improvinng photosynthesis efficiency in cultivated Brassica species.

scholarly journals The chloroplast genome evolution of Venus slipper (Paphiopedilum): IR expansion, SSC contraction, and highly rearranged SSC regions

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yan-Yan Guo ◽  
Jia-Xing Yang ◽  
Ming-Zhu Bai ◽  
Guo-Qiang Zhang ◽  
Zhong-Jian Liu
Keyword(s):  
Gene Order ◽  
Inverted Repeat ◽  
Single Copy ◽  
Gene Content ◽  
Comparative Genomic ◽  
Substitution Rates ◽  
Plastome Evolution ◽  
Chloroplast Genomes ◽  
Ideal System ◽  
Small Single Copy

Abstract Background Paphiopedilum is the largest genus of slipper orchids. Previous studies showed that the phylogenetic relationships of this genus are not well resolved, and sparse taxon sampling documented inverted repeat (IR) expansion and small single copy (SSC) contraction of the chloroplast genomes of Paphiopedilum. Results Here, we sequenced, assembled, and annotated 77 plastomes of Paphiopedilum species (size range of 152,130 – 164,092 bp). The phylogeny based on the plastome resolved the relationships of the genus except for the phylogenetic position of two unstable species. We used phylogenetic and comparative genomic approaches to elucidate the plastome evolution of Paphiopedilum. The plastomes of Paphiopedilum have a conserved genome structure and gene content except in the SSC region. The large single copy/inverted repeat (LSC/IR) boundaries are relatively stable, while the boundaries of the inverted repeat and small single copy region (IR/SSC) varied among species. Corresponding to the IR/SSC boundary shifts, the chloroplast genomes of the genus experienced IR expansion and SSC contraction. The IR region incorporated one to six genes of the SSC region. Unexpectedly, great variation in the size, gene order, and gene content of the SSC regions was found, especially in the subg. Parvisepalum. Furthermore, Paphiopedilum provides evidence for the ongoing degradation of the ndh genes in the photoautotrophic plants. The estimated substitution rates of the protein coding genes show accelerated rates of evolution in clpP, psbH, and psbZ. Genes transferred to the IR region due to the boundary shift also have higher substitution rates. Conclusions We found IR expansion and SSC contraction in the chloroplast genomes of Paphiopedilum with dense sampling, and the genus shows variation in the size, gene order, and gene content of the SSC region. This genus provides an ideal system to investigate the dynamics of plastome evolution.

scholarly journals Randomized scheduling algorithm for virtual output queuing switch at the presence of non-uniform traffic

2019 ◽  
Vol 8 (1) ◽  
pp. 50
Author(s):  
Ali Ghiasian ◽  
Majid Jamali
Keyword(s):  
Randomized Algorithms ◽  
High Speed ◽  
Time Slot ◽  
Scheduling Algorithm ◽  
Superior Performance ◽  
High Complexity ◽  
Maximum Weight ◽  
Switch Architecture ◽  
Simulation Results ◽  
Maximum Weight Matching

<span>Virtual Output Queuing (VOQ) is a well-known queuing discipline in data switch architecture that eliminates Head Of Line (HOL) blocking issue. In VOQ scheme, for each output port, a separate FIFO is maintained by each input port. Consequently, a scheduling algorithm is required to determine the order of service to virtual queues at each time slot. Maximum Weight Matching (MWM) is a well-known scheduling algorithm that achieves the entire throughput region. Despite of outstanding attainable throughput, high complexity of MWM makes it an impractical algorithm for implementation in high-speed switches. To overcome this challenge, a number of randomized algorithms have been proposed in the literature. But they commonly perform poorly when input traffic does not uniformly select output ports. In this paper, we propose two randomized algorithms that outperform the well-known formerly proposed solutions. We exploit a method to keep a parametric number of heavy edges from the last time matching and mix it by randomly generated matching to produce a new schedule. Simulation results confirm the superior performance of the proposed algorithms.</span>

scholarly journals Linear-Time Approximation for Maximum Weight Matching

2014 ◽  
Vol 61 (1) ◽  
pp. 1-23 ◽  
Author(s):  
Ran Duan ◽  
Seth Pettie
Keyword(s):  
Linear Time ◽  
Maximum Weight ◽  
Time Approximation ◽  
Maximum Weight Matching
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