scholarly journals Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuliya A. Putintseva ◽  
Eugeniya I. Bondar ◽  
Evgeniy P. Simonov ◽  
Vadim V. Sharov ◽  
Natalya V. Oreshkova ◽  
...  
Keyword(s):  
Dna Sequences ◽  
De Novo ◽  
Keystone Species ◽  
Siberian Larch ◽  
Larix Sibirica ◽  
Flowering Plant ◽  
Rrna Genes ◽  
Total Size ◽  
Protein Coding ◽  
Sequencing Project

Abstract Background Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibirica Ledeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plant Silene conica (11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.

scholarly journals Repetitive Elements in the Siberian Larch (Larix Sibirica Ledeb.) Nuclear Genome

2021 ◽  
Author(s):  
Kseniya A. Miroshnikova ◽  
Vasilina S. Akulova ◽  
Vladislav V. Biriukov ◽  
Eugeniya I. Bondar ◽  
Dmitry A. Kuzmin ◽  
...  
Keyword(s):  
Resistance Genes ◽  
De Novo ◽  
Plant Immunity ◽  
Nuclear Genome ◽  
Siberian Larch ◽  
Larix Sibirica ◽  
Repetitive Elements ◽  
Structural Element ◽  
Total Size ◽  
First Time

Abstract Background: Repetitive elements (REs) or repeats are sequences that occur multiple times in the genome. They represent a significant part of the gigantic conifer genomes (70-80%) relative to mammals and other plants and complicate whole genome sequencing and annotation. However, REs play important roles in evolution and adaptation processes in both plants and animals. Moreover, amino acid repeats play an important role in plant immunity being a structural element of the products of some disease resistance genes. Analysis of REs in conifer genomes is an important fundamental task.Results: REs were identified de novo and partly classified in the Siberian larch (Larix sibirica Ledeb.) nuclear genome for the first time. In total, 20.9 million REs were detected with the total size of 4.8 Gbp, which comprises about 39% of the 12.3 Gbp larch genome. Resistance genes with leucine-rich repeats (LRRs) were also identified and analyzed in the transcriptome data of autumn buds obtained using RNA-seq.Conclusions: For the first time, REs were identified and classified in the Siberian larch genome and transcriptome. In addition, LRRs and resistance genes were identified and analyzed in the Siberian larch transcriptomes from autumn buds. The larch genome contains twice as less RE compared to other conifers in the same Pinaceae family (39 vs 70-80%), and it might explain why it also has almost twice as smaller genome size (12 vs 18-31 Gbp).

The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

2020 ◽  
Author(s):  
Liyan Qu ◽  
Heng Zhang ◽  
Fengying Zhang ◽  
Wei Wang ◽  
Fenghua Tang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flying Fishes ◽  
Complete Mitochondrial Genomes

Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii.

scholarly journals Evolution of Pulmonate Gastropod Mitochondrial Genomes: Comparisons of Gene Organizations of Euhadra, Cepaea and Albinaria and Implications of Unusual tRNA Secondary Structures

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 749-758 ◽  
Author(s):  
Nika Yamazaki ◽  
Rei Ueshima ◽  
Jonathan A Terrett ◽  
Shin-ichi Yokobori ◽  
Masayuki Kaifu ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Rrna Genes ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Overlapping Genes ◽  
Protein Coding ◽  
Cepaea Nemoralis ◽  
Protein Coding Genes ◽  
Editing Process ◽  
Pulmonate Gastropod

Complete gene organizations of the mitochondrial genomes of three pulmonate gastropods, Euhadra herklotsi, Cepaea nemoralis and Albinaria coerulea, permit comparisons of their gene organizations. Euhadra and Cepaea are classified in the same superfamily, Helicoidea, yet they show several differences in the order of tRNA and protein coding genes. Albinaria is distantly related to the other two genera but shares the same gene order in one part of its mitochondrial genome with Euhadra and in another part with Cepaea. Despite their small size (14.1 – 14.5 kbp), these snail mtDNAs encode 13 protein genes, two rRNA genes and at least 22 tRNA genes. These genomes exhibit several unusual or unique features compared to other published metazoan mitochondrial genomes, including those of other molluscs. Several tRNAs predicted from the DNA sequences possess bizarre structures lacking either the T stem or the D stem, similar to the situation seen in nematode mt-tRNAs. The acceptor stems of many tRNAs show a considerable number of mismatched basepairs, indicating that the RNA editing process recently demonstrated in Euhadra is widespread in the pulmonate gastropods. Strong selection acting on mitochondrial genomes of these animals would have resulted in frequent occurrence of the mismatched basepairs in regions of overlapping genes.

scholarly journals GeneMark-HM: improving gene prediction in DNA sequences of human microbiome

2021 ◽  
Vol 3 (2) ◽  
Author(s):  
Alexandre Lomsadze ◽  
Christophe Bonny ◽  
Francesco Strozzi ◽  
Mark Borodovsky
Keyword(s):  
Dna Sequences ◽  
De Novo ◽  
Gene Annotation ◽  
Selection Process ◽  
Gene Prediction ◽  
Bacterial Species ◽  
Human Microbiome ◽  
Genome Database ◽  
Protein Coding ◽  
Pan Genome

Abstract Computational reconstruction of nearly complete genomes from metagenomic reads may identify thousands of new uncultured candidate bacterial species. We have shown that reconstructed prokaryotic genomes along with genomes of sequenced microbial isolates can be used to support more accurate gene prediction in novel metagenomic sequences. We have proposed an approach that used three types of gene prediction algorithms and found for all contigs in a metagenome nearly optimal models of protein-coding regions either in libraries of pre-computed models or constructed de novo. The model selection process and gene annotation were done by the new GeneMark-HM pipeline. We have created a database of the species level pan-genomes for the human microbiome. To create a library of models representing each pan-genome we used a self-training algorithm GeneMarkS-2. Genes initially predicted in each contig served as queries for a fast similarity search through the pan-genome database. The best matches led to selection of the model for gene prediction. Contigs not assigned to pan-genomes were analyzed by crude, but still accurate models designed for sequences with particular GC compositions. Tests of GeneMark-HM on simulated metagenomes demonstrated improvement in gene annotation of human metagenomic sequences in comparison with the current state-of-the-art gene prediction tools.

scholarly journals Development of microsatellite genetic markers in Siberian larch (Larix sibirica Ledeb.) based on the de novo whole genome sequencing

2017 ◽  
Vol 53 (11) ◽  
pp. 1194-1199 ◽  
Author(s):  
N. V. Oreshkova ◽  
Yu. A. Putintseva ◽  
V. V. Sharov ◽  
D. A. Kuzmin ◽  
K. V. Krutovsky
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
De Novo ◽  
Siberian Larch ◽  
Larix Sibirica ◽  
Whole Genome

scholarly journals The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiaolin Li ◽  
Lijiao Li ◽  
Zhijie Bao ◽  
Wenying Tu ◽  
Xiaohui He ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Fungal Species ◽  
Ectomycorrhizal Fungus ◽  
Open Reading Frames ◽  
Rrna Genes ◽  
Trna Genes ◽  
Total Size ◽  
Protein Coding

In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogenome of T. calosporum, involving gene relocations and position exchanges. The mitogenome of T. calosporum was found to have lost several tRNA genes encoding for cysteine, aspartate, histidine, etc. In addition, a pair of fragments with a total length of 32.91 kb in both the nuclear and mitochondrial genomes of T. calosporum was detected, indicating possible gene transfer events. A total of 12.83% intragenomic duplications were detected in the T. calosporum mitogenome. Phylogenetic analysis based on mitochondrial gene datasets obtained well-supported tree topologies, indicating that mitochondrial genes could be reliable molecular markers for phylogenetic analyses of Ascomycota. This study served as the first report on mitogenome in the family Tuberaceae, thereby laying the groundwork for our understanding of the evolution, phylogeny, and population genetics of these important ectomycorrhizal fungi.

scholarly journals Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica

2019 ◽  
Author(s):  
Fen Zhang ◽  
Wei Li ◽  
Cheng-wen Gao ◽  
Li-zhi Gao
Keyword(s):  
Rna Editing ◽  
Camellia Sinensis ◽  
De Novo ◽  
Single Copy ◽  
Rrna Genes ◽  
Protein Coding ◽  
Tea Tree ◽  
Protein Coding Genes ◽  
Cp Genome ◽  
Mt Genome

ABSTRACTTea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. Despite its enormous industrial, cultural and medicinal values, the chloroplast (cp) and mitochondrial (mt) genomes are not available for Camellia sinensis var. assamica. In this study, we de novo assembled the cp genome sequence of C. sinensis var. assamica into a circular contig of 157,100 bp in length with an overall GC content of 37.29%, comprising a large single-copy region (LSC, 86,649 bp) and a small single-copy region (SSC, 18,285 bp) separated by a pair of inverted repeats (IRs, 26,083 bp). We annotated a total of 141 cp genes, of which 87 are protein-coding genes, 46 are tRNA genes, and eight are rRNA genes. We also de novo assembled the mt genome of C. sinensis var. assamica into two complete circular scaffolds (702,253 bp and 178,082 bp) with overall GC contents of 45.63% and 45.81%, respectively. We annotated a total of 71 mt genes, including 44 protein-coding genes, 24 tRNAs, and 3 rRNAs. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878 bp and 149 bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are ∼4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamica presented in this study will become an invaluable resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.

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