scholarly journals The assembled Banana dihaploid mitochondrial genome is compact with a high number of gene copies

2022 ◽  
Author(s):  
Shruthy Priya Prakash ◽  
Vaidheki Chandrasekar ◽  
Selvi Subramanian ◽  
Rahamatthunnisha Ummar
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequence ◽  
Copy Number ◽  
Ribosomal Proteins ◽  
Tandem Repeats ◽  
Sequence Data ◽  
Crop Improvement ◽  
Whole Genome Sequence ◽  
Trna Genes ◽  
Mt Genome

Banana being a major food crop all around the world, attracts various research interests in crop improvement. In banana, complete genome sequences of Musa accuminata and Musa balbisiana are available. However, the mitochondrial genome is not sequenced or assembled. Mitochondrial (mt) genes play an important role in flower and seed development and in Cytoplasmic Male Sterility. Unraveling banana mt genome architecture will be a foundation for understanding inheritance of traits and their evolution. In this study, the complete banana mt genome is assembled from the whole genome sequence data of the Musa acuminata subsp. malaccensis DH-Pahang. The mt genome sequence acquired by this approach was 409574 bp and it contains, 54 genes coding for 25 respiratory complex proteins 15 ribosomal proteins, 12 tRNA genes and two ribosomal RNA gene. Except atpB, rps11 and rps19 other genes are in multiple copies. The copy number is 12 in tRNA genes. In addition, nearly 25% tandem repeats are also present in it. These mt proteins are identical to the mt proteins present in the other members of AA genome and share 98% sequence similarity with M. balbisiana. The C to U RNA editing is profoundly higher (87 vs 13%) in transcripts of M. balbisiana (BB) compared to M. accuminata (AA). The banana AA mitochondrial genome is tightly packed with 233 genes, with less rearrangements and just 5.3% chloroplast DNA in it. The maintenance of high copy number of functional mt genes suggest that they have a crucial role in the evolution of banana.

scholarly journals Variants in the Mitochondrial Genome Sequence of Rhyzopertha dominica (Fabricius) (Coleoptera: Bostrycidae)

Insects ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 387
Author(s):  
Lindsey C. Perkin ◽  
Timothy P. L. Smith ◽  
Brenda Oppert
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequence ◽  
Sequence Data ◽  
Laboratory Strain ◽  
Rhyzopertha Dominica ◽  
Whole Genome Sequence ◽  
Rrna Genes ◽  
Long Control Region ◽  
Trna Genes ◽  
Mitochondrial Genome Sequence

The lesser grain borer, Rhyzopertha dominica, is a coleopteran pest of stored grains and is mainly controlled by phosphine fumigation, but the increase in phosphine-resistant populations threatens efficacy. Some phosphine-resistant insects have reduced respiration, and thus studying the mitochondrial genome may provide additional information regarding resistance. Genomic DNA from an inbred laboratory strain of R. dominica was extracted and sequenced with both short (Illumina) and long (Pacific Biosciences) read technologies for whole genome sequence assembly and annotation. Short read sequences were assembled and annotated by open software to identify mitochondrial sequences, and the assembled sequence was manually annotated and verified by long read sequences. The mitochondrial genome sequence for R. dominica had a total length of 15,724 bp and encoded 22 trna genes, 2 rRNA genes, 13 protein coding genes (7 nad subunits, 3 cox, 2 atp, and 1 cytB), flanked by a long control region. We compared our predicted mitochondrial genome to that of another from a R. dominica strain from Jingziguan (China). While there was mostly agreement between the two assemblies, key differences will be further examined to determine if mutations in populations are related to insecticide control pressure, mainly that of phosphine. Differences in sequence data, assembly, and annotation also may result in different genome interpretations.

scholarly journals Whole-Genome Sequence of a Pantoea sp. Strain Isolated from an Olive (Olea europaea L.) Knot

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Gabriela Vuletin Selak ◽  
Marina Raboteg ◽  
Audrey Dubost ◽  
Danis Abrouk ◽  
Katja Žanić ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Trna Genes ◽  
Whole Genome ◽  
Ribosomal Operon ◽  
Adriatic Coast ◽  
Olive Trees

Here, we present the total genome sequence of Pantoea sp. strain paga, a plant-associated bacterium isolated from knots present on olive trees grown on the Adriatic Coast. The genome size of Pantoea sp. paga is 5.08 Mb, with a G+C content of 54%. The genome contains 4,776 predicted coding DNA sequences (CDSs), including 70 tRNA genes and 1 ribosomal operon. Obtained genome sequence data will provide insight on the physiology, ecology, and evolution of Pantoea spp.

scholarly journals The Whole Genome Assembly and Comparative Genomic Research ofThellungiella parvula(Extremophile Crucifer) Mitochondrion

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Xuelin Wang ◽  
Changwei Bi ◽  
Yiqing Xu ◽  
Suyun Wei ◽  
Xiaogang Dai ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Genomic Research ◽  
Comparative Genomic ◽  
Trna Genes ◽  
Protein Coding ◽  
Ssr Analysis ◽  
Brassicaceae Species ◽  
Mt Genome ◽  
Rna Genes

The complete nucleotide sequences of the mitochondrial (mt) genome of an extremophile speciesThellungiella parvula(T. parvula) have been determined with the lengths of 255,773 bp.T. parvulamt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome ofT. parvula, including 24 direct repeats, 28 tandem repeats (TRs), and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1%) through simple sequence repeat (SSR) analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes’ evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species,T. parvulais related toArabidopsis thalianawhose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants.

scholarly journals Analysis of copy number variations in Holstein-Friesian cow genomes based on whole-genome sequence data

2017 ◽  
Vol 100 (7) ◽  
pp. 5515-5525 ◽  
Author(s):  
M. Mielczarek ◽  
M. Frąszczak ◽  
R. Giannico ◽  
G. Minozzi ◽  
John L. Williams ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Copy Number ◽  
Sequence Data ◽  
Copy Number Variations ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Holstein Friesian

scholarly journals TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

2014 ◽  
Vol 24 (11) ◽  
pp. 1881-1893 ◽  
Author(s):  
Gavin Ha ◽  
Andrew Roth ◽  
Jaswinder Khattra ◽  
Julie Ho ◽  
Damian Yap ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Copy Number ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Cell Populations ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Clonal Cell

scholarly journals A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data

2018 ◽  
Vol 102 (1) ◽  
pp. 142-155 ◽  
Author(s):  
Brett Trost ◽  
Susan Walker ◽  
Zhuozhi Wang ◽  
Bhooma Thiruvahindrapuram ◽  
Jeffrey R. MacDonald ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Genome Sequence ◽  
Copy Number ◽  
Sequence Data ◽  
Read Depth ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Number Variation

scholarly journals Copy number variants in the sheep genome detected using multiple approaches

2016 ◽  
Author(s):  
Gemma M Jenkins ◽  
Michael E Goddard ◽  
Michael A Black ◽  
Rudiger Brauning ◽  
Benoit Auvray ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Copy Number ◽  
Sequence Data ◽  
Average Length ◽  
Copy Number Variants ◽  
Whole Genome Sequence ◽  
Small Subset ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Sheep Genome

Background.Copy number variants (CNVs) are a type of polymorphism found to underlie phenotypic variation, both in humans and livestock. Most surveys of CNV in livestock have been conducted in the cattle genome, and often utilise only a single approach for the detection of copy number differences. Here we performed a study of CNV in sheep, using multiple methods to identify and characterise copy number changes. Comprehensive information from small pedigrees (trios) was collected using multiple platforms (array CGH, SNP chip and whole genome sequence data), with these data then analysed via multiple approaches to identify and verify CNVs.Results.In total, 3,488 autosomal CNV regions (CNVRs) were identified in this study, which substantially builds on an initial survey of the sheep genome that identified 135 CNVRs. The average length of the identified CNVRs was 19kb (range of 1kb to 3.6Mb), with shorter CNVRs being more frequent than longer CNVRs. The total length of all CNVRs was 67.6Mbps, which equates to 2.7% of the sheep autosomes. For individuals this value ranged from 0.24 to 0.55%, and the majority of CNVRs were identified in single animals. Rather than being uniformly distributed throughout the genome, CNVRs tended to be clustered. Application of three independent approaches for CNVR detection facilitated a comparison of validation rates. CNVs identified on the Roche-NimbleGen 2.1M CGH array generally had low validation rates with lower density arrays, while whole genome sequence data had the highest validation rate (>60%).Conclusions.This study represents the first comprehensive survey of the distribution, prevalence and characteristics of CNVR in sheep. Multiple approaches were used to detect CNV regions and it appears that the best method for verifying CNVR on a large scale involves using a combination of detection methodologies. The characteristics of the 3,488 autosomal CNV regions identified in this study are comparable to other CNV regions reported in the literature and provide a valuable and sizeable addition to the small subset of published sheep CNVs.

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