scholarly journals The Multipartite Mitochondrial Genome of Marama (Tylosema esculentum)

2021 ◽  
Vol 12 ◽  
Author(s):  
Jin Li ◽  
Christopher Cullis
Keyword(s):  
Mitochondrial Genome ◽  
Chloroplast Genome ◽  
Hybrid Approach ◽  
Total Size ◽  
Millettia Pinnata ◽  
Genomics Research ◽  
Experimental Individual ◽  
Tylosema Esculentum ◽  
Wild Legume ◽  
Local Farmers

Tylosema esculentum (marama bean), a wild legume from tropical Africa, has long been considered as a potential crop for local farmers due to its rich nutritional value. Genomics research of marama is indispensable for the domestication and varietal improvement of the bean. The chloroplast genome of marama has been sequenced and assembled previously using a hybrid approach based on both Illumina and PacBio data. In this study, a similar method was used to assemble the mitochondrial genome of marama. The mitochondrial genome of the experimental individual has been confirmed to have two large circles OK638188 and OK638189, which do not recombine according to the data. However, they may be able to restructure into five smaller circles through recombination on the 4 pairs of long repeats (>1 kb). The total length of marama mitogenome is 399,572 bp. A 9,798 bp DNA fragment has been found that is homologous to the chloroplast genome of marama, accounting for 2.5% of the mitogenome. In the Fabaceae family, the mitogenome of Millettia pinnata is highly similar to marama, including for both the genes present and the total size. Some genes including cox2, rpl10, rps1, and sdh4 have been lost during the evolution of angiosperms and are absent in the mitogenomes of some legumes. However, these remain intact and functional in marama. Another set of genes, rpl2, rps2, rps7, rps11, rps13, and rps19 are either absent, or present as pseudogenes, in the mitogenome of marama.

scholarly journals Draft Genome Sequence of the d-Xylose-Fermenting Yeast Spathaspora xylofermentans UFMG-HMD23.3

2017 ◽  
Vol 5 (33) ◽  
Author(s):  
Daiane D. Lopes ◽  
Samuel P. Cibulski ◽  
Fabiana Q. Mayer ◽  
Franciele M. Siqueira ◽  
Carlos A. Rosa ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Total Size ◽  
Amazonian Forest

ABSTRACT Here, we report the draft genome sequence of the yeast Spathaspora xylofermentans UFMG-HMD23.3 (=CBS 12681), a d-xylose-fermenting yeast isolated from the Amazonian forest. The genome consists of 298 contigs, with a total size of 15.1 Mb, including the mitochondrial genome, and 5,948 predicted genes.

scholarly journals Long-read assemblies reveal structural diversity in genomes of organelles - an example with Acacia pycnantha

2020 ◽  
Author(s):  
Anna E. Syme ◽  
Todd G.B. McLay ◽  
Frank Udovicic ◽  
David J. Cantrill ◽  
Daniel J. Murphy
Keyword(s):  
Mitochondrial Genome ◽  
Chloroplast Genome ◽  
De Novo ◽  
Genomic Structure ◽  
Structural Diversity ◽  
Mitochondrial Genomes ◽  
Long Reads ◽  
Organelle Genomes ◽  
Long Read ◽  
Assembly Algorithms

AbstractAlthough organelle genomes are typically represented as single, static, circular molecules, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms. We sequenced and assembled chloroplast and mitochondrial genomes of the Golden Wattle, Acacia pycnantha, using long reads, iterative baiting to extract organelle-only reads, and several assembly algorithms to explore genomic structure. Using a de novo assembly approach agnostic to previous hypotheses about structure, we found different assemblies revealed contrasting arrangements of genomic segments; a hypothesis supported by mapped reads spanning alternate paths.

scholarly journals A chromosome-level assembly of the Atlantic herring – detection of a supergene and other signals of selection

2019 ◽  
Author(s):  
Mats E. Pettersson ◽  
Christina M. Rochus ◽  
Fan Han ◽  
Junfeng Chen ◽  
Jason Hill ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Genome Assembly ◽  
Large Scale ◽  
De Novo ◽  
Hybrid Approach ◽  
Ecological Adaptation ◽  
Atlantic Herring ◽  
Total Size ◽  
Bony Fishes ◽  
Chromosome Level

ABSTRACTThe Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining ade novoPacBio assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb. The development of a high-resolution linkage map confirmed the global chromosome organization and the linear order of genomic segments along the chromosomes. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few interchromosomal but frequent intrachromosomal rearrangements. The improved assembly makes the analysis of previously intractable large-scale structural variation more feasible; allowing, for example, the detection of a 7.8 Mb inversion on chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations from the northern and southern parts of the species distribution. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation in the Atlantic herring.

scholarly journals Draft Nuclear Genome, Complete Chloroplast Genome, and Complete Mitochondrial Genome for the Biofuel/Bioproduct Feedstock Species Scenedesmus obliquus Strain DOE0152z

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
S. R. Starkenburg ◽  
J. E. W. Polle ◽  
B. Hovde ◽  
H. E. Daligault ◽  
K. W. Davenport ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Chloroplast Genome ◽  
Green Alga ◽  
Industrial Production ◽  
Complete Mitochondrial Genome ◽  
Scenedesmus Obliquus ◽  
Nuclear Genome ◽  
Mitochondrial Genomes ◽  
Complete Chloroplast Genome ◽  
Draft Assembly

ABSTRACT The green alga Scenedesmus obliquus is an emerging platform species for the industrial production of biofuels. Here, we report the draft assembly and annotation for the nuclear, plastid, and mitochondrial genomes of S. obliquus strain DOE0152z.

scholarly journals Comparative analysis of nuclear, chloroplast, and mitochondrial genomes of watermelon and melon provides evidence of gene transfer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Haonan Cui ◽  
Zhuo Ding ◽  
Qianglong Zhu ◽  
Yue Wu ◽  
Boyan Qiu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Mitochondrial Genome ◽  
Chloroplast Genome ◽  
Genetic Material ◽  
Nuclear Genome ◽  
Plant Evolution ◽  
Total Length ◽  
Organelle Genomes ◽  
Nuclear Genomes ◽  
Genetic Communication

AbstractDuring plant evolution, there is genetic communication between organelle and nuclear genomes. A comparative analysis was performed on the organelle and nuclear genomes of the watermelon and melon. In the watermelon, chloroplast-derived sequences accounted for 7.6% of the total length of the mitochondrial genome. In the melon, chloroplast-derived sequences accounted for approximately 2.73% of the total mitochondrial genome. In watermelon and melon, the chloroplast-derived small-fragment sequences are either a subset of large-fragment sequences or appeared multiple times in the mitochondrial genome, indicating that these fragments may have undergone multiple independent migration integrations or emerged in the mitochondrial genome after migration, replication, and reorganization. There was no evidence of migration from the mitochondria to chloroplast genome. A sequence with a total length of about 73 kb (47%) in the watermelon chloroplast genome was homologous to a sequence of about 313 kb in the nuclear genome. About 33% of sequences in the watermelon mitochondrial genome was homologous with a 260 kb sequence in the nuclear genome. A sequence with a total length of about 38 kb (25%) in the melon chloroplast genome was homologous with 461 sequences in the nuclear genome, with a total length of about 301 kb. A 3.4 Mb sequence in the nuclear genome was homologous with a melon mitochondrial sequence. These results indicate that, during the evolution of watermelon and melon, a large amount of genetic material was exchanged between the nuclear genome and the two organelle genomes in the cytoplasm.

scholarly journals The Genome of the “Sea Vomit” Didemnum vexillum

Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1377
Author(s):  
Ernesto Parra-Rincón ◽  
Cristian A. Velandia-Huerto ◽  
Adriaan Gittenberger ◽  
Jörg Fallmann ◽  
Thomas Gatter ◽  
...  
Keyword(s):  
Hybrid Approach ◽  
Sister Group ◽  
Total Size ◽  
High Genetic Diversity ◽  
Didemnum Vexillum ◽  
Protein Coding ◽  
Draft Assembly ◽  
Sea Squirt ◽  
Genome Duplications ◽  
Non Coding Rnas

Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past, and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt Didemnum vexillum, commonly known as “sea vomit”, is a colonial tunicate considered an invasive species with substantial ecological and economical risk. We report the assembly of the D. vexillum genome using a hybrid approach that combines 28.5 Gb Illumina and 12.35 Gb of PacBio data. The new hybrid scaffolded assembly has a total size of 517.55 Mb that increases contig length about eightfold compared to previous, Illumina-only assembly. As a consequence of an unusually high genetic diversity of the colonies and the moderate length of the PacBio reads, presumably caused by the unusually acidic milieu of the tunic, the assembly is highly fragmented (L50 = 25,284, N50 = 6539). It is sufficient, however, for comprehensive annotations of both protein-coding genes and non-coding RNAs. Despite its shortcomings, the draft assembly of the “sea vomit” genome provides a valuable resource for comparative tunicate genomics and for the study of the specific properties of colonial ascidians.

Maternal inheritance of chloroplast genome and paternal inheritance of mitochondrial genome in bananas (Musa acuminata)

1994 ◽  
Vol 25 (3) ◽  
pp. 265-269 ◽  
Author(s):  
Sabine Faur� ◽  
Jean-Louis Noyer ◽  
Fran�oise Carreel ◽  
Jean-Pierre Horry ◽  
Fr�d�ric Bakry ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Chloroplast Genome ◽  
Maternal Inheritance ◽  
Musa Acuminata ◽  
Paternal Inheritance

scholarly journals A novel inversion in the chloroplast genome of marama (Tylosema esculentum)

2017 ◽  
Vol 68 (8) ◽  
pp. 2065-2072 ◽  
Author(s):  
Yunsoo Kim ◽  
Christopher Cullis
Keyword(s):  
Chloroplast Genome ◽  
Tylosema Esculentum

scholarly journals Inheritance and Evolution of the Cucurbit Organellar Genomes

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 601e-601
Author(s):  
M.J. Havey ◽  
J. McCreight ◽  
W. Rhodes ◽  
G. Taurick
Keyword(s):  
Mitochondrial Genome ◽  
Chloroplast Genome ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Mitochondrial Genomes ◽  
Maternal Transmission ◽  
Reciprocal Crosses ◽  
Organellar Genomes ◽  
Length Polymorphisms ◽  
Restriction Fragment Length

The cucurbits have several-fold size differences in their mitochondrial genomes. Watermelon possesses a relatively small mitochondrial genome of 330 kb. Squash has a larger mitochondrial genome of 840 kb. Cucumber and melon possess huge mitochondrial genomes of 1500 and 2400 kb, respectively. We demonstrated predominately paternal transmission of the mitochondrial genome in cucumber. Squash shows maternal transmission of the chloroplast genome. We generated reciprocal crosses and identified restriction fragment length polymorphisms in the chloroplast and mitochondrial genomes of melon, squash, and watermelon to establish their transmission. Our analyses also revealed that intergenomic transfers contributed to the evolution of extremely large mitochondrial genomes.

scholarly journals Structural and Comparative Analysis of the Complete Chloroplast Genome of a Mangrove Plant: Scyphiphora hydrophyllacea Gaertn. f. and Related Rubiaceae Species

Forests ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 1000 ◽  
Author(s):  
Ying Zhang ◽  
Jing-Wen Zhang ◽  
Yong Yang ◽  
Xin-Nian Li
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Gc Content ◽  
Conservation Strategies ◽  
Mangrove Species ◽  
Mangrove Plant ◽  
Total Size ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Rna Genes

Scyphiphora hydrophyllacea Gaertn. f. (Rubiaceae) is an endangered mangrove species found in China, and its only known location is in Hainan Island. Previous studies conducted on S. hydrophyllaceae have mainly focused on its location, biological characteristics, and medical effects. However, to date, there has been no published report regarding the genetics or genome of this endangered mangrove species. In this study, we developed valuable chloroplast genome-related molecular resources of S. hydrophyllaceae by comparing with it related Rubiaceae species. The chloroplast genome of S. hydrophyllaceae was found to be a circular molecule with a total size of 155,132 bp, and it is observed to have a quadripartite structure. The whole chloroplast genome contains 132 genes, of which 88 and 36 are protein-coding and transfer RNA genes, respectively; it also contains four ribosomal RNA genes with an overall GC content of 37.60%. A total of 52 microsatellites were detected in the S. hydrophyllacea chloroplast genome, and microsatellite marker detection identified A/T mononucleotides as majority simple sequence repeats in all nine Rubiaceae chloroplast genomes. Comparative analyses of these nine chloroplast genomes revealed variable regions, including matK, rps16, and atpF. All nine species shared 13 RNA-editing sites distributed across eight coding genes. Phylogenetic analyses based on the complete sequences of the chloroplast genomes revealed that the position of S. hydrophyllaceae is closer to the Coffeeae genus than to Cinchoneae, Naucleeae, Morindeae, and Rubieae in the Rubiaceae family. The genome information reported in this study could find further application in the evolution and population genetic studies, and it helps improve our understanding of the endangered mechanism and the development of conservation strategies of this endangered mangrove plant.

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