Comparative Mitogenomics of Two Critically Endangered Turtles, Batagur Kachuga and Batagur Dhongoka (Testudines: Geoemydidae): Implications in Phylogenetics of Freshwater Turtles

Abstract The Red-crowned roofed turtle (Batagur kachuga) and Three-striped roofed turtle (B. dhongoka) are ‘critically endangered’ turtles in the Geoemydidae family. Herein, we generated the novel mitochondrial genome sequence of B. kachuga (16,155) and B. dhongoka (15,620) and compared it with other turtles species. Batagur mitogenome has 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and one control region (CR). The genome composition was biased toward A + T, with positive AT-skew and negative GC-skew. In the examined species, all 13 PCGs were started by ATG codons, except COI gene, which was initiated by GTG. The majority of mito-genes were encoded on the heavy strand, except eight tRNAs and the ND6 region. We observed a typical cloverleaf structure for all tRNA, excluding tRNASer (AGN), where the base pairs of the dihydrouridine (DHU) arm were abridged. Bayesian Inference (BI) based phylogenetic analysis was constructed among 39 species from six Testudines families, exhibited a close genetic relationship between Batagur and Pangshura with a high supporting value (PP ~ 0.99). It provides additional mitogenomic resources for further study of the Testudines evolutionary patterns.

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Mitochondrial genome of the sweet potato hornworm, Agrius convolvuli (Lepidoptera: Sphingidae), and comparison with other Lepidoptera species

Genome ◽

10.1139/gen-2016-0058 ◽

2017 ◽

Vol 60 (2) ◽

pp. 128-138 ◽

Cited By ~ 6

Author(s):

Li-Shang Dai ◽

Sheng Li ◽

Hui-min Yu ◽

Guo-Qing Wei ◽

Lei Wang ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Cox1 Gene ◽

Base Pairs ◽

Protein Coding ◽

Transfer Rnas ◽

The Family ◽

Circular Molecule ◽

Cloverleaf Structure

In the present study, we sequenced the complete mitochondrial genome (mitogenome) of Agrius convolvuli (Lepidoptera: Sphingidae) and compared it with previously sequenced mitogenomes of lepidopteran species. The mitogenome was a circular molecule, 15 349 base pairs (bp) long, containing 37 genes. The order and orientation of genes in the A. convolvuli mitogenome were similar to those in sequenced mitogenomes of other lepidopterans. All 13 protein-coding genes (PCGs) were initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which seemed to be initiated by the codon CGA, as observed in other lepidopterans. Three of the 13 PCGs had the incomplete termination codon T, while the remainder terminated with TAA. Additionally, the codon distributions of the 13 PCGs revealed that Asn, Ile, Leu2, Lys, Phe, and Tyr were the most frequently used codon families. All transfer RNAs were folded into the expected cloverleaf structure except for tRNASer(AGN), which lacked a stable dihydrouridine arm. The length of the adenine (A) + thymine (T)-rich region was 331 bp. This region included the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)8 element next to the motif ATTTA. Phylogenetic analyses (maximum likelihood and Bayesian methods) showed that A. convolvuli belongs to the family Sphingidae.

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The mitochondrial genome of Coridius chinensis (Hemiptera: Dinidoridae)

Zootaxa ◽

10.11646/zootaxa.3537.1.2 ◽

2012 ◽

Vol 3537 (1) ◽

pp. 29 ◽

Cited By ~ 5

Author(s):

LI LIU ◽

HU LI ◽

FAN SONG ◽

WEN SONG ◽

XUN DAI ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Nucleotide Composition ◽

Rrna Genes ◽

Trna Genes ◽

Structural Domains ◽

Protein Coding ◽

Simple Loop ◽

Transfer Rnas ◽

Cloverleaf Structure

The nearly complete mitochondrial genome of Coridius chinensis (Dallas) is reported in this study. The mitogenome is a double-stranded circular molecule of more than 14,648 bp in length with an A+T content of 75.1%. It encoded 37 genes as in other insect mtDNAs, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and a control region (unsuccessful sequencing), and the gene order is the same as most other known heteropteran mitogenomes. All of the 22 transfer RNAs can be folded into the typical cloverleaf structure except tRNASer(AGN), which can only form a simple loop at the site of dihydrouridine (DHU) arm as known in other metazoans. The secondary structures of the large and small ribosomal RNAs of C. chinensis are similar to other presented insects. The rrnL consisted of six structural domains and 40 helices, and the rrnS consisted of three structural domains and 26 helices. Nine PCGs are initiated with the standard initiation codons (ATN), while ND6 and ND1 use GTG, and COI and ATP8 use TTG. All PCGs stopped with TAA/TAG termination codons except the COII terminated with a single T residue. Asymmetry in the nucleotide composition between J-strand and N-strand was observed in this mitogenome.

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Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus teitensis (Gesneriaceae)

BioMed Research International ◽

10.1155/2018/1507847 ◽

2018 ◽

Vol 2018 ◽

pp. 1-11 ◽

Cited By ~ 2

Author(s):

Cornelius M. Kyalo ◽

Andrew W. Gichira ◽

Zhi-Zhong Li ◽

Josphat K. Saina ◽

Itambo Malombe ◽

...

Keyword(s):

Chloroplast Genome ◽

Genome Structure ◽

Single Copy ◽

Iucn Red List ◽

Critically Endangered ◽

Protein Coding ◽

Complete Chloroplast Genome ◽

Transfer Rnas ◽

Critically Endangered Species ◽

Genome Information

Streptocarpus teitensis (Gesneriaceae) is an endemic species listed as critically endangered in the International Union for Conservation of Nature (IUCN) red list of threatened species. However, the sequence and genome information of this species remains to be limited. In this article, we present the complete chloroplast genome structure of Streptocarpus teitensis and its evolution inferred through comparative studies with other related species. S. teitensis displayed a chloroplast genome size of 153,207 bp, sheltering a pair of inverted repeats (IR) of 25,402 bp each split by small and large single-copy (SSC and LSC) regions of 18,300 and 84,103 bp, respectively. The chloroplast genome was observed to contain 116 unique genes, of which 80 are protein-coding, 32 are transfer RNAs, and four are ribosomal RNAs. In addition, a total of 196 SSR markers were detected in the chloroplast genome of Streptocarpus teitensis with mononucleotides (57.1%) being the majority, followed by trinucleotides (33.2%) and dinucleotides and tetranucleotides (both 4.1%), and pentanucleotides being the least (1.5%). Genome alignment indicated that this genome was comparable to other sequenced members of order Lamiales. The phylogenetic analysis suggested that Streptocarpus teitensis is closely related to Lysionotus pauciflorus and Dorcoceras hygrometricum.

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Phylogeny and evolution of Lasiopodomys in subfamily Arvivolinae based on mitochondrial genomics

PeerJ ◽

10.7717/peerj.10850 ◽

2021 ◽

Vol 9 ◽

pp. e10850

Author(s):

Luye Shi ◽

Likuan Liu ◽

Xiujuan Li ◽

Yue Wu ◽

Xiangyu Tian ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Early Pleistocene ◽

Individual Species ◽

Protein Coding ◽

Climatic Fluctuations ◽

Transfer Rnas ◽

Relative Contribution ◽

Gc Skew ◽

Phylogeny And Evolution

The species of Lasiopodomys Lataste 1887 with their related genera remains undetermined owing to inconsistent morphological characteristics and molecular phylogeny. To investigate the phylogenetic relationship and speciation among species of the genus Lasiopodomys, we sequenced and annotated the whole mitochondrial genomes of three individual species, namely Lasiopodomys brandtii Radde 1861, L. mandarinus Milne-Edwards 1871, and Neodon (Lasiopodomys) fuscus Büchner 1889. The nucleotide sequences of the circular mitogenomes were identical for each individual species of L. brandtii, L. mandarinus, and N. fuscus. Each species contained 13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs, with mitochondrial genome lengths of 16,557 bp, 16,562 bp, and 16,324 bp, respectively. The mitogenomes and PCGs showed positive AT skew and negative GC skew. Mitogenomic phylogenetic analyses suggested that L. brandtii, L. mandarinus, and L. gregalis Pallas 1779 belong to the genus Lasiopodomys, whereas N. fuscus belongs to the genus Neodon grouped with N. irene. Lasiopodomys showed the closest relationship with Microtus fortis Büchner 1889 and M. kikuchii Kuroda 1920, which are considered as the paraphyletic species of genera Microtus. TMRCA and niche model analysis revealed that Lasiopodomys may have first appeared during the early Pleistocene epoch. Further, L. gregalis separated from others over 1.53 million years ago (Ma) and then diverged into L. brandtii and L. mandarinus 0.76 Ma. The relative contribution of climatic fluctuations to speciation and selection in this group requires further research.

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The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

Scientific Reports ◽

10.1038/s41598-019-57065-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Vikas Kumar ◽

Kaomud Tyagi ◽

Rajasree Chakraborty ◽

Priya Prasad ◽

Shantanu Kundu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Start Codon ◽

Gene Arrangement ◽

Sister Relationship ◽

Protein Coding ◽

Relationship Of ◽

Rna Genes ◽

Boundary Mapping ◽

Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

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Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa018 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

John W Davey ◽

Carolina M C Catta-Preta ◽

Sally James ◽

Sarah Forrester ◽

Maria Cristina M Motta ◽

...

Keyword(s):

Chromosome Number ◽

Noncoding Rnas ◽

Nuclear Genome ◽

Supernumerary Chromosome ◽

Ribosomal Rnas ◽

Protein Coding ◽

Transfer Rnas ◽

Protein Coding Genes ◽

Oxford Nanopore ◽

Genome Assemblies

Abstract Angomonas deanei is an endosymbiont-bearing trypanosomatid with several highly fragmented genome assemblies and unknown chromosome number. We present an assembly of the A. deanei nuclear genome based on Oxford Nanopore sequence that resolves into 29 complete or close-to-complete chromosomes. The assembly has several previously unknown special features; it has a supernumerary chromosome, a chromosome with a 340-kb inversion, and there is a translocation between two chromosomes. We also present an updated annotation of the chromosomal genome with 10,365 protein-coding genes, 59 transfer RNAs, 26 ribosomal RNAs, and 62 noncoding RNAs.

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Conserved long-range base pairings are associated with pre-mRNA processing of human genes

Nature Communications ◽

10.1038/s41467-021-22549-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Svetlana Kalmykova ◽

Marina Kalinina ◽

Stepan Denisov ◽

Alexey Mironov ◽

Dmitry Skvortsov ◽

...

Keyword(s):

Long Range ◽

Rna Folding ◽

Current Knowledge ◽

Rna Structures ◽

Base Pairs ◽

Protein Coding ◽

Proximity Ligation ◽

Transcriptional Suppression ◽

Human Genes ◽

Cleavage And Polyadenylation

AbstractThe ability of nucleic acids to form double-stranded structures is essential for all living systems on Earth. Current knowledge on functional RNA structures is focused on locally-occurring base pairs. However, crosslinking and proximity ligation experiments demonstrated that long-range RNA structures are highly abundant. Here, we present the most complete to-date catalog of conserved complementary regions (PCCRs) in human protein-coding genes. PCCRs tend to occur within introns, suppress intervening exons, and obstruct cryptic and inactive splice sites. Double-stranded structure of PCCRs is supported by decreased icSHAPE nucleotide accessibility, high abundance of RNA editing sites, and frequent occurrence of forked eCLIP peaks. Introns with PCCRs show a distinct splicing pattern in response to RNAPII slowdown suggesting that splicing is widely affected by co-transcriptional RNA folding. The enrichment of 3’-ends within PCCRs raises the intriguing hypothesis that coupling between RNA folding and splicing could mediate co-transcriptional suppression of premature pre-mRNA cleavage and polyadenylation.

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Evolutionary Patterns of Sex-Biased Genes in Three Species of Haplodiploid Insects

Insects ◽

10.3390/insects11060326 ◽

2020 ◽

Vol 11 (6) ◽

pp. 326

Author(s):

Yu-Jun Wang ◽

Hua-Ling Wang ◽

Xiao-Wei Wang ◽

Shu-Sheng Liu

Keyword(s):

Gene Expression ◽

Slow Rate ◽

Species Complex ◽

Evolutionary Patterns ◽

Protein Coding ◽

Coding Sequences ◽

Species Comparisons ◽

Differential Gene ◽

Males And Females ◽

And Behavior

Females and males often differ obviously in morphology and behavior, and the differences between sexes are the result of natural selection and/or sexual selection. To a great extent, the differences between the two sexes are the result of differential gene expression. In haplodiploid insects, this phenomenon is obvious, since males develop from unfertilized zygotes and females develop from fertilized zygotes. Whiteflies of the Bemisia tabaci species complex are typical haplodiploid insects, and some species of this complex are important pests of many crops worldwide. Here, we report the transcriptome profiles of males and females in three species of this whitefly complex. Between-species comparisons revealed that non-sex-biased genes display higher variation than male-biased or female-biased genes. Sex-biased genes evolve at a slow rate in protein coding sequences and gene expression and have a pattern of evolution that differs from those of social haplodiploid insects and diploid animals. Genes with high evolutionary rates are more related to non-sex-biased traits—such as nutrition, immune system, and detoxification—than to sex-biased traits, indicating that the evolution of protein coding sequences and gene expression has been mainly driven by non-sex-biased traits.

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Adaptation, Ecology, and Evolution of the Halophilic Stromatolite ArchaeonHalococcus hamelinensisInferred through Genome Analyses

Archaea ◽

10.1155/2015/241608 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 10

Author(s):

Reema K. Gudhka ◽

Brett A. Neilan ◽

Brendan P. Burns

Keyword(s):

Unknown Function ◽

Energy Production ◽

Extreme Environment ◽

Evolutionary Significance ◽

Base Pairs ◽

Protein Coding ◽

Inorganic Ion ◽

Damage Repair ◽

Genome Analyses

Halococcus hamelinensiswas the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome ofH. hamelinensisconsisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of theH. hamelinensisgenome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome ofH. hamelinensisalso revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes ofH. hamelinensisagainst various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

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Nucleotide sequence of the putative regulatory region of mouse lactate dehydrogenase-A gene

Biochemical Journal ◽

10.1042/bj2350435 ◽

1986 ◽

Vol 235 (2) ◽

pp. 435-439 ◽

Cited By ~ 15

Author(s):

K M Fukasawa ◽

S S L Li

Keyword(s):

Lactate Dehydrogenase ◽

Nucleotide Sequence ◽

Cyclic Amp ◽

Regulatory Region ◽

Base Pairs ◽

Protein Coding ◽

Untranslated Sequence ◽

Eukaryotic Genes ◽

Putative Regulatory Region ◽

Processed Pseudogene

The nucleotide sequence of approx. 3 kilobases including the regulatory region, a non-coding exon and the first protein-coding exon from mouse lactate dehydrogenase-A (LDH-A) gene has been determined. The putative initiation sites of transcription and translation were deduced by comparing the nucleotide sequence of mouse LDH-A gene with those of a mouse LDH-A processed pseudogene and the LDH-A full-length cDNAs from rat and human. The tentative TATA and CAAT boxes, and the hexanucleotides CCGCCC have been identified. The sequence of AAATCTTGCTCAA of mouse LDH-A gene has also been found to show striking homology to the cyclic AMP-responsive sequences of eukaryotic genes regulated by cyclic AMP. It has been reported previously that the protein-coding sequence of mouse LDH-A gene is interrupted by six introns and the 3′ untranslated sequence of 485 nucleotides is not interrupted [Li, Tiano, Fukasawa, Yagi, Shimiza, Sharief, Nakashima & Pan (1985) Eur. J. Biochem. 149, 215-225]. An additional intron of 1653 base-pairs was found in the 5′ untranslated sequence of 101 nucleotides at 24 nucleotides upstream to the translation start site. Thus, mouse LDH-A gene containing seven introns spans approx. 11 kilobases and its length of mature mRNA is 1582 nucleotides, excluding the poly(A) tail.

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