Analysis of synonymous codon usage pattern of genes in unique non–blood‐sucking leech <i>Whitmania pigra</i>

Khan, Muhammad Salabat; Guan, De‐Long; Ma, Li; Xie, Jun; Xu, Sheng‐Quan

doi:10.1002/jcb.28267

Cited by 3 publications

(3 citation statements)

References 30 publications

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“…The ’mutation-selection drift’ theory has been employed to depict the origin of codon usage bias (CUB) of a gene [ 55 , 56 ]. The theory explains that evolutionary forces such as the selection of compositional constraints, mutation pressure, along with genetic drift in a population might play an effective role in the usage of codon bias [ 57 ]. Earlier studies have reported that genes within a species exhibit similar patterns of codon usage [ 58 , 59 ].…”

Section: Discussionmentioning

confidence: 99%

Analysis of Codon Usage of Speech Gene FoxP2 among Animals

Mazumder¹,

Alqahtani

et al. 2021

Biology

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The protein-coding gene FoxP2 (fork head box protein P2) plays a major role in communication and evolutionary changes. The present study carried out a comprehensive codon usage bias analysis in the FoxP2 gene among a diverse group of animals including fishes, birds, reptiles, and mammals. We observed that in the genome of fishes for the FoxP2 gene, codons ending with C or G were most frequently used, while in birds, reptiles, and mammals, codons ending with T or A were most frequently used. A higher ENC value was observed for the FoxP2 gene indicating a lower CUB. Parity role two-bias plots suggested that apart from mutation pressure, other factors such as natural selection might have influenced the CUB. The frequency distribution of the ENC observed and ENC expected ratio revealed that mutation pressure plays a key role in the patterns of codon usage of FoxP2. Besides, correspondence analysis exposed the composition of the nucleobase under mutation bias affects the codon usage of the FoxP2 gene. However, neutrality plots revealed the major role of natural selection over mutation pressure in the CUB of FoxP2. In addition, the codon usage patterns for FoxP2 among the selected genomes suggested that nature has favored nearly all the synonymous codons for encoding the corresponding amino acid. The uniform usage of 12 synonymous codons for FoxP2 was observed among the species of birds. The amino acid usage frequency for FoxP2 revealed that the amino acids Leucine, Glutamine, and Serine were predominant over other amino acids among all the species of fishes, birds, reptiles, and mammals.

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Section: Discussionmentioning

confidence: 99%

Analysis of Codon Usage of Speech Gene FoxP2 among Animals

Mazumder¹,

Alqahtani

et al. 2021

Biology

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“…Whitmania pigra , as a nonblood‐feeding species, is the most commonly available leech from the traditional Chinese medicine market, which mainly relies on artificial farming (Luo et al, 2019 ; Lynn, 2019 ). Currently, W. pigra is being threatened by several diseases during farming, including edema disease, white spot disease, and withered disease, which have cumulatively caused a devastating drop (70%) in W. pigra production (Wei et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Dysbiosis of intestinal homeostasis contribute to Whitmania pigra edema disease

Dai

Chen

Qian

et al. 2023

Microbial Biotechnology

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Whitmania pigra is widely used in traditional Chinese medicine. However, W. pigra is being threatened by an edema disease with unknown causes (WPE). In this study, a comprehensive exploration of virome, microbiome, and metabolome aberrations in the intestine of W. pigra was performed to address the aetiology of WPE. Virome analysis indicated that eukaryotic viruses did not contribute to WPE, whereas an expansion of Caudovirales was observed in WPE. Compared to the control, the microbial richness and diversity in diseased W. pigra decreased remarkably. Nine genera, including Aeromonas, Anaerotruncus, Vibrio, Proteocatella, Acinetobacter, and Brachyspira were overrepresented in WPE, whereas eleven genera, including Bifidobacterium, Phascolarctobacterium, Lactobacillus, Bacillus and AF12, were enriched in healthy individuals. Furthermore, certain metabolites, especially amino acids, short‐chain fatty acids, and bile acids, were found to be linked to intestinal microbiota alterations in WPE. An integration of the microbiome and metabolome in WPE found that dysbiosis of the gut microbiota or metabolites caused WPE. Notably, W. pigra accepted intestinal microbiota transplantation from WPE donors developed WPE clinical signs eventually, and the dysbiotic intestinal microbiota can be recharacterized in this recipient W. pigra. Strikingly, pathological features of metanephridium and uraemic toxin enrichment in the gut indicated a putative interconnection between the gut and metanephridium in WPE, which represents the prototype of the gut–kidney axis in mammals. These finding exemplify the conservation of “microecological Koch's postulates” from annelids to insects and other vertebrates, which provides a direction of prevention and treatment for WPE and opens a new insight into the pathogenesis of aquatic animal diseases from an ecological perspective.

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“…Reports suggest that W. pigra is microphagous, non-blood-sucking and mostly prey on eld snails (Weisblat, 2003;Kuo and Lai, 2019). Although it exhibits nonblood feeding character, many researchers have identi ed anticoagulation peptides from this leech and located the molecular basis to the synthesis of such substances (Chu et al, 2016;Khan et al, 2019a;Khan et al, 2019b;Hu et al, 2020;Huang et al, 2020). Phylogenetically, W. pigra belongs to the family Hirudinidae.…”

Section: Introductionmentioning

confidence: 99%

Single-Molecule Long-Read Sequencing Facilitates Transcriptomic Research For Whitmania Pigra, The Most Utilized Medical Leech In Chinese Traditional Medicine For Anticoagulant Therapy

Song

Guan

et al. 2021

Preprint

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Although leeches are of great medical and economic value in anticoagulant therapy, full-length transcriptomes for leeches remain scarce. Here, we generated the first full-length transcriptome for the paddy leech Whitmania pigra (the most widely utilized medical leech in Chinese traditional medicine) through Pacific Biosciences (Pacbio) single-molecule long-read sequencing. A total of 191,676 full-length non-chimeric (FLNC) reads were obtained, 30,660 were high-quality unique full-length transcripts. The BUSCO (Bench-marking Universal Single-Copy Orthologues) accession of completeness demonstrated that 74.8% of BUSCOs were complete. We functionally annotated 28,144 transcripts were in public databases, including NR, gene ontology (GO), Pfam, etc. Furthermore, 1,314 long non-coding RNAs (LncRNAs), 2,574 alternative splicing (AS) events, 932 transcript factors (TFs), and 33,258 simple sequence repeats (SSRs) we identified across all transcripts. From the generated data, a total of 426 anticoagulant genes, including 122 Antistasins, 124 with the Fibrinogen beta and gamma chains, and 62 Kazal-type serine protease inhibitors were screened out. Twenty-five novel proteins were revealed following the evaluation of the annotations and products of these anticoagulant transcripts. The regulation network between LncRNAs and corresponding coding transcripts was found with the typical mang-to-many pattern, especially obvious in a specific type of protein, Guamerin. Collectively, the present findings provide a rich set of full-length cDNA sequences for W. pigra, which will greatly facilitate research on transcriptomic genetic for this species and leeches.

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Analysis of synonymous codon usage pattern of genes in unique non–blood‐sucking leech Whitmania pigra

Cited by 3 publications

References 30 publications

Analysis of Codon Usage of Speech Gene FoxP2 among Animals

Analysis of Codon Usage of Speech Gene FoxP2 among Animals

Dysbiosis of intestinal homeostasis contribute to Whitmania pigra edema disease

Single-Molecule Long-Read Sequencing Facilitates Transcriptomic Research For Whitmania Pigra, The Most Utilized Medical Leech In Chinese Traditional Medicine For Anticoagulant Therapy

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