Bipartite mitogenome of Fargesia angustissima reveals repeat-mediated structural dynamics, inter-organellar DNA transfers, and phylogenetic discordance.
The F. angustissima mitogenome exemplifies a paradigm of structural plasticity, post-transcriptional constraint, and phylogenetic discordance by overcoming the low nucleotide diversity barrier inherent to temperate bamboos, a structurally and functionally derived marker framework was established.
Abstract
Background
As an endemic bamboo and a critical dietary staple for the endangered giant panda, Fargesia angustissima T. P. Yi is integral to the ecological stability of Western Sichuan's forest ecosystems. Nevertheless, the absence of a complete mitogenome has constrained investigations into its complex genomic architecture, evolutionary history, and the genetic basis underlying the montane adaptation.
Results
Using a hybrid sequencing strategy (BGI short reads and PacBio HiFi long reads), we de novo assembled and characterized the bipartite mitogenome of F. angustissima (429,279 bp, 44.18% GC content). The mitogenome encodes a conserved repertoire of 37 unique protein-coding genes (PCGs), exhibiting a pronounced A/U-ending codon bias driven by directional mutation pressure. Long-read mapping validated that a 7,368 bp palindromic repeat (R1) maintained major bipartite isomers (45.45% recombinant frequency), while 39 tetrameric Simple Sequence Repeats (SSRs) and 298 dispersed repeat pairs mediate localized structural variations. To counteract sequence-level mutational drift, 488 C-to-U RNA-editing sites impose strict functional stringency. These modifications predominantly convert hydrophilic Ser/Pro to hydrophobic Leu (42.0%) to ensure the proper membrane integration of respiratory complexes, while also generating obligate stop codons in atp6, atp9, and ccmFC. Moreover, we identified 27 plastid-derived sequences (MTPTs) spanning 20.151 kb, demonstrating an asymmetric intracellular DNA migration pattern; the plastid Large Single Copy (LSC) region (e.g., MTPT27) serves as an evolutionary hotspot for sequence transfer, contrasting with the structural conservatism of the Inverted Repeat (IR) regions (MTPT1, MTPT11, and MTPT12). Despite high sequence identity (> 99.8%) across the Bambusoideae, synteny analyses revealed extensive structural rearrangements. Subsequent phylogenetic reconstruction uncovered significant inter-organellar topological conflicts, providing genomic evidence for historical reticulate evolution and incomplete lineage sorting (ILS) during the rapid diversification of the Fargesia genus.
Conclusions
The F. angustissima mitogenome exemplifies a paradigm of structural plasticity, post-transcriptional constraint, and phylogenetic discordance. By overcoming the low nucleotide diversity barrier inherent to temperate bamboos, a structurally and functionally derived marker framework was established. The genomic reference and the associated candidate loci provide a molecular blueprint for non-destructive population genetics and data-driven conservation within giant panda habitats.
The intergeneric attraction of Pammene nemorosa to sex pheromone traps targeting the Oriental fruit moth, Grapholita molesta (Lepidoptera: Tortricidae), may compromise the reliability of pest monitoring in apple orchards, yet the evolutionary context of this behavioral overlap remains unclear. Here, we sequenced and characterized the first complete mitochondrial genome (mitogenome) of P. nemorosa and assessed its phylogenetic position within the tribe Grapholitini. The circular mitogenome is 15,457 bp long and contains the canonical set of 37 genes, including 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with a gene order typical of ditrysian Lepidoptera. The genome exhibits a pronounced A + T bias (80.1%), and its 484-bp control region contains a tandem duplication of an approximately 215-bp sequence unit, with each repeat copy marked by an ATAGA motif. Phylogenetic analyses based on Neighbor-Joining, Maximum Likelihood, and Bayesian Inference consistently recovered P. nemorosa as sister to the Grapholita clade (G. dimorpha + G. molesta), with strong Bayesian support (posterior probability = 0.999), highlighting a potential discordance between its mitochondrial phylogenetic position and its current morphological classification within Pammene. These findings establish the first complete mitogenomic resource for P. nemorosa and provide a phylogenetic framework for interpreting its close evolutionary affinity with Grapholita species. Although mitochondrial data alone cannot establish the functional mechanisms underlying heterospecific pheromone attraction, the genomic resource established here provides a baseline for future integrative studies combining nuclear genomics, transcriptomics, and chemical ecology, and contributes to a broader understanding of the evolutionary relationships and ecological interactions within Grapholitini.
Jae-in Oh, Kyung Hyun Kim, I. Kim et al.· Scientific Reports· 0 citations
Background: Leptobotia tchangi is a loach species endemic to South China, but its mitochondrial genome has not yet been characterized, limiting understanding of its evolutionary relationships and conservation genetics. Methods: Here, we report the first complete mitochondrial genome of L. tchangi, using next-generation sequencing, assembly and bioinformatics analyses. Results: The double-stranded circular mitogenome has 16,590 bp and contains: 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region (D-loop) containing conserved ETAS and CSB motifs. The overall base composition is 25.0% thymine (T), 27.9% cytosine (C), 31.1% adenine (A), and 16.0% guanine (G), showing a clear A + T bias (56.1%) which is consistent with other Botiidae mitogenomes. To infer the phylogenetic placement of L. tchangi within Botiidae, we conducted both Bayesian inference and maximum-likelihood phylogenetic analyses based on the concatenated PCG sequences. Our results strongly support (1) the monophyly of the subfamilies Leptobotiinae and Botiinae, as well as the monophyly of each genus within the family Botiidae; (2) three sister-group relationships within Botiinae: (Botia + Chromobotia), (Ambastaia + Sinibotia), and (Syncrossus + Yasuhikotakia), with the latter two species groups also being sister groups; (3) L. tchangi being most closely related to Leptobotia taeniops. Conclusions: These findings not only provide essential molecular markers for the species identification and conservation genetics of L. tchangi, but also clarify the taxonomic status of L. tchangi within Botiidae.
Nucleotide diversity and evolutionary rate analyses across mitogenomes of Oedipodinae revealed pervasive purifying selection acting on all 13 PCGs, which strongly supported M. wagneri as a monophyletic lineage within the subfamily Oedipodinae.
Abstract The complete mitochondrial genome of Plagiognathops microlepis was sequenced using Illumina NovaSeq and PacBio Sequel II platforms. The circular mitogenome is 16,632 bp in length and contains 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding control region (D-loop). The genome exhibits an AT content of 56.7%, with an AT skew of 0.104 and a GC skew of −0.255. COX1 initiates with GTG and CYTB with ATA, whereas the remaining 11 PCGs employ ATG; four PCGs (COX2, COX3, ND3, and ND4) terminate with incomplete stop codons (T or TA). Relative synonymous codon usage (RSCU) analysis revealed 27 preferred codons (RSCU > 1), with a strong bias toward A- and T-ending codons. All 22 tRNAs display conventional cloverleaf secondary structures. Maximum likelihood (ML), Bayesian inference (BI) and Neighbor joining (NJ) analyses consistently recovered P. microlepis as sister species to Xenocypris davidi (NJ bootstrap = 1, ML UFBoot = 67, BI posterior probability = 0.977), confirming its phylogenetic position within the genus Xenocypris. These findings provide molecular evidence for the taxonomic placement of P. microlepis and genomic resources for species delimitation, conservation genetics and evolutionary studies within Xenocyprinae.
Huiming Zhou, Guo-Yong Xiong, Jiaxin Yuan et al.· Mitochondrial DNA. Part A, D...· 0 citations
Gymnosperm mitochondrial genomes exhibit substantial variation in size and structure, yet the evolutionary dynamics of Cycadales remain insufficiently explored beyond the genus Cycas.
We assembled the complete mitochondrial genome of Zamia integrifolia using Oxford Nanopore long-read and MGI short-read sequencing. Genome assembly, polishing, and annotation were performed through an integrated bioinformatics pipeline. Repetitive elements and mitochondrial plastid DNA transfers (MTPTs) were characterized. Whole-genome synteny and structural rearrangements were analyzed. Phylogenomic relationships and topological discordance (gene and site concordance factors, gCF/sCF) were evaluated with gene. Lineage-specific substitution rates (
dN
,
dS
, and
ω
) were estimated under a branch-specific model.
The genome (487,460 bp) reveals a ~74 kb expansion relative to Cycas, driven primarily by the accumulation of non-redundant repeats (107,836 bp) and extensive plastid DNA integration (63,674 bp). Quantitative metrics indicate a process of active turnover where ancestral spacers are purged and replaced by lineage-specific elements. Despite this structural flux, the gene content and local order remain conserved under purifying selection. Our phylogenetic reconstruction positions Cycadales as the sister group to all other extant gymnosperms, although gene-tree support for this node is low (gCF = 34.8%; sCF = 44.0%),and this topology is discordant with the Cycadales–Ginkgoales clade often recovered in nuclear datasets. We discuss how the exceptionally low substitution rates in cycad mitogenomes may preserve ancestral polymorphisms, leading to incomplete lineage sorting (ILS) that confounds deep node resolution, and we also consider long-branch attraction (LBA) and other sources of systematic error as alternative explanations for the observed discordance.
These findings highlight a distinct evolutionary mode in Zamiaceae involving structural fluidity amidst sequence stasis and underscore the complexity of resolving gymnosperm phylogeny using organellar markers.
Zhao-Wu Zhang, S. Dong, Zhi-Jing Qiu et al.· Frontiers in Plant Science· 0 citations
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