Sequence Divergence Research Articles

A new jewel-like species of the pill-millipede genus Sphaerobelum Verhoeff, 1924 (Diplopoda, Sphaerotheriida, Zephroniidae) from Thailand.

A new species of the giant pill millipede genus Sphaerobelum is described: Sphaerobelumturcosasp. nov. from the northeastern part of Thailand. Species delimitation is based on morphological characters and COI sequence data. The new species can be clearly discriminated from congeners by its greenish-blue body color, the face mask-like appearance of the thoracic and anal shields jointly when rolled up, and the combination of the following four characters: (1) the coxa of the second leg laterally with a sharp and long process, (2) the tarsi of legs 4-21 with 6-7 ventral spines, (3) the anterior telopods consisting of four conspicuous telopoditomeres, and (4) the immovable, slender (not strongly humped) and distally curved finger of the posterior telopods without a membranous spot. The interspecific COI sequence divergence between the new species and other Sphaerobelum species ranges from 17% to 23% (mean 20%). The intergeneric COI sequence divergence between the new species and Zephronia species ranges from 18% to 21% (mean 20%). The relationships among Sphaerobelum and Zephronia species based on the COI sequence data were not resolved in this study. Sphaerobelumturcosasp. nov. is restricted to limestone habitat in Loei province and is probably endemic for the Thai fauna.

Integrative taxonomy reveals the conspecific status of Xerotricha madritensis (Rambur, 1868) and Helicella candoni Thach, 2018 (Gastropoda, Geomitridae)

The Mediterranean region is a biodiversity hotspot. Mollusks represent the second most diverse phylum, with high species richness, endemism, and significant numbers of threatened species. The non-marine species are an especially vulnerable group. New taxa are frequently described although the descriptions often lack biological support. This is true for Helicella candoni Thach, 2018, originally described from Puerto de Santa María, Cádiz, Spain. Thatch (2018) considered H. candoni to be similar to Xerotricha madritensis (Rambur, 1868) but the comparison was made on the basis of basic conchological characters. The present study analyzed topotypes of X. madritensis and H. candoni using integrative taxonomy to evaluate the relationship of the two taxa and their status within Helicella A. Férussac, 1821 and Xerotricha Monterosato, 1892 respectively. A matrix of the mitochondrial cytochrome c oxidase subunit I (COI) yielded a total of 618 bp. Bayesian and Maximum Likelihood analyses showed that H. candoni and X. madritensis clustered closely together along with Helicella itala. Mean sequence divergence for COI between H. candoni and X. madritensis was 1.42 %. Both taxa are similar in shell shape and colour. Genitalia dimensions of H. condoni were very similar to those of X. madritensis. These data indicate that H. candoni is a junior synonym of X. madritensis. The phylogenetic analyses showed that, despite its morphological similarities, X. madritensis is a species of Helicella instead of Xerotricha.

Allopatric montane wren-babblers exhibit similar song notes but divergent vocal sequences

Allopatric montane wren-babblers exhibit similar song notes but divergent vocal sequences

High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres

Centromere positioning and organization are crucial for genome evolution; however, research on centromere biology is largely influenced by the quality of available genome assemblies. Here, we combined Oxford Nanopore and Pacific Biosciences technologies to de novo assemble two high-quality reference genomes for Gossypium hirsutum (TM-1) and Gossypium barbadense (3-79). Compared with previously published reference genomes, our assemblies show substantial improvements, with the contig N50 improved by 4.6-fold and 5.6-fold, respectively, and thus represent the most complete cotton genomes to date. These high-quality reference genomes enable us to characterize 14 and 5 complete centromeric regions for G. hirsutum and G. barbadense, respectively. Our data revealed that the centromeres of allotetraploid cotton are occupied by members of the centromeric repeat for maize (CRM) and Tekay long terminal repeat families, and the CRM family reshapes the centromere structure of the At subgenome after polyploidization. These two intertwined families have driven the convergent evolution of centromeres between the two subgenomes, ensuring centromere function and genome stability. In addition, the repositioning and high sequence divergence of centromeres between G. hirsutum and G. barbadense have contributed to speciation and centromere diversity. This study sheds light on centromere evolution in a significant crop and provides an alternative approach for exploring the evolution of polyploid plants.

Evolutionary analyses of gene expression divergence in Panicum hallii: exploring constitutive and plastic responses using reciprocal transplants.

The evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis- polymorphisms and through more widespread effects driven by trans-regulatory factors. Here, we explore expression and sequence divergence in a large sample of Panicum hallii accessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibiting genotype-by-site interactions. We used a modified Fst-Qst outlier approach (QPC analysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction as QPC outliers. Constitutive QPC outlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging earlier expression quantitative trait loci (eQTL) results (Lovell et al. 2018), we found a strong enrichment of expression divergence, including for QPC outliers, in genes previously identified with cis and cis-environment interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence of promoters and coding sequence of constitutive expression outliers, but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence in P. hallii.

Novel genes and alleles of the BTB/POZ protein family in Oryza rufipogon

The BTB/POZ family of proteins is widespread in plants and animals, playing important roles in development, growth, metabolism, and environmental responses. Although members of the expanded BTB/POZ gene family (OsBTB) have been identified in cultivated rice (Oryza sativa), their conservation, novelty, and potential applications for allele mining in O. rufipogon, the direct progenitor of O. sativa ssp. japonica and potential wide-introgression donor, are yet to be explored. This study describes an analysis of 110 BTB/POZ encoding gene loci (OrBTB) across the genome of O. rufipogon as outcomes of tandem duplication events. Phylogenetic grouping of duplicated OrBTB genes was supported by the analysis of gene sequences and protein domain architecture, shedding some light on their evolution and functional divergence. The O. rufipogon genome encodes nine novel BTB/POZ genes with orthologs in its distant cousins in the family Poaceae (Sorghum bicolor, Brachypodium distachyon), but such orthologs appeared to have been lost in its domesticated descendant, O. sativa ssp. japonica. Comparative sequence analysis and structure comparisons of novel OrBTB genes revealed that diverged upstream regulatory sequences and regulon restructuring are the key features of the evolution of this large gene family. Novel genes from the wild progenitor serve as a reservoir of potential new alleles that can bring novel functions to cultivars when introgressed by wide hybridization. This study establishes a foundation for hypothesis-driven functional genomic studies and their applications for widening the genetic base of rice cultivars through the introgression of novel genes or alleles from the exotic gene pool.

Teunomyces gombertii f.a., sp. nov., Teunomyces landelliae f.a., sp. nov., Teunomyces ledahaglerae f.a., sp. nov. and Teunomyces paulamoraisiae f.a., sp. nov., four yeast species isolated from mushrooms and drosophilids in a Brazilian Amazonian rainforest biome.

Ten yeast isolates representing four candidate novel species of the genus Teunomyces were obtained from different species of mushrooms and drosophilids collected in an Amazonian Forest biome in Brazil. Sequence analyses of the ITS 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that four isolates were phylogenetically related to Teunomyces stri, two isolates related to Teunomyces atbi, two isolates related to Teunomyces aglyptinius, and another two isolates related to Teunomyces aglyptinius, Teunomyces barrocoloradensis, Teunomyces gatunensis and Teunomyces stri. The four novel species differ by 3 % or more of sequence divergence in D1/D2 domains from their closest relatives. These species were isolated from basidiocarps of the mushrooms Marasmiellus volvatus, Tricholomopsis aurea, Hydropus sp. and Favolus tenuiculus, or drosophilids feeding on these substrates. The names Teunomyces gombertii f.a., sp. nov. (holotype CBS 16168T; Mycobank MB849065), Teunomyces landelliae f.a., sp. nov. (holotype =CBS 16169T; Mycobank MB 849066), Teunomyces ledahaglerae f.a., sp. nov. (holotype CBS 16170T; Mycobank MB 849067) and Teunomyces paulamoraisiae f.a., sp. nov. (holotype CBS 16120T; Mycobank MB 849068) are proposed for these species.

PLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models.

The detection of homology through sequence comparison is a typical first step in the study of protein function and evolution. In this work, we explore the applicability of protein language models to this task. We introduce pLM-BLAST, a tool inspired by BLAST, that detects distant homology by comparing single-sequence representations (embeddings) derived from a protein language model, ProtT5. Our benchmarks reveal that pLM-BLAST maintains a level of accuracy on par with HHsearch for both highly similar sequences (with >50% identity) and markedly divergent sequences (with <30% identity), while being significantly faster. Additionally, pLM-BLAST stands out among other embedding-based tools due to its ability to compute local alignments. We show that these local alignments, produced by pLM-BLAST, often connect highly divergent proteins, thereby highlighting its potential to uncover previously undiscovered homologous relationships and improve protein annotation. pLM-BLAST is accessible via the MPI Bioinformatics Toolkit as a web server for searching precomputed databases (https://toolkit.tuebingen.mpg.de/tools/plmblast). It is also available as a standalone tool for building custom databases and performing batch searches (https://github.com/labstructbioinf/pLM-BLAST).

&lt;italic&gt;Fissipedicella orientalis&lt;/italic&gt; gen. et sp. nov. (Ralfsiales, Phaeophyceae), a new crustose brown alga from Korea based on molecular and morphological analyses

The crustose brown algal family Ralfsiaceae comprises four genera: Analipus, Endoplura, Heteroralfsia, and Ralfsia. This study provides a detailed description of Fissipedicella orientalis gen. et sp. nov. based on molecular and morphological analyses. Our phylogenetic analyses from rbcL and concatenated dataset (rbcL + 5′ region of cytochrome c oxidase subunit I [COI-5P]) reveal that specimens collected in Korea are nested in a distinct new clade within Ralfsiaceae with robust bootstrap support and Bayesian posterior probabilities. The sequence divergences for rbcL and COI-5P between F. orientalis and other genera within Ralfsiaceae are 7.4–10.1 and 17.5–21.2%, respectively. Fissipedicella orientalis is characterized by crustose thalli with a hypothallial basal layer and erect perithallial filaments, tufts of hairs in pits, a single chloroplast per cell, plurangia with 1–3 sterile cells, and unangia on stalks composed of 1–6 vertically or obliquely cleaved cells. We propose that F. orientalis can be recognized as a new genus-level taxon within Ralfsiaceae, even though a single species represents it. Our new genus, Fissipedicella, is distinguished from the other members within the Ralfsiaceae by the type of thallus, the number of chloroplasts and tufts of hairs in pits, and the development of unangia.

Analysis of a Novel Peptide That Is Capable of Inhibiting the Enzymatic Activity of the Protein Kinase A Catalytic Subunit-Like Protein from Trypanosoma equiperdum.

A 26-residue peptide possessing the αN-helix motif of the protein kinase A (PKA) regulatory subunit-like proteins from the Trypanozoom subgenera (VAP26, sequence = VAPYFEKSEDETALILKLLTYNVLFS), was shown to inhibit the enzymatic activity of the Trypanosoma equiperdum PKA catalytic subunit-like protein, in a similar manner that the mammalian heat-stable soluble PKA inhibitor known as PKI. However, VAP26 does not contain the PKI inhibitory sequence. Bioinformatics analyzes of the αN-helix motif from various Trypanozoon PKA regulatory subunit-like proteins suggested that the sequence could form favorable peptide-protein interactions of hydrophobic nature with the PKA catalytic subunit-like protein, which possibly may represent an alternative PKA inhibitory mechanism. The sequence of the αN-helix motif of the Trypanozoon proteins was shown to be highly homologous but significantly divergent from the corresponding αN-helix motifs of their Leishmania and mammalian counterparts. This sequence divergence contrasted with the proposed secondary structure of the αN-helix motif, which appeared conserved in every analyzed regulatory subunit-like protein. In silico mutation experiments at positions I234, L238 and F244 of the αN-helix motif from the Trypanozoon proteins destabilized both the specific motif and the protein. On the contrary, mutations at positions T239 and Y240 stabilized the motif and the protein. These results suggested that the αN-helix motif from the Trypanozoon proteins probably possessed a different evolutionary path than their Leishmania and mammalian counterparts. Moreover, finding stabilizing mutations indicated that new inhibitory peptides may be designed based on the αN-helix motif from the Trypanozoon PKA regulatory subunit-like proteins.

Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives.

Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.

Genome-wide methylation patterns from canine nanopore assemblies.

Recent advances in long-read sequencing have enabled the creation of reference-quality genome assemblies for multiple individuals within a species. In particular, 8 long-read genome assemblies have recently been published for the canine model (dogs and wolves). These assemblies were created using a range of sequencing and computational approaches, with only limited comparisons described among subsets of the assemblies. Here we present 3 high-quality de novo reference assemblies based upon Oxford Nanopore long-read sequencing: 2 Bernese Mountain Dogs (BD & OD) and a Cairn terrier (CA611). These breeds are of particular interest due to the enrichment of unresolved genetic disorders. Leveraging advancement in software technologies, we utilized published data of Labrador Retriever (Yella) to generate a new assembly, resulting in a ∼280-fold increase in continuity (N50 size of 91 kbp vs 25.75 Mbp). In conjunction with these 4 new assemblies, we uniformly assessed 8 existing assemblies for generalized quality metrics, sequence divergence, and a detailed BUSCO assessment. We identified a set of ∼400 conserved genes during the BUSCO analysis missing in all assemblies. Genome-wide methylation profiles were generated from the nanopore sequencing, resulting in broad concordance with existing whole-genome and reduced-representation bisulfite sequencing, while highlighting superior overage of mobile elements. These analyses demonstrate the ability of Nanopore sequencing to resolve the sequence and epigenetic profile of canine genomes.

Comparative Analysis of the Chloroplast Genome of Sicyos angulatus with Other Seven Species of Cucurbitaceae Family.

Sicyos angulatus (SA) is an annual plant from the Cucurbitaceae family that is native to the eastern part of North America. This study aims to assemble and annotate the chloroplast genome of S. angulatus, and then compare it with plastomes of the other species representing the Cucurbitaceae family. The chloroplast genome size of S. angulatus is 154,986 bp, including a pair of inverted repeats (IR) of 26,276 bp, and small single-copy region (SSC) of 18,079 bp and large single-copy region (LSC) of 84,355 bp. Compared to other Cucurbitaceae species, the chloroplast genome of S. angulatus is almost 4222 bp smaller than the plastome Gynostemma pentaphyllum. All other seven species have an identical set of tRNA (37), except Citrullus laevigata, which contains 36 tRNA. The IRa/LSC junction in all eight species is located upstream of rpl2 and downstream of trnH gene. Moreover, variation in the size of the gene and the presence of pseudogene ycf1 has been seen because of the IR contraction and expansion. The highest number of tandem repeats was seen in G. pentaphyllum, and then Corynocarpus leavigata. The sequence divergence analysis and topology of the phylogenetic tree indicate that S. angulatus is more similar to genus Citrullus as compared to genus Gynostemma. These findings contribute to developing the genomic marker for the purpose of future genetic studies.

DNA barcoding of the genus Apaidia Hampson, 1900 for species delimitation from Western Mediterranean fauna (Lepidoptera, Erebidae).

The genus Apaidia Hampson, 1900 is a relict Western Mediterranean genus in the South-western part of Europe and the North-western areas of the Mediterranean Africa comprising so far three species, Apaidia rufeola (Rambur, 1832), Apaidia mesogona (Godart, [1824]) and Apaidia barbarica Legrand, 1939. According to the examined material, COI mitochondrial DNA sequences and adult morphology integration supports the existence of three main lineages of Apaidia with sequence divergence rates of approximately 4.5%, which are within the range reported for other well-defined insect species. In addition, we recovered three different BINS, suggesting the presence of different species with unique and specific identifier for A. mesogona (AEC6797), A. rufeola (AEI9539), and the Iberian-Balearic A. barbarica (AEI9540). This study contributes to a better understanding of the taxonomy of the genus Apaidia and challenges future revision of this genus in Northern Africa, as well as the presence of the Apaidia species in Western Mediterranean islands and populations located in Italy.

A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley

Leaf rust, caused by Puccinia hordei, is one of the most widespread and damaging foliar diseases affecting barley. The barley leaf rust resistance locus Rph7 has been shown to have unusually high sequence and haplotype divergence. In this study, we isolate the Rph7 gene using a fine mapping and RNA-Seq approach that is confirmed by mutational analysis and transgenic complementation. Rph7 is a pathogen-induced, non-canonical resistance gene encoding a protein that is distinct from other known plant disease resistance proteins in the Triticeae. Structural analysis using an AlphaFold2 protein model suggests that Rph7 encodes a putative NAC transcription factor with a zinc-finger BED domain with structural similarity to the N-terminal DNA-binding domain of the NAC transcription factor (ANAC019) from Arabidopsis. A global gene expression analysis suggests Rph7 mediates the activation and strength of the basal defence response. The isolation of Rph7 highlights the diversification of resistance mechanisms available for engineering disease control in crops.

Divergent amplifications of CYP9A cytochrome P450 genes provide two noctuid pests with differential protection against xenobiotics

Here, we provide mechanistic support for the involvement of the CYP9A subfamily of cytochrome P450 monooxygenases in the detoxification of host plant defense compounds and chemical insecticides in Spodoptera exigua and Spodoptera frugiperda. Our comparative genomics shows that a large cluster of CYP9A genes occurs in the two species but with significant differences in its contents, including several species-specific duplicates and substantial sequence divergence, both between orthologs and between duplicates. Bioassays of CRISPR-Cas9 knockouts of the clusters show that, collectively, the CYP9As can detoxify two furanocoumarin plant defense compounds (imperatorin and xanthotoxin) and insecticides representing three different chemotypes (pyrethroids, avermectins, and oxadiazines). However, in vitro metabolic assays of heterologously expressed products of individual genes show several differences between the species in the particular CYP9As with activities against these compounds. We also find that the clusters show tight genetic linkage with high levels of pyrethroid resistance in field strains of the two species. We propose that their divergent amplifications of the CYP9A subfamily have not only contributed to the development of the broad host ranges of these species over long evolutionary timeframes but also supplied them with diverse genetic options for evolving resistance to chemical insecticides in the very recent past.

Molecular assessment of specimens previously assigned to Cirrulicarpus (Kallymeniaceae, Rhodophyta) in Brazil, with the description of Meredithia dichotoma sp. nov.

ABSTRACT Molecular sequence analyses of specimens previously identified as Cirrulicarpus sp. in the southeastern Brazil (Espírito Santo coast), indicated that they are more closely related to the genus Meredithia than to the genus Cirrulicarpus. The new species Meredithia dichotoma is herein proposed to accommodate this uncommon and endemic taxon, morphologically characterized by an erect, narrow, strap-shaped thallus, up to 16 cm long, mostly dichotomously branched, with regular constrictions, densely to moderately filamentous medulla, with occasional ganglionic cells, and an expanded medullary region in the basal transverse sections, resembling a midrib in surface view. The species is also supported by the sequence divergence from its congeners: ≥4.3% and 2.2% in the COI-5P and rbcL markers, respectively. Meredithia dichotoma differs from other 11 species of the genus by its dimensions and general habit, never forming expanded blades. This is a new genus record for Brazil and the first species of Meredithia known to occur in the western South Atlantic, increasing the known diversity in the red algal family Kallymeniaceae.

Assessing Global-Local Secondary Structure Fingerprints to Classify RNA Sequences With Deep Learning.

RNA elements that are transcribed but not translated into proteins are called non-coding RNAs (ncRNAs). They play wide-ranging roles in biological processes and disorders. Just like proteins, their structure is often intimately linked to their function. Many examples have been documented where structure is conserved across taxa despite sequence divergence. Thus, structure is often used to identify function. Specifically, the secondary structure is predicted and ncRNAs with similar structures are assumed to have same or similar functions. However, a strand of RNA can fold into multiple possible structures, and some strands even fold differently in vivo and in vitro. Furthermore, ncRNAs often function as RNA-protein complexes, which can affect structure. Because of these, we hypothesized using one structure per sequence may discard information, possibly resulting in poorer classification accuracy. Therefore, we propose using secondary structure fingerprints, comprising two categories: a higher-level representation derived from RNA-As-Graphs (RAG), and free energy fingerprints based on a curated repertoire of small structural motifs. The fingerprints take into account the difference between global and local structural matches. We also evaluated our deep learning architecture with k-mers. By combining our global-local fingerprints with 6-mer, we achieved an accuracy, precision, and recall of 91.04%, 91.10%, and 91.00%.

Comparative analysis of Camelina sativa and fungal industrial lipases used for biodiesel production

Aim. To identify the genes of false flax (Camelina sativa) endogenous lipases and to analyze the sequence similarity of their key functional domains with those of commercially available lipases. Methods. A detailed search of the databases was carried out in order to identify the sequences of lipases of various species, as well as their sequences were aligned, conservative sequence motifs were identified, the domain structure of the detected proteins was established, and phylogenetic analysis was carried out. Results. 15 triacylglycerol lipase genes were identified, and corresponding sequences of lipases for commercially available products were identified as well. Their domain structure was analyzed, and the level of sequence divergence of their functional regions was also revealed. Conclusions. The lipases that are most similar in terms of sequence and domain organization to the lipases of false flax have been identified, and therefore could potentially be used for more effective transesterification of oil with a specific fatty acid composition for this species.

Gene duplication is the primary driver of intraspecific genomic divergence in coral algal symbionts.

Dinoflagellates in the order Suessiales include the family Symbiodiniaceae, which have essential roles as photosymbionts in corals, and their cold-adapted sister group, Polarella glacialis. These diverse taxa exhibit extensive genomic divergence, although their genomes are relatively small (haploid size < 3 Gbp) when compared with most other free-living dinoflagellates. Different strains of Symbiodiniaceae form symbiosis with distinct hosts and exhibit different regimes of gene expression, but intraspecific whole-genome divergence is poorly understood. Focusing on three Symbiodiniaceae species (the free-living Effrenium voratum and the symbiotic Symbiodinium microadriaticum and Durusdinium trenchii) and the free-living outgroup P. glacialis, for which whole-genome data from multiple isolates are available, we assessed intraspecific genomic divergence with respect to sequence and structure. Our analysis, based on alignment and alignment-free methods, revealed a greater extent of intraspecific sequence divergence in Symbiodiniaceae than in P. glacialis. Our results underscore the role of gene duplication in generating functional innovation, with a greater prevalence of tandemly duplicated single-exon genes observed in the genomes of free-living species than in symbionts. These results demonstrate the remarkable intraspecific genomic divergence in dinoflagellates under the constraint of reduced genome sizes, shaped by genetic duplications and symbiogenesis events during the diversification of Symbiodiniaceae.