Related Species Research Articles

Convergent reductive evolution in bee-associated lactic acid bacteria.

Several lactic acid bacteria (LAB) species are intimately associated with bees and exhibit unique biochemical properties with potential for food applications and honeybee health. Using a machine-learning based approach, our study shows that adaptation of LAB to the bee environment was accompanied by a distinctive genomic trajectory deeply shaped by gene loss. Several of these gene losses occurred independently in distantly related species and are linked to some of their unique biotechnologically relevant traits, such as the preference of fructose over glucose (fructophily). This study underscores the potential of machine learning in identifying fingerprints of adaptation and detecting instances of convergent evolution. Furthermore, it sheds light onto the genomic and phenotypic particularities of bee-associated bacteria, thereby deepening the understanding of their positive impact on honeybee health.

Mesobacterium hydrothermale sp. nov., isolated from shallow-sea hydrothermal systems off Kueishantao Island.

A Gram-negative, rod-shaped, non-motile, aerobic bacterium, designated as strain TK19101T, was isolated from the intermediate seawater of yellow vent in the shallow-sea hydrothermal system located near Kueishantao Island. The strain was found to grow at 10-40°C (optimum, 35°C), at pH 6.0-8.0 (optimum, 7.0), and in 0-5% (w/v) NaCl (optimum, 1%). Strain TK19101T was catalase-positive and oxidase-positive. The predominant fatty acids (> 10%) in strain TK19101T cells were C16:0, summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), and C18:0. The predominant isoprenoid quinone of strain TK19101T was ubiquinone-10. The polar lipids of strain TK19101T comprised phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phospholipid, and unknown polar lipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TK19101T belonged to the genus Mesobacterium. Strain TK19101T exhibited highest 16S rRNA gene sequence similarity value to Mesobacterium pallidum MCCC M24557T (97.48%). The estimated average nucleotide identity and digital DNA-DNA hybridization values between strain TK19101T and the closest related species Mesobacterium pallidum MCCC M24557T were 74.88% and 20.30%, respectively. The DNA G + C content was 63.49mol%. On the basis of the analysis of 16S rRNA gene sequences, genotypic and phylogenetic data, strain TK19101T has a unique phylogenetic status and represents a novel species of genus Mesobacterium, for which the name Mesobacterium hydrothermale sp. nov. is proposed. The type strain is TK19101T (= MCCC 1K08936T = KCTC 8354T).

Among-species variation in six decades of changing migration timings explained through ecology, life-history and local migratory abundance.

Species exploiting seasonal environments must alter timings of key life-history events in response to large-scale climatic changes in order to maintain trophic synchrony with required resources. Yet, substantial among-species variation in long-term phenological changes has been observed. Advancing from simply describing such variation towards predicting future phenological responses requires studies that rigorously quantify and explain variation in the direction and magnitude of changing timings across diverse species in relation to key ecological and life-history variables. Accordingly, we fitted multi-quantile regressions to 59 years of multi-species data on spring and autumn bird migration timings through northern Scotland. We demonstrate substantial variation in changes in timings among 72 species, and tested whether such variation can be explained by species ecology, life-history and changes in local abundance. Consistent with predictions, species that advanced their migration timing in one or both seasons had more seasonally restricted diet types, fewer suitable breeding habitat types, shorter generation lengths and capability to produce multiple offspring broods per year. In contrast, species with less seasonally restricted diet types and that produce single annual offspring broods, showed no change. Meanwhile, contrary to prediction, long-distance and short-distance migrants advanced migration timings similarly. Changes in migration timing also varied with changes in local migratory abundance, such that species with increasing seasonal abundance apparently altered their migration timing, whilst species with decreasing abundance did not. Such patterns broadly concur with expectation given adaptive changes in migration timing. However, we demonstrate that similar patterns can be generated by numerical sampling given changing local abundances. Any apparent phenology-abundance relationships should, therefore, be carefully validated and interpreted. Overall, our results show that migrant bird species with differing ecologies and life-histories showed systematically differing phenological changes over six decades contextualised by large-scale environmental changes, potentially facilitating future predictions and altering temporal dynamics of seasonal species co-occurrences.

Facilitated introgression from domestic goat into Alpine ibex at immune loci.

Hybridization can result in the transfer of adaptive genetic material from one species to another, known as adaptive introgression. Bottlenecked (and hence genetically depleted) species are expected to be particularly receptive to adaptive introgression, since introgression can introduce new or previously lost adaptive genetic variation. The Alpine ibex (Capra ibex), which recently recovered from near extinction, is known to hybridize with the domestic goat (Capra aegagrus hircus), and signals of introgression previously found at the major histocompatibility complex were suggested to potentially be adaptive. Here, we combine two ancient whole genomes of Alpine ibex with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate the genome-wide patterns of introgression and confirm the potential relevance of immune loci. We identified low rates of admixture in modern Alpine ibex through various F statistics and screening for putative introgressed tracts. Further results based on demographic modelling were consistent with introgression to have occurred during the last 300 years, coinciding with the known species bottleneck, and that in each generation, 1-2 out of 100 Alpine ibex had a domestic goat parent. The putatively introgressed haplotypes were enriched at immune-related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage. While interbreeding with domestic species is a prevalent issue in species conservation, in this specific case, it resulted in putative adaptive introgression. Our findings highlight the complex interplay between hybridization, adaptive evolution, and the potential risks and benefits associated with anthropogenic influences on wild species.

Assemble and comparative analysis of the mitochondrial genome of Rhododendron delavayi: Insights into phylogenetic relationships and genomic variations

Rhododendron delavayi, a notable ornamental plant primarily found in regions of China like Yunnan and Guizhou provinces, holds substantial horticultural value. To elucidate the systematic phylogenetic relationships and organelle genomic differences within R. delavayi and related Rhododendron species, we conducted sequencing and assembly of the complete mitochondrial genome of R. delavayi. The full-length mitochondrial genome of it was a singular circular molecule spanning 1,009,263 bp, comprising 53 protein-coding genes, including 18 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and 32 protein-coding genes. A total of 1,182 simple sequence repeats (SSRs) loci were identified in the R. delavayi mitochondrial genome, primarily consisting of single nucleotide, dinucleotide, and trinucleotide repeats. Nucleotide diversity analysis highlighted five genes (atp6, atp9, cox2, nad1, and rpl10) with the highest diversity within the mitochondrial genomes of Rhododendron genus. Comparative analysis of the mitochondrial genome of R. delavayi with those of four other Rhododendron species indicated complex rearrangements in 21 genes, including rps4, nad6, rps3, atp6, cob, atp9, nad7, among others. The mitochondrial phylogenetic tree revealed a close relationship between R. delavayi and R. decorum, forming a sister clade to R. × pulchrum and R. simsii. Furthermore, 126 plastid-to-mitochondrial gene transfers in R. delavayi were identified, ranging from 30 bp to 19,385 bp. These fragments collectively constituted 47.54 % and 9.52 % of the chloroplast and mitochondrial genomes (202,169 bp), respectively. Complex mitochondrial-to-mitochondrial transfers were also observed, with 843 identified fragments totaling 312,036 bp (30.92 % of the mitochondrial genome). Segments exceeding 10 kb may mediate homologous recombination within the mitochondrial molecules. Remarkably, our study underscores that the mitochondrial genome of R. delavayi was the largest reported within the Rhododendron genus to date. The intricate rearrangements observed in the mitochondrial genomes of Rhododendron species, alone with the identification of five potential molecular marker sites, provided valuable insights for species classification and parentage identification within the Rhododendron genus.

Complete Mitochondrial Genome of Clupeonella abrau (Maliatsky, 1930) (Clupeiformes), an Endemic Freshwater Fish from the Lake Abrau (Russia).

The Abrau sprat (tyulka or sardelka) Clupeonella abrau (Maliatsky, 1930) is an endemic fish of the Lake Abrau (Krasnodar Krai, Russia). The full C. abrau mitochondrial genome (16 650 bp) showed a gene arrangement conserved in Clupeidae and 98.8% similarity with the mitochondrial genome of the related species Black and Caspian Sea sprat C. cultriventris from the Black Sea. The COX1 gene sequence was additionally studied in a museum specimen collected in the Lake Abrau in 1938. Variability in modern Abrau sprat COX1 gene locus was estimated at approximately 0.15%, the difference between C. abrau and C. cultriventris was 1.2%, and the difference between the museum and modern C. abrau specimens from the Lake Abrau was 0.92%. The study confirmed that the Abrau sprat is present in the fish community and is capable of reproducing in the lake. Various scenarios were proposed to explain colonization of the Lake Abrau by C. abrau.

Aquibaculum arenosum gen. nov., sp. nov., a novel member of the family Rhodovibrionaceae, isolated from sea sand.

A Gram-negative, non-motile, and creamy-white coloured bacterium, designated CAU 1616T, was isolated from sea sand collected at Ayajin Beach, Goseong-gun, Republic of Korea. The bacterium was found to grow optimally at 37 °C, pH 8.0-8.5, and with 1-5 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequences placed strain CAU 1616T within the order Rhodospirillales. The highest 16S rRNA gene sequence similarity was to Fodinicurvata fenggangensis YIM D812T (94.1 %), Fodinicurvata sediminis YIM D82T (93.7 %), Fodinicurvata halophila BA45ALT (93.6 %) and Algihabitans albus HHTR 118T (92.3 %). Comparing strain CAU 1616T with closely related species (Fodinicurvata fenggangensis YIM D812T and Fodinicurvata sediminis YIM D82T), the average nucleotide identity based on blast+ values were 69.7-69.8 %, the average amino acid identity values were 61.3-61.4 %, and the digital DNA-DNA hybridization values were 18.4-18.5 %. The assembled draft genome of strain CAU 1616T had 29 contigs with an N50 value of 385.8 kbp, a total length of 3 490 371 bp, and a DNA G+C content of 65.1 mol%. The predominant cellular fatty acids were C18 : 1 2-OH, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The major respiratory quinone was Q-10. Based on phenotypic, phylogenetic, and chemotaxonomic evidence, strain CAU 1616T represents a novel genus in the family Rhodovibrionaceae, for which the name Aquibaculum arenosum gen. nov., sp. nov. is proposed. The type strain is CAU 1616T (=KCTC 82428T=MCCC 1K06089T).

Lacrimispora brassicae sp. nov. isolated from fermented cabbage, and proposal of Clostridium indicum Gundawar et al. 2019 and Clostridium methoxybenzovorans Mechichi et al. 1999 as heterotypic synonyms of Lacrimispora amygdalina (Parshina et al. 2003) Haas and Blanchard 2020 and Lacrimispora indolis (McClung and McCoy 1957) Haas and Blanchard 2020, respectively.

A Gram-stain-negative, endospore-forming, rod-shaped, indole-producing bacterial strain, designated YZC6T, was isolated from fermented cabbage. Strain YZC6T grew at 10-37 °C, pH 5.5-8.5, and with up to 2 % (w/v) NaCl. The major cellular fatty acids were C16 : 0 and C18 : 1 cis 11 dimethyl acetal. Phylogenetic analysis of the 16S rRNA gene revealed that strain YZC6T belonged to the genus Lacrimispora and was closely related to Lacrimispora aerotolerans DSM 5434T (98.3 % sequence similarity), Lacrimispora saccharolytica WM1T (98.1 %), and Lacrimispora algidixylanolytica SPL73T (98.1 %). The average nucleotide identity based on blast (below 87.8 %) and digital DNA-DNA hybridization (below 36.1 %) values between the novel isolate and its corresponding relatives showed that strain YZC6T could be readily distinguished from its closely related species. Based on genotypic, phenotypic, and chemotaxonomic data, a novel Lacrimispora species, Lacrimispora brassicae sp. nov., was proposed, with YZC6T as the type strain (=MAFF 212518T=JCM 32810T=DSM 112100T). This study also proposed Clostridium indicum Gundawar et al. 2019 as a later heterotypic synonym of Lacrimispora amygdalina (Parshina et al. 2003) Haas and Blanchard 2020 and Clostridium methoxybenzovorans Mechichi et al. 1999 as a later heterotypic synonym of Lacrimispora indolis (McClung and McCpy 1957) Haas and Blanchard 2020.

Rarity and life-history strategies shape inbreeding and outbreeding effects on early plant fitness

Local abundance and regional distribution are two aspects of a species’ rarity. They are suggested to differentially alter genetic processes in plants: Locally rare species are hypothesized to suffer less from inbreeding and outbreeding than locally common species, thanks to genetic purging through long inbreeding histories and weaker local adaptations, respectively. Regionally rare species are hypothesized to be more susceptible to outbreeding, but less to inbreeding, compared to regionally common ones, due to small and declining range size. While this has major implications for plant conservation practices, we lack evidences and general understanding on how breeding effects on a plant’s early life fitness are related to its local and regional rarity. To investigate effects of inbreeding and outbreeding on plants’ early fitness, we performed self-, within- and between-population pollinations in eight pairs of closely related species differing in regional and local rarity. To avoid biases due to context dependency, we took species competitive ability, habitat resource-richness and resource-allocation strategy into account in the analyses. We then tested how inbreeding and outbreeding affected five fruit-, seed- and seedling-related traits. Inbreeding did not generally have more negative effects on early fitness of regionally rare and non-competitive species than on regionally common and competitive ones. Outbreeding was generally beneficial to early fitness of plant species across the gradients of regional rarity, competitive ability and habitat resource-richness. Our results show that outbreeding may be beneficial to the early fitness of plant species, including rare and non-competitive ones and may be considered for conservation strategies.

Role of prey refuge and fear level in fractional prey-predator model with anti-predator

Ecological modeling is an effective tool for studying the interactions between predator and prey species by considering various functional responses and ecological effects. Employing computational or mathematical models allows us to determine the impact of specific human interventions or animal behaviors on the evolution of these species. The fear experienced by prey due to the presence of predators plays a crucial role in shaping the dynamics of their interactions. The manuscript focuses on developing and examining a novel prey-predator model that considers predation fear, prey refuge, and anti-predator effects. Caputo fractional derivative is utilized in the construction and analysis of the model, which integrates ecological principles like memory effects to improve our comprehension of species relationship. The study investigates aspects such as stability, well-posedness, and solution uniqueness for the proposed model. We carried out extensive numerical simulation to support theoretical results. Graphical results are provided for the model encompassing a broad spectrum of fractional order values. The effect of the fear level, growth rate of prey, saturation rate and prey refuse on the behavior of the solution are discussed.

Phylogenomic analysis of the Candida auris- Candida haemuli clade and related taxa in the Metschnikowiaceae, and proposal of thirteen new genera, fifty-five new combinations and nine new species

Candida is a polyphyletic genus of sexually reproducing yeasts in the Saccharomycotina with more than 400 species that occur in almost all families of the subclass and its name is strongly connected with the infectious disease candidiasis. During the last two decades, approximately half of the Candida species have been reassigned into more than 36 already existing genera and 14 newly proposed genera, but the polyphyletic feature of the genus largely remained. Candida auris is an important, globally emerging opportunistic pathogen that has caused life-threatening outbreaks in healthcare facilities worldwide. This species belongs to the Candida auris - Candida haemuli (CAH) clade in the Metschnikowiaceae, a clade that contains multidrug-resistant clinically relevant species, but also species isolated from natural environments. The clade is phylogenetically positioned remotely from the type species of the genus Candida that is Candida vulgaris (currently interpreted as a synonym of Candida tropicalis) and belongs to the family Debaryomycetaceae. Although previous phylogenetic and phylogenomic studies confirmed the position of C. auris in the Metschnikowiaceae, these analyses failed to resolve the position of the CAH clade within the family and its delimitation from the genera Clavispora and Metschnikowia. To resolve the position of the CAH clade, phylogenomic and comparative genomics analyses were carried out to address the phylogenetic position of C. auris and related species in the Metschnikowiaceae using several metrics, such as the average amino acid identity (AAI) values, the percentage of conserved proteins (POCP), and the presence-absence patterns of orthologs (PAPO).Based on those approaches, 13 new genera are proposed for various Candida and Hyphopichia species, including members of the CAH clade in the Metschnikowiaceae. As a result, C. auris and related species are reassigned to the genus Candidozyma. Fifty-five new combinations and nine new species are introduced, and this will reduce the polyphyly of the genus Candida.

Co-Invasion of Congeneric Invasive Plants Adopts Different Strategies Depending on Their Origins.

Plant communities may be co-invaded by invasive plants, sometimes even by congeneric invasive plants (CIPs). Despite the growing understanding of co-invasion in the environment, little is known about how CIP interactions and mechanisms regulate co-invasion. Darwin's naturalisation conundrum predicts that the coexistence of closely related species is difficult due to their structural and behavioural similarities. Nevertheless, communities containing closely related species are more susceptible to being invaded because close relatives may favour similar environments; therefore, this hypothesis should be followed in the co-invasion of CIPs. To explore whether the phylogenetic relatedness and origins of invasive species to CIPs can promote or hinder co-invasion, we conducted a controlled interaction and soil-legacy greenhouse experiment to quantify the growth response of invasive plants and their congeners. We consistently found that CIPs of identical origin were more likely to co-invade compared to CIPs of distinct origins. CIPs of distinct origins exhibited an antagonistic effect on co-invasion by allelopathy. Invasive plant-conditioned soil was more conducive to the growth of CIPs of identical origin than CIPs of distinct origins. Our results revealed the different effects of invader-invader phylogenetic relatedness on co-invader success and impact, suggesting the operation of different mechanisms across co-invasion.

Augmenting bacterial similarity measures using a graph-based genome representation.

Given the prevalence and necessity of the 16S rRNA measure in bacterial identification and analysis, this additional analysis adds a functional and synteny-based layer to the identification of relatives and clustering of bacteria genomes. It is also of computational interest to model the bacterial genome as a graph structure, which presents new avenues of genomic analysis for bacteria and their closely related strains and species.

Inference of Essential Genes of the Parasite Haemonchus contortus via Machine Learning.

Over the years, comprehensive explorations of the model organisms Caenorhabditis elegans (elegant worm) and Drosophila melanogaster (vinegar fly) have contributed substantially to our understanding of complex biological processes and pathways in multicellular organisms generally. Extensive functional genomic-phenomic, genomic, transcriptomic, and proteomic data sets have enabled the discovery and characterisation of genes that are crucial for life, called 'essential genes'. Recently, we investigated the feasibility of inferring essential genes from such data sets using advanced bioinformatics and showed that a machine learning (ML)-based workflow could be used to extract or engineer features from DNA, RNA, protein, and/or cellular data/information to underpin the reliable prediction of essential genes both within and between C. elegans and D. melanogaster. As these are two distantly related species within the Ecdysozoa, we proposed that this ML approach would be particularly well suited for species that are within the same phylum or evolutionary clade. In the present study, we cross-predicted essential genes within the phylum Nematoda (evolutionary clade V)-between C. elegans and the pathogenic parasitic nematode H. contortus-and then ranked and prioritised H. contortus proteins encoded by these genes as intervention (e.g., drug) target candidates. Using strong, validated predictors, we inferred essential genes of H. contortus that are involved predominantly in crucial biological processes/pathways including ribosome biogenesis, translation, RNA binding/processing, and signalling and which are highly transcribed in the germline, somatic gonad precursors, sex myoblasts, vulva cell precursors, various nerve cells, glia, or hypodermis. The findings indicate that this in silico workflow provides a promising avenue to identify and prioritise panels/groups of drug target candidates in parasitic nematodes for experimental validation in vitro and/or in vivo.

Unraveling emergent network indeterminacy in complex ecosystems: A random matrix approach

Indeterminacy of ecological networks-the unpredictability of ecosystem responses to persistent perturbations-is an emergent property of indirect effects a species has on another through interaction chains. Thus, numerous indirect pathways in large, complex ecological communities could make forecasting the long-term outcomes of environmental changes challenging. However, a comprehensive understanding of ecological structures causing indeterminacy has not yet been reached. Here, using random matrix theory (RMT), we provide mathematical criteria determining whether network indeterminacy emerges across various ecological communities. Our analytical and simulation results show that indeterminacy intricately depends on the characteristics of species interaction. Specifically, contrary to conventional wisdom, network indeterminacy is unlikely to emerge in large competitive and mutualistic communities, while it is a common feature in top-down regulated food webs. Furthermore, we found that predictable and unpredictable perturbations can coexist in the same community and that indeterminate responses to environmental changes arise more frequently in networks where predator-prey relationships predominate than competitive and mutualistic ones. These findings highlight the importance of elucidating direct species relationships and analyzing them with an RMT perspective on two fronts: It aids in 1) determining whether the network's responses to environmental changes are ultimately indeterminate and 2) identifying the types of perturbations causing less predictable outcomes in a complex ecosystem. In addition, our framework should apply to the inverse problem of network identification, i.e., determining whether observed responses to sustained perturbations can reconstruct their proximate causalities, potentially impacting other fields such as microbial and medical sciences.

On the subgenus Eurysunius Reitter of Turkey IX. Three new species from central northern Anatolia, with an identification key to Turkish species (Coleoptera: Staphylinidae: Paederinae, Astenus)

In this study, three new species belonging to the subgenus Eurysunius Reitter of the genus Astenus Dejean (Coleoptera: Staphylinidae: Paederinae) are described and illustrated from central northern Anatolia, in Turkey, and compared with the related species: Astenus corumensis sp. n. and A. hititicus sp. n. (Çorum province), and A. kaspareki sp. n. (Amasya province). A improved key to Turkish species of Eurysunius is provided as well. The distributions of 28 species in Turkey are mapped.

Fleas (Siphonaptera) of Gerbils in the Caucasus

Representatives of the gerbil subfamily (Gerbillinae) are the main components of biocenoses in deserts and semi-deserts. They are the hosts of many flea species and the main vectors of the causative plague agent in a number of natural plague foci. The taxonomic diversity, distribution pattern and host-parasite relationships of flea species noted as parasites of gerbils in the Caucasus are analyzed. Gerbils and their fleas entered the Caucasus from southwest Asia in the Pliocene in parallel to the migration of floral psammophilic complexes. In the Holocene, semi-desert and desert Turanian plants were introduced from the northeast to the Pre-Caucasus, and the fauna of gerbils and their fleas was replenished with several species and subspecies. In accordance with the settlement of carriers and vectors, sandy natural plague foci in Transcaucasia could have existed already in the Pliocene, and in the Pre-Caucasus they were formed no earlier than the Holocene.

Knock-Out of ACY-1 Like Gene in Spodoptera litura Supports the Notion that FACs Improve Nitrogen Metabolism.

Volicitin [N-(17-hydroxylinolenoyl)-L-glutamine] and N-linolenoyl-L-glutamine were originally identified in the regurgitant of Spodoptera exigua larvae. These fatty acid amino acid conjugates (FACs) are known to be elicitors that induce plants to release volatile compounds which in turn attract natural enemies of the larvae such as parasitic wasps. FAC concentrations are regulated by enzymatic biosynthesis and hydrolysis in the intestine of Lepidoptera larvae. It has been proposed that FAC metabolism activates glutamine synthetase and plays an important role in nitrogen metabolism in larvae. In this study, we identified candidate genes encoding a FACs hydrolase in Spodoptera litura using genomic information of various related lepidopteran species in which FACs hydrolases have been reported. We analyzed the importance of FAC hydrolysis on caterpillar performance with CRISPR/Cas9 knock outs. Larvae of strains with an inactive FACs hydrolase excreted FACs in their feces. They absorbed 30% less nitrogen from the diet compared to WT caterpillars resulting in a reduction of their body weight of up to 40% compared to wild type caterpillars. These results suggest that the hydrolysis of FACs is an important metabolism for insects and that FACs are important for larval growth.

Iris luojiensis (Iridaceae), a new species from southwest China

Iris luojiensis Z.Y. Wang, H.W. Huang and R. Li sp. nov. from southwest China is described and illustrated. This species occurs on shrub slopes in mountainous regions of southwest China. Iris luojiensis is morphologically similar to Iris japonica Thunb., Iris calcicola Z. C. Lu, Z.P. Huang and Yan Liu and Iris wattii Baker, but easily distinguished from them by its bluish‐violet flowers, 3–6 flowering‐stem branches, leaf size, particularly the upper leaves, and by only having two to three (seldom one) flowers per bract. A phylogenetic analysis based on the complete plastid genome supports the separation of I. luojiensis from other morphologically related species. According to morphological and molecular evidence, I. luojiensis can be placed in the I. sect. Lophiris.

Temporal dynamics of chloroplast biogenesis revealed initiation of photosynthesis-related gene expression and protein complexes during alfalfa seed germination

The chloroplast biogenesis occurs in cotyledon during alfalfa seed germination before true leaf formation, and is extremely important for the followed plant development and growth. In this study, we conducted a simulation of alfalfa seed germination in the soil by using tin foil and focused on 10 pivotal time points of chloroplast biogenesis in cotyledons before and after light exposure, which showed significant differences in multispectral images, and covered the whole process of chloroplast biogenesis from proplastid, etioplast to mature chloroplast. We revealed three phases that referred to the programmed involvements of photosynthesis promotion, ultrastructure maturity, transcriptomic expression, and protein complex construction, and observed distinct transcriptional expressions of genes from nuclear and chloroplast genomes. In phase I at dark germination before light exposure, chloroplast-encoded genes showed up-regulated expressions together with the importation of chloroplast proteins. In phase II for the first day after light exposure, nuclear-encoded genes’ expressions were initiated at 2 h after light exposure (E2h), followed by swift assembly of chloroplast thylakoid membrane protein complexes, and roaring Fv/Fm and contents of chlorophyll a, chlorophyll b and carotenoid. The initiation at E2h was pronounced by the observation of gradual accumulation of single lamella, and facilitated the formation of granum stacks (thylakoid) at E8h in phase II. In phase III from the second day after light exposure, chloroplast became gradually complete with the fully established photosynthetic capacity. Altogether, our results layed a theoretical foundation for enhancing potential photosynthetic efficiency in alfalfa and related species.