Lack Of Genome Information Research Articles

Populus cathayana genome and population resequencing provide insights into its evolution and adaptation.

Populus cathayana Rehder, an indigenous poplar species of ecological and economic importance, is widely distributed in a high-elevation range from southwest to northeast China. Further development of this species as a sustainable poplar resource has been hindered by a lack of genome information the at the population level. Here, we produced a chromosome-level genome assembly of P. cathayana, covering 406.55Mb (scaffold N50 = 20.86Mb) and consisting of 19 chromosomes, with 35 977 protein-coding genes. Subsequently, we made a genomic variation atlas of 438 wild individuals covering 36 representative geographic areas of P. cathayana, which were divided into four geographic groups. It was inferred that the Northwest China regions served as the genetic diversity centers and a population bottleneck happened during the history of P. cathayana. By genotype-environment association analysis, 947 environment-association loci were significantly associated with temperature, solar radiation, precipitation, and altitude variables. We identified local adaptation genes involved in DNA repair and UV radiation response, among which UVR8, HY5, and CUL4 had key roles in high-altitude adaptation of P. cathayana. Predictions of adaptive potential under future climate conditions showed that P. cathayana populations in areas with drastic climate change were anticipated to have greater maladaptation risk. These results provide comprehensive insights for understanding wild poplar evolution and optimizing adaptive potential in molecular breeding.

Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands.

Cordia subcordata trees or shrubs, belonging to the Boraginaceae family, have strong resistance and have adapted to their habitat on a tropical coral island in China, but the lack of genome information regarding its genetic background is unclear. In this study, the genome was assembled using both short/long whole genome sequencing reads and Hi-C reads. The assembled genome was 475.3 Mb, with 468.7 Mb (99.22%) of the sequences assembled into 16 chromosomes. Repeat sequences accounted for 54.41% of the assembled genome. A total of 26,615 genes were predicted, and 25,730 genes were functionally annotated using different annotation databases. Based on its genome and the other 17 species, phylogenetic analysis using 336 single-copy genes obtained from ortholog analysis showed that C. subcordata was a sister to Coffea eugenioides, and the divergence time was estimated to be 77 MYA between the two species. Gene family evolution analysis indicated that the significantly expanded gene families were functionally related to chemical defenses against diseases. These results can provide a reference to a deeper understanding of the genetic background of C. subcordata and can be helpful in exploring its adaptation mechanism on tropical coral islands in the future.

Genomes of the human filarial parasites Mansonella perstans and Mansonella ozzardi

The filarial parasites Mansonella ozzardi and Mansonella perstans, causative agents of mansonellosis, infect hundreds of millions of people worldwide, yet remain among the most understudied of the human filarial pathogens. M. ozzardi is highly prevalent in Latin American countries and Caribbean Islands, while M. perstans is predominantly found in sub-Saharan Africa as well as in a few areas in South America. In addition to the differences in their geographical distribution, the two parasites are transmitted by different insect vectors, as well as exhibit differences in their responses to commonly used anthelminthic drugs. The lack of genome information has hindered investigations into the biology and evolution of Mansonella parasites and understanding the molecular basis of the clinical differences between species. In the current study, high quality genomes of two independent clinical isolates of M. perstans from Cameroon and two M. ozzardi isolates one from Brazil and one from Venezuela are reported. The genomes are approximately 76 Mb in size, encode about 10,000 genes each, and are largely complete based on BUSCO scores of about 90%, similar to other completed filarial genomes. These sequences represent the first genomes from Mansonella parasites and enabled a comparative genomic analysis of the similarities and differences between Mansonella and other filarial parasites. Horizontal DNA transfers (HDT) from mitochondria (nuMTs) as well as transfers from genomes of endosymbiotic Wolbachia bacteria (nuWTs) to the host nuclear genome were identified and analyzed. Sequence comparisons and phylogenetic analysis of known targets of anti-filarial drugs diethylcarbamazine (DEC), ivermectin and mebendazole revealed that all known target genes were present in both species, except for the DEC target encoded by gon-2 gene, which is fragmented in genome assemblies from both M. ozzardi isolates. These new reference genome sequences will provide a valuable resource for further studies on biology, symbiosis, evolution and drug discovery.

Chromosome Genome Assembly and Annotation of the Capitulum mitella With PacBio and Hi-C Sequencing Data.

A pedunculate barnacle Capitulum mitella (Linnaeus, 1758) is a dominant intertidal cirripede (Lee et al., 2000). C. mitella distribute in the mid- and high-intertidal zone of tropical and subtropical coasts and is common in the East Sea and South Sea of China. C. mitella has a great commercial value in China, the petiole muscle of which has been a source of traditional delicious seafood (Yuan et al., 2016). The local market demand led to high-intensity catching activity, and this behavior caused significant decrease in quantity and habitat destruction in recent years. Artificial aquaculture of fishery resources will help to reduce overexploitation of natural stocks and meet market needs for fishery products. In general, the barnacle life cycle consists of six nauplius instars and a nonfeeding cyprid instar. In the barnacle life history, the cyprid is a transitory phase between the pelagic and sessile lifestyle. The cyprid role is responsible for locating, exploring, and attaching to a suitable substratum; subsequently, a complex metamorphosis and permanent settlement happen (Lagersson and Hoeg, 2002). Cypris attachment and metamorphosis are also known as “cypris settlement” (Clare and Matsumura, 2000; Franco et al., 2016). The cypris settlement is a crucial event for the survival and development of both adults and subsequent generations. Within the last three decades, the basic biology of C. mitella such as reproductive characteristics, sperm ultrastructure, and larval culture conditions was investigated in our lab. C. mitella cyprids have been cultured on a relatively large scale. However, they cannot attach and metamorphose into juveniles in an artificial environment, so they would die eventually and interrupt their life history. In recent years, the cypris morphology of C. mitella has been depicted minutely using SEM (Rao and Lin, 2014). After we had successfully induced metamorphosis of the C. mitella cyprids into juveniles, we described a time line and specific morphological changes during the metamorphosis under microscopy and SEM (Lin and Rao, 2017). The impacts of external (i.e., water temperature and salinity) and internal (i.e., cyprid age) factors on the metamorphosis of C. mitella were researched (Rao and Lin, 2020). These efforts are possible for completing the life history in an artificial environment and aquaculture of C. mitella. Not only is the artificial aquaculture for C. mitella a production activity but also it helps to reduce the stress on overexploited populations. Barnacles are frequently dominant marine foulings and widely distributed around the world that play crucial roles in marine ecology (Marechal and Hellio, 2011). Recently, there are a few transcriptome researches on barnacles, such as a model animal Amphibalanus amphitrite (Chen et al., 2011; Yan et al., 2012; Chandramouli et al., 2015; Sarah et al., 2016), a giant barnacle Megabalanus volcano (Yan et al., 2017) and a stalked barnacle Neolepas marisindica (Ryu et al., 2019). These efforts showed that the transcriptome databases could greatly promote the research on molecular mechanisms of barnacle settlement. Genome sequencing has been performed for an acorn barnacle Amphibalanus amphitrite, but there is still no genome sequencing information for a stalked barnacle. Numerous reports on C. mitella were mainly related to mitochondrial DNA sequencing and quantitative proteomics analyses (Song and Yoon, 2013; Yoon et al., 2013; Yuan et al., 2016; Tian et al., 2020). So far, no genome literature on the C. mitella is available. Whereas a lack of genome information on the barnacles has obstructed further inquiry on the molecular mechanisms with development, attachment, metamorphosis, genetic evolution, and so on, so does on C. mitella. Accordingly, in this study, we aimed to sequence and assemble the genome of C. mitella. The baseline data obtained from this study will be very useful in taxonomical identification, phylogenetic analysis, larval settlement mechanisms, artificial breeding and aquaculture, and species protection for C. mitella.

Chloroplast genome characteristics and phylogenetic analysis of the medicinal plant Blumea balsamifera (L.) DC.

Blumea balsamifera (L.) DC., a medicinal plant with high economic value in the Asteraceae family, is widely distributed in China and Southeast Asia. However, studies on the population structure or phylogenetic relationships with other related species are rare owing to the lack of genome information. In this study, through high-throughput sequencing, we found that the chloroplast genome of B. balsamifera was 151,170 bp in length, with a pair of inverted repeat regions (IRa and IRb) comprising 24,982 bp, a large single-copy (LSC) region comprising 82,740 bp, and a small single-copy (SSC) region comprising 18,466 bp. A total of 130 genes were identified in the chloroplast genome of B. balsamifera, including 85 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes; furthermore, sequence analysis identified 53 simple sequence repeats. Whole chloroplast genome comparison indicated that the inverted regions (IR) were more conserved than large single-copy and SSC regions. Phylogenetic analysis showed that B. balsamifera is closely related to Pluchea indica. Conclusively, the chloroplast genome of B. balsamifera was helpful for species identification and analysis of the genetic diversity and evolution in the genus Blumea and family Asteraceae.

Development of a species-specific transformation system using the novel endogenous promoter calreticulin from oleaginous microalgae Ettlia sp.

Microalgae not only serve as raw materials for biofuel but also have uses in the food, pharmaceutical, and cosmetic industries. However, regulated gene expression in microalgae has only been achieved in a few strains due to the lack of genome information and unstable transformation. This study developed a species-specific transformation system for an oleaginous microalga, Ettlia sp. YC001, using electroporation. The electroporation was optimized using three parameters (waveform, field strength, and number of pulses), and the final selection was a 5 kV cm−1 field strength using an exponential decay wave with one pulse. A new strong endogenous promoter CRT (Pcrt) was identified using transcriptome and quantitative PCR analysis of highly expressed genes during the late exponential growth phase. The activities of this promoter were characterized using a codon optimized cyan fluorescent protein (CFP) as a reporter. The expression of CFP was similar under Pcrt and under the constitutive promoter psaD (PpsaD). The developed transformation system using electroporation with the endogenous promoter is simple to prepare, is easy to operate with high repetition, and utilizes a species-specific vector for high expression. This system could be used not only in molecular studies on microalgae but also in various industrial applications of microalgae.

Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta.

The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants is a major evolutionary event that has transformed the planet. So far, lack of genome information on unicellular charophyte algae hinders the understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high‐quality reference genome and transcriptome of Mesostigma viride, a single‐celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for the evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age‐old questions of the evolution of multicellularity and the origin of land plants.

Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism.

Parasitic plants in the genus Striga, commonly known as witchweeds, cause major crop losses in sub-Saharan Africa and pose a threat to agriculture worldwide. An understanding of Striga parasite biology, which could lead to agricultural solutions, has been hampered by the lack of genome information. Here, we report the draft genome sequence of Striga asiatica with 34,577 predicted protein-coding genes, which reflects gene family contractions and expansions that are consistent with a three-phase model of parasitic plant genome evolution. Striga seeds germinate in response to host-derived strigolactones (SLs) and then develop a specialized penetration structure, the haustorium, to invade the host root. A family of SL receptors has undergone a striking expansion, suggesting a molecular basis for the evolution of broad host range among Striga spp. We found that genes involved in lateral root development in non-parasitic model species are coordinately induced during haustorium development in Striga, suggesting a pathway that was partly co-opted during the evolution of the haustorium. In addition, we found evidence for horizontal transfer of host genes as well as retrotransposons, indicating gene flow to S.asiatica from hosts. Our results provide valuable insights into the evolution of parasitism and a key resource for the future development of Striga control strategies.

Combining Targeted Metabolites Analysis and Transcriptomics to Reveal Chemical Composition Difference and Underlying Transcriptional Regulation in Maca (Lepidium Meyenii Walp.) Ecotypes

Maca (Lepidium meyenii Walp.) is a traditional Andean crop with great potential for various sanitarian and medical functions, which is attracting increased research attention. The majority of previous Maca studies were focused on biochemistry and pharmacodynamics, while the genetic basis of its unique characteristics lagged due to a lack of genome information. The authors perform gas chromatography-mass spectrometry (GC/MS) analysis in the hypocotyls of three Maca ecotypes and identify 79 compounds. Among them, 62 compounds have distinct profiles among Maca ecotypes. To reveal the underlying regulatory mechanism of the chemical composition differences, de novo transcriptome sequencing is performed and the transcription profiles of three Maca ecotypes are comparatively analyzed. Functional analysis indicates several key pathways, including “starch and sucrose metabolism,” “phenylpropanoid biosynthesis,” “phenylalanine metabolism” and “plant-pathogen interaction,” are involved in regulating the chemical compositions of Maca. Combining metabolomics and transcriptomics analysis indicates transcription factors such as MYB and WRKY and mediators such as protein kinase and bifunctional inhibitors might be critical regulators of chemical composition in Maca. The transcriptome reference genome and differentially expressed genes (DEGs) obtained in this study might serve as an initial step to illustrate the genetic differences in nutrient component, secondary metabolites content, medicinal function and stress resistance in Maca.

Identification and characterization of miRNAs involved in adventitious branches formation of Gracilaria lichenoides in vitro

The main morphological response of Gracilaria lichenoides explants to wounding in vitro was the direct production of adventitious branches (ABs) within a short period rather than callus formation, similar to other seaweeds. However, the underlying mechanism remains unclear because of the lack of genome information. MicroRNAs (miRNAs) play a role in plant growth and development by targeting mRNAs for translational repression or cleavage. Here, we investigated small RNA-mediated regulation of ABs formation by examining the post-transcriptional profiles of different treatment samples of G. lichenoides using the Illumina sequencing platform. The results showed that miR156g-3p, miR2597, miR3447-3p, miR169j-3p and other miRNAs families play significant roles in ABs formation in G. lichenoides through their predicted targets, including phospholipase D (PLD), auxin response factor (ARF), protein phosphatase 2C (PP2C), CTR1 and adenylate isopentenyltransferase (IPT). In addition, we identified 30 putative unique Gracilariales miRNAs in two small RNA libraries that may be involved in ABs induction. Profiling of miRNAs and their target genes of G. lichenoides provide new insight on miRNAs networks involved in ABs formation in seaweed.

Molecular characterization and genome organization of temperature insensitive necrosis inducing strain of BCMV infecting common bean in India

BCMV strain NL-1n differing from already reported BCMV strains has been encountered on common bean in the entire North-Western Himalayan region. Unlike other strains of BCMV, this strain induced mosaic symptoms in cultivars possessing recessive “i” alleles and temperature insensitive necrosis (below and above 30 °C) on differential cv. Jubila carrying the dominant allele “I″. Despite the importance of the crop and the virus there is lack of genome information about any strain of this virus in the Indian subcontinent. In this study, complete genome sequence of NL-1n was determined to understand its relationship with other BCMV strains. The genome was 10,081 nucleotides long containing an open reading frame of 3222 amino acids that encoded a single polyprotein of approximately 365.99 kDa which is cleaved into ten proteins typical of Potyvirus. Pair wise comparison and phylogenetic analysis revealed that BCMV-NL-1n is more closely related to BCMV-NL-1 though clustered along with other strains and isolates of BCMV. Recombination analysis also revealed BCMV-NL-1n to be a recombinant showing two unique events. Based on these features, we propose to designate NL-1n as a recombinant of NL-1 and RU-1 strains. This is the first report of a BCMV strain inducing temperature-insensitive local necrosis on I gene carrying differential cv. Jubila as well as its complete genome sequence from India.

Development and Identification of SSR Markers Associated with Starch Properties and β-Carotene Content in the Storage Root of Sweet Potato (Ipomoea batatas L.).

Sweet potato (Ipomoea batatas L.) is a nutritious food crop and, based on the high starch content of its storage root, a potential bioethanol feedstock. Enhancing the nutritional value and starch quantity of storage roots are important goals of sweet potato breeding programs aimed at developing improved varieties for direct consumption, processing, and industrial uses. However, developing improved lines of sweet potato is challenging due to the genetic complexity of this plant and the lack of genome information. Short sequence repeat (SSR) markers are powerful molecular tools for tracking important loci in crops and for molecular-based breeding strategies; however, few SSR markers and marker-trait associations have hitherto been identified in sweet potato. In this study, we identified 1824 SSRs by using a de novo assembly of publicly available ESTs and mRNAs in sweet potato, and designed 1476 primer pairs based on SSR-containing sequences. We mapped 214 pairs of primers in a natural population comprised of 239 germplasms, and identified 1278 alleles with an average of 5.972 alleles per locus and a major allele frequency of 0.7702. Population structure analysis revealed two subpopulations in this panel of germplasms, and phenotypic characterization demonstrated that this panel is suitable for association mapping of starch-related traits. We identified 32, 16, and 17 SSR markers associated with starch content, β-carotene content, and starch composition in the storage root, respectively, using association analysis and further evaluation of a subset of sweet potato genotypes with various characteristics. The SSR markers identified here can be used to select varieties with desired traits and to investigate the genetic mechanism underlying starch and carotenoid formation in the starchy roots of sweet potato.

Transcriptome and proteome dynamics in larvae of the barnacle Balanus Amphitrite from the Red Sea.

BackgroundThe barnacle Balanus amphitrite is widely distributed in marine shallow and tidal waters, and has significant economic and ecological importance. Nauplii, the first larval stage of most crustaceans, are extremely abundant in the marine zooplankton. However, a lack of genome information has hindered elucidation of the molecular mechanisms of development, settlement and survival strategies in extreme marine environments. We sequenced and constructed the genome dataset for nauplii to obtain comprehensive larval genetic information. We also investigated iTRAQ-based protein expression patterns to reveal the molecular basis of nauplii development, and to gain information on larval survival strategies in the Red Sea marine environment.ResultsA nauplii larval transcript dataset, containing 92,117 predicted open reading frames (ORFs), was constructed and used as a reference for the proteome analysis. Genes related to translation, oxidative phosphorylation and cytoskeletal development were highly abundant. We observed remarkable plasticity in the proteome of Red Sea larvae. The proteins associated with development, stress responses and osmoregulation showed the most significant differences between the two larval populations studied. The synergistic overexpression of heat shock and osmoregulatory proteins may facilitate larval survival in intertidal habitats or in extreme environments.ConclusionsWe presented, for the first time, comprehensive transcriptome and proteome datasets for Red Sea nauplii. The datasets provide a foundation for future investigations focused on the survival mechanisms of other crustaceans in extreme marine environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2262-1) contains supplementary material, which is available to authorized users.

Genome-scale resources for Thermoanaerobacterium saccharolyticum.

BackgroundThermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. A major project was undertaken to develop this organism into an industrial biocatalyst, but the lack of genome information and resources were recognized early on as a key limitation.ResultsHere we present a set of genome-scale resources to enable the systems level investigation and development of this potentially important industrial organism. Resources include a complete genome sequence for strain JW/SL-YS485, a genome-scale reconstruction of metabolism, tiled microarray data showing transcription units, mRNA expression data from 71 different growth conditions or timepoints and GC/MS-based metabolite analysis data from 42 different conditions or timepoints. Growth conditions include hemicellulose hydrolysate, the inhibitors HMF, furfural, diamide, and ethanol, as well as high levels of cellulose, xylose, cellobiose or maltodextrin. The genome consists of a 2.7 Mbp chromosome and a 110 Kbp megaplasmid. An active prophage was also detected, and the expression levels of CRISPR genes were observed to increase in association with those of the phage. Hemicellulose hydrolysate elicited a response of carbohydrate transport and catabolism genes, as well as poorly characterized genes suggesting a redox challenge. In some conditions, a time series of combined transcription and metabolite measurements were made to allow careful study of microbial physiology under process conditions. As a demonstration of the potential utility of the metabolic reconstruction, the OptKnock algorithm was used to predict a set of gene knockouts that maximize growth-coupled ethanol production. The predictions validated intuitive strain designs and matched previous experimental results.ConclusionThese data will be a useful asset for efforts to develop T. saccharolyticum for efficient industrial production of biofuels. The resources presented herein may also be useful on a comparative basis for development of other lignocellulose degrading microbes, such as Clostridium thermocellum.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-015-0159-x) contains supplementary material, which is available to authorized users.

Development in rice genome research based on accurate genome sequence.

Rice is one of the most important crops in the world. Although genetic improvement is a key technology for the acceleration of rice breeding, a lack of genome information had restricted efforts in molecular-based breeding until the completion of the high-quality rice genome sequence, which opened new opportunities for research in various areas of genomics. The syntenic relationship of the rice genome to other cereal genomes makes the rice genome invaluable for understanding how cereal genomes function. Producing an accurate genome sequence is not an easy task, and it is becoming more important as sequence deviations among, and even within, species highlight functional or evolutionary implications for comparative genomics.

The response of Mannheimia haemolytica to iron limitation: Implications for the acquisition of iron in the bovine lung

Mannheimia haemolytica is the major causative agent of shipping fever, a severe pneumonia in cattle causing high morbidity and mortality. A prerequisite of successful lung colonization by M. haemolytica is the necessity to adapt to the paucity of iron. The lack of genome information has precluded an assessment of the genetic repertoire available to M. haemolytica to adapt to low iron environments. To close this knowledge-gap, we have determined 90% of a virulent M. haemolytica serotype A1 genome sequence and produced a microarray in order to study gene expression under iron-limiting growth for 15, 30 and 60 min. M. haemolytica responded to iron limitation by the up-regulation of transcripts coding for receptors and ABC-type transporters of transferrin, haemoglobin, haem and siderophores. Real time PCR analysis of lung tissue from Mannheimia-infected calves demonstrated the in vivo transcription of two potential haemoglobin receptors, hmbR1 and hmbR2. The relative hmbR1 and hmbR2 transcript levels in the infected lung tissue were comparable to the induced levels observed under iron-limiting growth, demonstrating in vivo induction of receptor transcription in the context of an infection. When the iron response of M. haemolytica was compared to the iron response of Pasteurella multocida, another pathogen colonizing the bovine lung, only few homologous genes were induced in both organisms. These included the haemoglobin receptor hmbR2 and the periplasmic transport systems yfeABCD and fbpABC. The comparative analysis suggests that the two pathogens use different strategies to adapt to the iron-limiting environment in the bovine host.