Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement

Abstract Background The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. Results Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. Conclusions The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues.

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Development of stable transgenic maize plants tolerant for drought by manipulating ABA signaling through Agrobacterium-mediated transformation

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-021-00195-2 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Sridevi Muppala ◽

Pavan Kumar Gudlavalleti ◽

Kodandarami Reddy Malireddy ◽

Sateesh Kumar Puligundla ◽

Premalatha Dasari

Keyword(s):

Abiotic Stress ◽

Inbred Line ◽

Biochemical Characterization ◽

Abiotic Stress Tolerance ◽

Crop Improvement ◽

Maximum Frequency ◽

Aba Signaling ◽

Tolerant Plants ◽

Maize Plants ◽

Gateway Technology

Abstract Background In crop plants, to cope up with the demand of food for rising population, revolutionary crop improvement programmes are being implemented for higher and higher yields. Abiotic stress, especially at flowering stage, causes drastic effect on yield in plants. Deforestation and urbanization made the water table very low and changed the climate which led to untimely and unforeseen rains which affect the yield of a crop through stress, both by lack of water as well as water logging (abiotic stress). Development of tolerant plants through breeding is a time-consuming programme and does not perform well in normal conditions. Development of stress-tolerant plants through transgenic technology is the better solution. Maize is a major crop used as food and fodder and has the commercial value in ethanol production. Hence, the genes viz., nced (9-cis-epoxycarotenoid dioxygenase) and rpk (receptor-like protein kinase), which play the key roles in the abscisic acid pathway and upstream component in ABA signaling have been transferred into maize plants through Agrobacterium-mediated transformation by optimizing several parameters to obtain maximum frequency of transformation. Results Cultures raised from immature embryos of 2-mm size isolated from maize cobs, 12–15 days after pollination, were used for transformation. rpk and nced genes under the control of leaP and salT promoters respectively, cloned using gateway technology, have been introduced into elite maize inbred lines. Maximum frequency of transformation was observed with the callus infected after 20 days of inoculation by using 100 μM acetosyringone, 10 min infection time, and 2 days incubation period after co-cultivation resulted in maximum frequency of transformation (6%) in the NM5884 inbred line. Integration of the genes has been confirmed with molecular characterization by performing PCRs with marker as well as gene-specific primers and through southern hybridization. Physiological and biochemical characterization was done in vitro (artificial stress) and in vivo (pot experiments). Conclusions Changes in the parameters which affect the transformation frequency yielded maximum frequency of transformation with 20-day-old callus in the NM5884 inbred line. Introducing two or more genes using gateway technology is useful for developing stable transgenic plants with desired characters, abiotic stress tolerance in this study.

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A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

Genome Biology and Evolution ◽

10.1093/gbe/evz228 ◽

2019 ◽

Vol 11 (11) ◽

pp. 3144-3157 ◽

Cited By ~ 12

Author(s):

Yutaka Satou ◽

Ryohei Nakamura ◽

Deli Yu ◽

Reiko Yoshida ◽

Mayuko Hamada ◽

...

Keyword(s):

Genome Size ◽

Inbred Line ◽

Genome Assembly ◽

Ciona Intestinalis ◽

Type A ◽

Chromosomal Evolution ◽

Sequence Information ◽

A Genome ◽

Biological Studies ◽

Wide Range

Abstract Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114–120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.

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Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

10.1101/2020.09.09.289611 ◽

2020 ◽

Author(s):

Guifang Lin ◽

Cheng He ◽

Jun Zheng ◽

Dal-Hoe Koo ◽

Ha Le ◽

...

Keyword(s):

Inbred Line ◽

Genome Assembly ◽

Single Copy ◽

Maize Inbred Line ◽

Genome Comparison ◽

Carotenoid Cleavage Dioxygenase ◽

Elevated Expression ◽

Enhanced Expression ◽

Low Expression ◽

Chromosome Level

ABSTRACTThe highly embryogenic and transformable maize inbred line A188 is an attractive model for analyzing maize gene function. Here we constructed a chromosome-level genome assembly of A188 using long reads and optical maps. Genome comparison of A188 with the reference line B73 identified pervasive structural variation, including a 1.8 Mb duplication on the Gametophyte factor1 locus for unilateral cross-incompatibility and six inversions of 0.7 Mb or greater. Increased copy number of the gene, carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression together with low expression of yellow endosperm 1 (y1) condition reduced carotenoid accumulation, which accounts for the white seed phenotype of A188 that contrasts with the yellow seed of B73 that has high expression of y1 and low expression of the single-copy ccd1. Further, transcriptome and epigenome analyses with the A188 reference genome revealed enhanced expression of defense pathways and altered DNA methylation patterns of embryonic callus.

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An Improved Oil Palm Genome Assembly as a Valuable Resource for Crop Improvement and Comparative Genomics in the Arecoideae Subfamily

Plants ◽

10.3390/plants9111476 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1476

Author(s):

Ai-Ling Ong ◽

Chee-Keng Teh ◽

Sean Mayes ◽

Festo Massawe ◽

David Ross Appleton ◽

...

Keyword(s):

Comparative Genomics ◽

Genome Assembly ◽

Oil Palm ◽

Date Palm ◽

Physical Map ◽

Association Studies ◽

Cocos Nucifera ◽

Crop Improvement ◽

Genome Wide Association Studies ◽

Palm Species

Oil palm (Elaeis guineensis Jacq.) is the most traded crop among the economically important palm species. Here, we report an extended version genome of E. guineensis that is 1.2 Gb in length, an improvement of the physical genome coverage to 79% from the previous 43%. The improvement was made by assigning an additional 1968 originally unplaced scaffolds that were available publicly into the physical genome. By integrating three ultra-dense linkage maps and using them to place genomic scaffolds, the 16 pseudomolecules were extended. As we show, the improved genome has enhanced the mapping resolution for genome-wide association studies (GWAS) and permitted further identification of candidate genes/protein-coding regions (CDSs) and any non-coding RNA that may be associated with them for further studies. We then employed the new physical map in a comparative genomics study against two other agriculturally and economically important palm species—date palm (Phoenix dactylifera L.) and coconut palm (Cocos nucifera L.)—confirming the high level of conserved synteny among these palm species. We also used the improved oil palm genome assembly version as a palm genome reference to extend the date palm physical map. The improved genome of oil palm will enable molecular breeding approaches to expedite crop improvement, especially in the largest subfamily of Arecoideae, which consists of 107 species belonging to Arecaceae.

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Genome assembly of the maize inbred line A188 provides a new reference genome for functional genomics

The Crop Journal ◽

10.1016/j.cj.2021.08.002 ◽

2021 ◽

Author(s):

Fei Ge ◽

Jingtao Qu ◽

Peng Liu ◽

Lang Pan ◽

Chaoying Zou ◽

...

Keyword(s):

Functional Genomics ◽

Inbred Line ◽

Genome Assembly ◽

Reference Genome ◽

Maize Inbred Line

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High-quality genome assembly, annotation and evolutionary analysis of the mungbean (Vigna radiata) genome

10.22541/au.160587196.63922177/v1 ◽

2020 ◽

Author(s):

Qiang Yan ◽

Qiong Wang ◽

Cheng Xuzhen ◽

Lixia Wang ◽

Prakit Somta ◽

...

Keyword(s):

Genome Assembly ◽

Vigna Radiata ◽

Crop Improvement ◽

Repetitive Sequences ◽

Gene Families ◽

Close Relative ◽

Specific Gene ◽

Evolutionary Analysis ◽

High Quality ◽

High Quality Genome

Mungbean (Vigna radiata [L.]) is an important economic crop grown in South, and East Asia. The low contiguity of the current assembly of V. radiata genome has limited its application. Here, we report a high-quality chromosome-scale assembled genome of V. radiata to facilitate the investigation of its genome characteristics and evolution. By combination of Nanopore long reads, Illumina short reads and Hi-C data, we generated a high-quality genome assembly of V. radiata, with 473.67 megabases assembled into 11 chromosomes with contig N50 and scaffold N50 of 11.3 and 42.4 megabases, respectively. A total of 52.8% of the genome was annotated as repetitive sequences, among which LTRs (long terminal repeats) were predominant (33.9%). The genome of V. radiata was predicted to contain 33,924 genes, 32,470 (95.7%) of which could be functionally annotated. Evolutionary analysis revealed an estimated divergence time of V. radiata from its close relative V. angularis of ~11.66 million years ago. In addition, 277 V. radiata specific gene families, 18 positively selected genes were detected and functionally annotated. This high-quality mungbean genome will provide valuable resources for further genetic analysis and crop improvement of mungbean and other legume species.

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