抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way.

/pdf/de-novo-assembly-of-human-genomes-with-massively-parallel-16x5duki0i.pdf

De novo assembly of human genomes with massively parallel short read sequencing

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Methylthioalkylmalate synthases (MAMs) encoded by MAM genes are central to the diversification of the glucosinolates, which are important secondary metabolites in Brassicaceae species. However, the evolutionary pathway of MAM genes is poorly understood. We analyzed the phylogenetic and synteny relationships of MAM genes from 13 sequenced Brassicaceae species. Based on these analyses, we propose that the syntenic loci of MAM genes, which underwent frequent tandem duplications, divided into two independent lineage-specific evolution routes and were driven by positive selection after the divergence from Aethionema arabicum. In the lineage I species Capsella rubella, Camelina sativa, Arabidopsis lyrata, and A. thaliana, the MAM loci evolved three tandem genes encoding enzymes responsible for the biosynthesis of aliphatic glucosinolates with different carbon chain-lengths. In lineage II species, the MAM loci encode enzymes responsible for the biosynthesis of short-chain aliphatic glucosinolates. Our proposed model of the evolutionary pathway of MAM genes will be useful for understanding the specific function of these genes in Brassicaceae species.

/pdf/lineage-specific-evolution-of-methylthioalkylmalate-406tjio3ku.pdf

Lineage-specific evolution of Methylthioalkylmalate synthases (MAMs) involved in glucosinolates biosynthesis.

Sulforaphane, the hydrolytic product of glucoraphanin glucosinolate, is a potent anticarcinogen that possesses preventive effects against several human cancers. However, in most B. rapa vegetables, glucoraphanin is undetectable or only present in trace amounts, since the glucoraphanin that is present is converted to gluconapin by three functional BrAOP2 genes. In this study, to enrich beneficial glucoraphanin content in B. rapa, the functional BrAOP2 alleles were replaced by non-functional counterparts through marker-assisted backcrossing. We identified non-functional mutations of two BrAOP2 genes from B. rapa. The backcross progenies with introgression of both non-functional braop2.2 and braop2.3 alleles significantly increased the glucoraphanin content by 18 times relative to the recurrent parent. In contrast, replacement or introgression of single non-functional braop2.2 or braop2.3 locus did not change glucoraphanin content. Our results suggest that replacement of these two functional BrAOP2 genes with non-functional alleles has the potential for producing improved Brassica crops with enriched beneficial glucoraphanin content.

/pdf/enriching-glucoraphanin-in-brassica-rapa-through-replacement-5bqx5imlcu.pdf

Enriching Glucoraphanin in Brassica rapa Through Replacement of BrAOP2.2/BrAOP2.3 with Non-functional Genes.

The species Brassica rapa includes several important vegetable crops. The draft reference genome of B. rapa ssp. pekinensis was completed in 2011, and it has since been updated twice. The pangenome with structural variations of 18 B. rapa accessions was published in 2021. Although extensive genomic analysis has been conducted on B. rapa, a comprehensive genome annotation including gene structure, alternative splicing (AS) events, and non-coding genes is still lacking. Therefore, we used the Pacific Biosciences (PacBio) single-molecular long-read technology to improve gene models and produced the annotated genome version 3.5. In total, we obtained 753,041 full-length non-chimeric (FLNC) reads and collapsed these into 92,810 non-redundant consensus isoforms, capturing 48% of the genes annotated in the B. rapa reference genome annotation v3.1. Based on the isoform data, we identified 830 novel protein-coding genes that were missed in previous genome annotations, defined the untranslated regions (UTRs) of 20,340 annotated genes and corrected 886 wrongly spliced genes. We also identified 28,564 AS events and 1,480 long non-coding RNAs (lncRNAs). We produced a relatively complete and high-quality reference transcriptome for B. rapa that can facilitate further functional genomic research.

/pdf/improved-reference-genome-annotation-of-brassica-rapa-by-1bdmzzbi.pdf

Improved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing

A High Density Linkage Map Facilitates QTL Mapping of Flowering Time in Brassica rapa

In Chinese cabbage (Brassica rapa L. ssp. pekinensis), the locus associated with orange inner leaves has been mapped. The mechanism responsible for carotenoid pigment synthesis in orange inner leaves of Chinese cabbage is still unclear, however, and limited molecular research has been conducted on the candidate gene. In this study, high-performance liquid chromatographic analysis indicated that orange leaf coloration in Chinese cabbage is due to accumulation of prolycopene and other carotenoid pigments. Mapping of simple sequence repeat and insertion/deletion markers from 269 individuals of an F2 population pinpointed the Bror locus within a 1.0-cM interval, with the physical distance of 65.555 kb, on B. rapa chromosome A09. Using B. rapa genome annotation information, the candidate gene BrCRTISO (Bra031539) was predicted to reside within the mapped Bror locus. Coding and promoter regions were sequenced in white- and orange-type homozygous lines. A 6-bp deletion and 53 single nucleotide polymorphisms (SNPs), corresponding to two glutamic acid deletions and 12 amino acid mutations, were identified in the coding sequence of the orange-type cultivar. The orange-type promoter was approximately 141 bp shorter than that of the white type, and many SNPs were located in the promoter region. Two functional markers were designed and found to cosegregate with the Bror locus in F2 individuals. Expression analysis demonstrated that BrCRTISO transcription levels were higher in white-type Chinese cabbage than in the orange-type cultivar. These results offer insights into the molecular mechanism of carotenoid biosynthesis and lay the foundation for molecular breeding of orange-type Chinese cabbage.

Carotenoid identification and molecular analysis of carotenoid isomerase-encoding BrCRTISO , the candidate gene for inner leaf orange coloration in Chinese cabbage

Xiaowu Wang

Papers

Lineage-specific evolution of Methylthioalkylmalate synthases (MAMs) involved in glucosinolates biosynthesis.

Enriching Glucoraphanin in Brassica rapa Through Replacement of BrAOP2.2/BrAOP2.3 with Non-functional Genes.

Improved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing

A High Density Linkage Map Facilitates QTL Mapping of Flowering Time in Brassica rapa

Carotenoid identification and molecular analysis of carotenoid isomerase-encoding BrCRTISO , the candidate gene for inner leaf orange coloration in Chinese cabbage